Study Comparison Entry Entrez_id Entrez_name Entrez_description Map_method n_studies n_comparisons n_total_samples net_fold_change net_direction net_direction_score n_disagreements up_down avg_fold_change n_comparisons_FC n_total_samples_FC max_fold_change min_fold_change Probe_Tag_Acc Probe Tag Accession Description Gene Fold_change Std_Fold_Change up_down_cond1_vs_cond2 RT-PCR Western IHC Class_predictor Signif Pvalue_listed Cond1 Cond2 n_cond1 n_cond2 Source Comment PMID 25 34 1628 29 ABR active BCR-related gene affy_probe_2_Entrez 1 1 55 2.15 up 1 0 1/0 2.15 1 55 2.15 2.15 212895_s_at 212895_s_at active BCR-related gene ABR 2.147 2.15 up 0.001479792 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 15 22 1040 31 ACACA acetyl-Coenzyme A carboxylase alpha Gene_symbol_2_NCBI_Entrez 1 1 7 -2 down 1 0 0/1 -2 1 7 -2.00 -2.00 Acetyl-Coenzyme A carboxylase ACACA 0.5 -2.00 down FTC FA 3 4 publication 15475448 5 10 385 48 ACO1 aconitase 1, soluble tag_2_refseq_or_mgc_2_Entrez 1 1 3 0 up 1 0 1/0 0 0 0 0 0 GATAGGTCGG GATAGGTCGG ACO1 up no FTC FA;Norm 1 2 publication 15085203 16 24 1239 97 ACYP1 acylphosphatase 1, erythrocyte (common) type Gene_symbol_2_NCBI_Entrez 1 1 63 -1.94 down 1 0 0/1 -1.94 1 63 -1.94 -1.94 ACYP1 0.516587678 -1.94 down 0.01 PTC;FVPTC FA;HN 32 31 publication 15087409 15 22 1023 107 ADCY1 adenylate cyclase 1 (brain) Gene_symbol_2_NCBI_Entrez 1 1 7 4 up 1 0 1/0 4 1 7 4.00 4.00 Adenylate cyclase 1 ADCY1 4 4.00 up FTC FA 3 4 publication 15475448 25 34 1724 125 ADH1B alcohol dehydrogenase IB (class I), beta polypeptide affy_probe_2_Entrez 1 1 55 -4.72 down 1 0 0/1 -4.72 1 55 -4.72 -4.72 209612_s_at 209612_s_at alcohol dehydrogenase IB (class I), beta polypeptide ADH1B -3.897 -3.90 down 1.11929E-07 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1736 125 ADH1B alcohol dehydrogenase IB (class I), beta polypeptide affy_probe_2_Entrez 1 1 55 -4.72 down 1 0 0/1 -4.72 1 55 -4.72 -4.72 209613_s_at 209613_s_at alcohol dehydrogenase IB (class I), beta polypeptide ADH1B -4.720 -4.72 down 1.3149E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1607 132 ADK adenosine kinase affy_probe_2_Entrez 1 1 55 2.76 up 1 0 1/0 2.76 1 55 2.76 2.76 204120_s_at 204120_s_at adenosine kinase ADK 2.762 2.76 up 0.002061785 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 864 133 ADM adrenomedullin clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 2.8 up 2 0 2/0 2.8 1 59 2.80 2.80 D14874 D14874 Adrenomedullin ADM up FTC FA 9 10 publication 12738736 18 31 1328 133 ADM adrenomedullin clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 2.8 up 2 0 2/0 2.8 1 59 2.80 2.80 D14874 D14874 Adrenomedullin AM 2.8 2.80 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 3 6 124 134 ADORA1 adenosine A1 receptor clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 8.1 up 1 0 1/0 8.1 1 16 8.10 8.10 L22214 L22214 Adenosine A1 receptor ADORA1 8.1 8.10 up yes 0.0003 PTC Norm 8 8 suppl. materials 11752453 24 33 1505 143 PARP4 poly (ADP-ribose) polymerase family, member 4 Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 32 2.07 up 1 0 1/0 2.07 1 32 2.07 2.07 ADP-ribosyltransferase (NAD+; poly(ADP-ribose) polymerase)-like 1 ADPRTL1 1.05 2.07 up PTC Norm 16 16 publication 15735049 12 19 849 196 AHR aryl hydrocarbon receptor clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 21 3.2 up 1 0 1/0 3.2 1 21 3.20 3.20 L19872 L19872 AHR 3.2 3.20 up PTC Norm 18 3 publication 12538453 18 31 1379 221 ALDH3B1 aldehyde dehydrogenase 3 family, member B1 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 114 7.12 up 2 0 2/0 3.56 2 114 5.02 2.10 U10868 U10868 Aldehyde dehydrogenase 7 ALDH7 2.1 2.10 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1577 221 ALDH3B1 aldehyde dehydrogenase 3 family, member B1 affy_probe_2_Entrez 2 2 114 7.12 up 2 0 2/0 3.56 2 114 5.02 2.10 205640_at 205640_at aldehyde dehydrogenase 3 family, member B1 ALDH3B1 5.022 5.02 up 0.006205547 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 17 29 1288 226 ALDOA aldolase A, fructose-bisphosphate tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 GCGACCGTCA GCGACCGTCA up PTC FA 1 1 publication 11076659 25 34 1639 274 BIN1 bridging integrator 1 affy_probe_2_Entrez 1 1 55 -2.05 down 1 0 0/1 -2.05 1 55 -2.05 -2.05 202931_x_at 202931_x_at bridging integrator 1 BIN1 -2.045 -2.05 down 0.000707103 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 18 31 1337 284 ANGPT1 angiopoietin 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2.7 down 1 0 0/1 -2.7 1 59 -2.70 -2.70 U83508 U83508 Angiopoietin-1 ANG1 2.7 -2.70 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1725 287 ANK2 ankyrin 2, neuronal affy_probe_2_Entrez 1 1 55 -3.91 down 1 0 0/1 -3.91 1 55 -3.91 -3.91 202920_at 202920_at ankyrin 2, neuronal ANK2 -3.907 -3.91 down 0.001598156 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 18 31 1352 301 ANXA1 annexin A1 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 83 5.5 up 2 0 2/0 2.75 2 83 3.1 2.40 X05908 X05908 Lipocortin LPC1 2.4 2.40 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 9 14 640 301 ANXA1 annexin A1 affy_probe_2_Entrez 2 2 83 5.5 up 2 0 2/0 2.75 2 83 3.1 2.40 201012_at 201012_at annexin A1 -3.1 3.1 up 0.000433 FA FTC 12 12 provided by authors 15713710 11 18 779 302 ANXA2 annexin A2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 D00017 D00017 Annexin A2 up ACL;ATC Norm 21 10 publication 15613457 25 34 1710 316 AOX1 aldehyde oxidase 1 affy_probe_2_Entrez 1 1 55 -5.42 down 1 0 0/1 -5.42 1 55 -5.42 -5.42 205082_s_at 205082_s_at aldehyde oxidase 1 AOX1 -3.450 -3.45 down 0.000290156 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1746 316 AOX1 aldehyde oxidase 1 affy_probe_2_Entrez 1 1 55 -5.42 down 1 0 0/1 -5.42 1 55 -5.42 -5.42 205083_at 205083_at aldehyde oxidase 1 AOX1 -5.418 -5.42 down 2.51791E-10 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 15 22 1059 328 APEX1 APEX nuclease (multifunctional DNA repair enzyme) 1 Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 7 -5 down 1 0 0/1 -5 1 7 -5.00 -5.00 Multifunctional DNA repair enzyme APEX 0.2 -5.00 down FTC FA 3 4 publication 15475448 9 14 649 334 APLP2 amyloid beta (A4) precursor-like protein 2 affy_probe_2_Entrez 1 1 24 3.24 up 1 0 1/0 3.24 1 24 3.24 3.24 214875_x_at 214875_x_at amyloid beta (A4) precursor-like protein 2 -3.24 3.24 up 0.0001 FA FTC 12 12 provided by authors 15713710 3 6 158 347 APOD apolipoprotein D clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 -6.1 down 1 0 0/1 -6.1 1 16 -6.10 -6.10 J02611 J02611 Apolipoprotein D APOD -6.1 -6.10 down no 0.0133 PTC Norm 8 8 suppl. materials 11752453 18 31 1329 348 APOE apolipoprotein E clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 2.8 up 1 0 1/0 2.8 1 59 2.80 2.80 M12529 M12529 Apolipoprotein E precursor APOE 2.8 2.80 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 11 18 792 361 AQP4 aquaporin 4 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 38 -2 down 2 0 0/2 -2 1 7 -2.00 -2.00 D63412 D63412 Aquaporin down ACL;ATC Norm 21 10 publication 15613457 15 22 1038 361 AQP4 aquaporin 4 Gene_symbol_2_NCBI_Entrez 2 2 38 -2 down 2 0 0/2 -2 1 7 -2.00 -2.00 Aquaporin 4 AQP4 0.5 -2.00 down FTC FA 3 4 publication 15475448 11 18 813 379 ARF4L ADP-ribosylation factor 4-like clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 NM_001661 NM_001661 ADP-ribosylation factor down ACL;ATC Norm 21 10 publication 15613457 5 10 381 384 ARG2 arginase, type II tag_2_refseq_or_mgc_2_Entrez 1 1 3 0 up 1 0 1/0 0 0 0 0 0 TTTCACAACA TTTCACAACA ARG2 up yes FTC FA;Norm 1 2 publication 15085203 15 22 1048 400 ARL1 ADP-ribosylation factor-like 1 Gene_symbol_2_NCBI_Entrez 1 1 7 -2.5 down 1 0 0/1 -2.5 1 7 -2.50 -2.50 ADP-ribosylation factor-like 1 ARL1 0.4 -2.50 down FTC FA 3 4 publication 15475448 13 20 865 440 ASNS asparagine synthetase clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 43 -3.09 even 1 1 1/1 -3.09 1 24 -3.09 -3.09 M27396 M27396 Asparagine synthetase ASNS up FTC FA 9 10 publication 12738736 9 14 613 440 ASNS asparagine synthetase affy_probe_2_Entrez 2 2 43 -3.09 even 1 1 1/1 -3.09 1 24 -3.09 -3.09 205047_s_at 205047_s_at asparagine synthetase 3.09 -3.09 down 0.002073 FA FTC 12 12 provided by authors 15713710 11 18 815 479 ATP12A ATPase, H+/K+ transporting, nongastric, alpha polypeptide clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U02076 U02076 ATP-driven ion pump (ATP1AL1) down ACL;ATC Norm 21 10 publication 15613457 11 18 777 498 ATP5A1 ATP synthase, H+ transporting, mitochondrial F1 complex, alpha subunit, isoform 1, cardiac muscle clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 BT007209 BT007209 ATP5A1 up yes ACL;ATC Norm 21 10 publication 15613457 16 24 1224 501 ALDH7A1 aldehyde dehydrogenase 7 family, member A1 Gene_symbol_2_NCBI_Entrez 1 1 63 -1.68 down 1 0 0/1 -1.68 1 63 -1.68 -1.68 ALDH7A1 0.596273292 -1.68 down 0.04 PTC;FVPTC FA;HN 32 31 publication 15087409 13 20 867 581 BAX BCL2-associated X protein clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 U19599 U19599 Bcl-2-associated X protein BAX up FTC FA 9 10 publication 12738736 14 21 995 595 CCND1 cyclin D1 (PRAD1: parathyroid adenomatosis 1) Gene_symbol_2_NCBI_Entrez 3 3 101 5.86 up 3 0 3/0 2.93 2 87 3.37 2.49 cyclin D1 CCND1 up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 24 33 1499 595 CCND1 cyclin D1 (PRAD1: parathyroid adenomatosis 1) Gene_symbol_2_NCBI_Entrez 3 3 101 5.86 up 3 0 3/0 2.93 2 87 3.37 2.49 Cyclin D1 (PRAD1: parathyroid adenomatosis 1) CCND1 1.315 2.49 up PTC Norm 16 16 publication 15735049 25 34 1591 595 CCND1 cyclin D1 (PRAD1: parathyroid adenomatosis 1) affy_probe_2_Entrez 3 3 101 5.86 up 3 0 3/0 2.93 2 87 3.37 2.49 208712_at 208712_at cyclin D1 (PRAD1: parathyroid adenomatosis 1) CCND1 3.547 3.55 up 9.91401E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1594 595 CCND1 cyclin D1 (PRAD1: parathyroid adenomatosis 1) affy_probe_2_Entrez 3 3 101 5.86 up 3 0 3/0 2.93 2 87 3.37 2.49 208711_s_at 208711_s_at cyclin D1 (PRAD1: parathyroid adenomatosis 1) CCND1 3.368 3.37 up 0.007940327 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 138 596 BCL2 B-cell CLL/lymphoma 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 -2.2 down 1 0 0/1 -2.2 1 16 -2.20 -2.20 M14745 M14745 Bcl-2 BCL2 -2.2 -2.20 down no 0.0005 PTC Norm 8 8 suppl. materials 11752453 18 31 1396 622 BDH 3-hydroxybutyrate dehydrogenase (heart, mitochondrial) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2 down 1 0 0/1 -2 1 59 -2.00 -2.00 M93107 M93107 Heart (R)-3-hydroxybutyrate dehydrogenase BDH 2 -2.00 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1509 649 BMP1 bone morphogenetic protein 1 Gene_symbol_2_NCBI_Entrez 2 2 87 4.03 up 2 0 2/0 2.015 2 87 2.08 1.95 Bone morphogenetic protein 1 BMP1 0.965 1.95 up PTC Norm 16 16 publication 15735049 25 34 1633 649 BMP1 bone morphogenetic protein 1 affy_probe_2_Entrez 2 2 87 4.03 up 2 0 2/0 2.015 2 87 2.08 1.95 205574_x_at 205574_x_at bone morphogenetic protein 1 BMP1 2.080 2.08 up 0.015787118 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1697 650 BMP2 bone morphogenetic protein 2 affy_probe_2_Entrez 1 1 55 -3.11 down 1 0 0/1 -3.11 1 55 -3.11 -3.11 205290_s_at 205290_s_at bone morphogenetic protein 2 BMP2 -3.107 -3.11 down 0.001274387 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 14 21 1005 653 BMP5 bone morphogenetic protein 5 Gene_symbol_2_NCBI_Entrez 1 1 14 0 up 1 0 1/0 0 0 0 0 0 BMP5 BMP5 up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 11 18 829 658 BMPR1B bone morphogenetic protein receptor, type IB clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U89326 U89326 Bone morphogenetic protein receptor type I (ALK-6) down ACL;ATC Norm 21 10 publication 15613457 2 4 98 663 BNIP2 BCL2/adenovirus E1B 19kDa interacting protein 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -8.2 down 1 0 0/1 -8.2 1 2 -8.20 -8.20 NM_004330 NM_004330 BCL2/adenovirus E1B 19kd interacting protein 2 BNP2 8.2 -8.20 down PCL Norm 1 1 publication 15785240 15 22 1050 664 BNIP3 BCL2/adenovirus E1B 19kDa interacting protein 3 Gene_symbol_2_NCBI_Entrez 1 1 7 -3.33 down 1 0 0/1 -3.33 1 7 -3.33 -3.33 BCL2 interacting protein 3 BNIP3 0.3 -3.33 down FTC FA 3 4 publication 15475448 18 31 1371 672 BRCA1 breast cancer 1, early onset clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2.2 down 1 0 0/1 -2.2 1 59 -2.20 -2.20 L78833 L78833 L21 ribosomal protein pseudogene PSCP 2.2 -2.20 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 18 31 1372 678 ZFP36L2 zinc finger protein 36, C3H type-like 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2.2 down 1 0 0/1 -2.2 1 59 -2.20 -2.20 U07802 U07802 Tis11d early response gene TIS11D 2.2 -2.20 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 13 20 866 682 BSG basigin (OK blood group) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 X64364 X64364 Basigin (OK blood group) BSG up yes FTC FA 9 10 publication 12738736 16 24 1244 744 C11orf8 chromosome 11 open reading frame 8 Gene_symbol_2_NCBI_Entrez 3 3 134 -21.14 down 3 0 0/3 -7.04666666666667 3 134 -2.25 -12.49 C11orf8 0.444444444 -2.25 down yes 0.02 PTC;FVPTC FA;HN 32 31 publication 15087409 25 34 1751 744 C11orf8 chromosome 11 open reading frame 8 affy_probe_2_Entrez 3 3 134 -21.14 down 3 0 0/3 -7.04666666666667 3 134 -2.25 -12.49 215692_s_at 215692_s_at chromosome 11 open reading frame 8 C11orf8 -5.823 -5.82 down 1.41784E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1778 744 C11orf8 chromosome 11 open reading frame 8 affy_probe_2_Entrez 3 3 134 -21.14 down 3 0 0/3 -7.04666666666667 3 134 -2.25 -12.49 205413_at 205413_at chromosome 11 open reading frame 8 C11orf8 -12.491 -12.49 down 0.001239578 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 159 744 C11orf8 chromosome 11 open reading frame 8 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 134 -21.14 down 3 0 0/3 -7.04666666666667 3 134 -2.25 -12.49 U57911 U57911 Chromosome 11 open reading frame 8 C11ORF8 -6.4 -6.40 down no 0.003 PTC Norm 8 8 suppl. materials 11752453 13 20 873 753 C18orf1 chromosome 18 open reading frame 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 AF009426 AF009426 Chromosome 18 open-reading frame 1 C18orf1 up FTC FA 9 10 publication 12738736 16 24 1223 757 TMEM50B transmembrane protein 50B Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 63 -1.67 down 1 0 0/1 -1.67 1 63 -1.67 -1.67 C21orf4 0.597402597 -1.67 down yes 0.0001 PTC;FVPTC FA;HN 32 31 publication 15087409 13 20 925 762 CA4 carbonic anhydrase IV clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 157 -4.18 down 3 1 1/3 -1.39333333333333 3 138 3.13 -4.61 M83670 M83670 Carbonic anhydrase IV CA4 down FTC FA 9 10 publication 12738736 18 31 1338 762 CA4 carbonic anhydrase IV clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 157 -4.18 down 3 1 1/3 -1.39333333333333 3 138 3.13 -4.61 M83670 M83670 Carbonic anhydrase IV CAIV 2.7 -2.70 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1733 762 CA4 carbonic anhydrase IV affy_probe_2_Entrez 4 4 157 -4.18 down 3 1 1/3 -1.39333333333333 3 138 3.13 -4.61 206209_s_at 206209_s_at carbonic anhydrase IV CA4 -4.612 -4.61 down 0.002308296 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 643 762 CA4 carbonic anhydrase IV affy_probe_2_Entrez 4 4 157 -4.18 down 3 1 1/3 -1.39333333333333 3 138 3.13 -4.61 206209_s_at 206209_s_at carbonic anhydrase IV -3.13 3.13 up 0.002362 FA FTC 12 12 provided by authors 15713710 11 18 808 771 CA12 carbonic anhydrase XII clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 109 3.3 up 2 1 2/1 3.3 1 59 3.30 3.30 AF037335 AF037335 Carbonic anhydrase precursor (CA 12) down ACL;ATC Norm 21 10 publication 15613457 13 20 869 771 CA12 carbonic anhydrase XII clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 109 3.3 up 2 1 2/1 3.3 1 59 3.30 3.30 AF037335 AF037335 Carbonic anhydrase XII CA12 up FTC FA 9 10 publication 12738736 18 31 1319 771 CA12 carbonic anhydrase XII clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 109 3.3 up 2 1 2/1 3.3 1 59 3.30 3.30 AF037335 AF037335 Carbonic anhydrase precursor CA 12 3.3 3.30 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 13 20 908 778 CACNA1F calcium channel, voltage-dependent, alpha 1F subunit clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 U93305 U93305 Proteolipid protein 2 PLP2 up FTC FA 9 10 publication 12738736 11 18 830 811 CALR calreticulin clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 M84739 M84739 Autoantigen calreticulin (CALR) down ACL;ATC Norm 21 10 publication 15613457 2 2 71 837 CASP4 caspase 4, apoptosis-related cysteine protease clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -7.6 down 1 0 0/1 -7.6 1 2 -7.60 -7.60 NM_001225 NM_001225 Caspase 4, apoptosis-related cysteine protease CASP4 7.6 -7.60 down FCL Norm 1 1 publication 15785240 15 22 1036 846 CASR calcium-sensing receptor (hypocalciuric hypercalcemia 1, severe neonatal hyperparathyroidism) Gene_symbol_2_NCBI_Entrez 1 1 7 -2 down 1 0 0/1 -2 1 7 -2.00 -2.00 Calcium-sensing receptor CASR 0.5 -2.00 down FTC FA 3 4 publication 15475448 25 34 1665 862 RUNX1T1 runt-related transcription factor 1; translocated to, 1 (cyclin D-related) affy_probe_2_Entrez 1 1 55 -2.49 down 1 0 0/1 -2.49 1 55 -2.49 -2.49 205529_s_at 205529_s_at core-binding factor, runt domain, alpha subunit 2; translocated to, 1; cyclin D-related CBFA2T1 -2.493 -2.49 down 0.000490859 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 874 875 CBS cystathionine-beta-synthase clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 L00972 L00972 Cystathionine-beta-synthetase CBS up FTC FA 9 10 publication 12738736 2 2 79 894 CCND2 cyclin D2 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 58 7.8 up 2 1 2/1 2.6 3 58 11.72 -6.40 NM_001759 NM_001759 Cyclin D2 CCND2 6.4 -6.40 down FCL Norm 1 1 publication 15785240 24 33 1500 894 CCND2 cyclin D2 Gene_symbol_2_NCBI_Entrez 3 3 58 7.8 up 2 1 2/1 2.6 3 58 11.72 -6.40 Cyclin D2 CCND2 1.31 2.48 up PTC Norm 16 16 publication 15735049 9 14 677 894 CCND2 cyclin D2 affy_probe_2_Entrez 3 3 58 7.8 up 2 1 2/1 2.6 3 58 11.72 -6.40 200953_s_at 200953_s_at cyclin D2 -3.9 3.9 up 0.000164 FA FTC 12 12 provided by authors 15713710 9 14 700 894 CCND2 cyclin D2 affy_probe_2_Entrez 3 3 58 7.8 up 2 1 2/1 2.6 3 58 11.72 -6.40 200952_s_at 200952_s_at cyclin D2 -11.72 11.72 up 0.00255 FA FTC 12 12 provided by authors 15713710 14 21 979 900 CCNG1 cyclin G1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 2.8 up 1 0 1/0 2.8 1 14 2.80 2.80 AA082943 AA082943 Cyclin G1 2.8 2.80 up PTC Norm 7 7 publication 15041723 14 21 994 902 CCNH cyclin H Gene_symbol_2_NCBI_Entrez 1 1 14 0 up 1 0 1/0 0 0 0 0 0 Tetracycline transporter-like protein Cyclin H CCNH up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 11 18 834 909 CD1A CD1A antigen, a polypeptide clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 X04450 X04450 CD1a antigen (CD1a gene) down ACL;ATC Norm 21 10 publication 15613457 11 18 795 947 CD34 CD34 antigen clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 S53911 S53911 CD34 down ACL;ATC Norm 21 10 publication 15613457 9 14 657 948 CD36 CD36 antigen (collagen type I receptor, thrombospondin receptor) affy_probe_2_Entrez 1 1 24 3.42 up 1 0 1/0 3.42 1 24 3.42 3.42 206488_s_at 206488_s_at CD36 antigen (collagen type I receptor, thrombospondin receptor) -3.42 3.42 up 0.000077 FA FTC 12 12 provided by authors 15713710 25 34 1551 953 ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 affy_probe_2_Entrez 2 2 79 15.22 up 2 0 2/0 7.61 2 79 8.82 6.40 209474_s_at 209474_s_at ectonucleoside triphosphate diphosphohydrolase 1 ENTPD1 14.021 14.02 up 0.000215841 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1558 953 ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 affy_probe_2_Entrez 2 2 79 15.22 up 2 0 2/0 7.61 2 79 8.82 6.40 207691_x_at 207691_x_at ectonucleoside triphosphate diphosphohydrolase 1 ENTPD1 9.429 9.43 up 0.001074251 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1568 953 ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 affy_probe_2_Entrez 2 2 79 15.22 up 2 0 2/0 7.61 2 79 8.82 6.40 209473_at 209473_at ectonucleoside triphosphate diphosphohydrolase 1 ENTPD1 6.398 6.40 up 0.005195822 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 684 953 ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 affy_probe_2_Entrez 2 2 79 15.22 up 2 0 2/0 7.61 2 79 8.82 6.40 209473_at 209473_at ectonucleoside triphosphate diphosphohydrolase 1 -4.2 4.2 up 0.005397 FA FTC 12 12 provided by authors 15713710 9 14 693 953 ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 affy_probe_2_Entrez 2 2 79 15.22 up 2 0 2/0 7.61 2 79 8.82 6.40 207691_x_at 207691_x_at ectonucleoside triphosphate diphosphohydrolase 1 -5.01 5.01 up 0.007791 FA FTC 12 12 provided by authors 15713710 9 14 699 953 ENTPD1 ectonucleoside triphosphate diphosphohydrolase 1 affy_probe_2_Entrez 2 2 79 15.22 up 2 0 2/0 7.61 2 79 8.82 6.40 209474_s_at 209474_s_at ectonucleoside triphosphate diphosphohydrolase 1 -8.82 8.82 up 0.007519 FA FTC 12 12 provided by authors 15713710 24 33 1504 960 CD44 CD44 antigen (homing function and Indian blood group system) Gene_symbol_2_NCBI_Entrez 3 3 111 9.38 up 3 0 3/0 3.12666666666667 3 111 4.51 2.24 CD44 antigen (homing function and Indian blood group system) CD44 1.165 2.24 up PTC Norm 16 16 publication 15735049 25 34 1605 960 CD44 CD44 antigen (homing function and Indian blood group system) affy_probe_2_Entrez 3 3 111 9.38 up 3 0 3/0 3.12666666666667 3 111 4.51 2.24 204490_s_at 204490_s_at CD44 antigen (homing function and Indian blood group system) CD44 2.831 2.83 up 0.005179358 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1606 960 CD44 CD44 antigen (homing function and Indian blood group system) affy_probe_2_Entrez 3 3 111 9.38 up 3 0 3/0 3.12666666666667 3 111 4.51 2.24 212014_x_at 212014_x_at CD44 antigen (homing function and Indian blood group system) CD44 2.819 2.82 up 0.009385995 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1610 960 CD44 CD44 antigen (homing function and Indian blood group system) affy_probe_2_Entrez 3 3 111 9.38 up 3 0 3/0 3.12666666666667 3 111 4.51 2.24 209835_x_at 209835_x_at CD44 antigen (homing function and Indian blood group system) CD44 2.628 2.63 up 0.024470493 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 655 960 CD44 CD44 antigen (homing function and Indian blood group system) affy_probe_2_Entrez 3 3 111 9.38 up 3 0 3/0 3.12666666666667 3 111 4.51 2.24 212014_x_at 212014_x_at CD44 antigen (homing function and Indian blood group system) -3.3 3.3 up 0.001058 FA FTC 12 12 provided by authors 15713710 9 14 665 960 CD44 CD44 antigen (homing function and Indian blood group system) affy_probe_2_Entrez 3 3 111 9.38 up 3 0 3/0 3.12666666666667 3 111 4.51 2.24 209835_x_at 209835_x_at CD44 antigen (homing function and Indian blood group system) -3.62 3.62 up 0.000999 FA FTC 12 12 provided by authors 15713710 9 14 666 960 CD44 CD44 antigen (homing function and Indian blood group system) affy_probe_2_Entrez 3 3 111 9.38 up 3 0 3/0 3.12666666666667 3 111 4.51 2.24 212063_at 212063_at CD44 antigen (homing function and Indian blood group system) -3.63 3.63 up 0.000459 FA FTC 12 12 provided by authors 15713710 9 14 670 960 CD44 CD44 antigen (homing function and Indian blood group system) affy_probe_2_Entrez 3 3 111 9.38 up 3 0 3/0 3.12666666666667 3 111 4.51 2.24 217523_at 217523_at ESTs, Highly similar to CD44_HUMAN CD44 antigen precursor -3.73 3.73 up 0.000505 FA FTC 12 12 provided by authors 15713710 9 14 676 960 CD44 CD44 antigen (homing function and Indian blood group system) affy_probe_2_Entrez 3 3 111 9.38 up 3 0 3/0 3.12666666666667 3 111 4.51 2.24 204490_s_at 204490_s_at CD44 antigen (homing function and Indian blood group system) -3.9 3.9 up 0.000901 FA FTC 12 12 provided by authors 15713710 9 14 689 960 CD44 CD44 antigen (homing function and Indian blood group system) affy_probe_2_Entrez 3 3 111 9.38 up 3 0 3/0 3.12666666666667 3 111 4.51 2.24 204489_s_at 204489_s_at CD44 antigen (homing function and Indian blood group system) -4.51 4.51 up 0.001994 FA FTC 12 12 provided by authors 15713710 15 22 1025 961 CD47 CD47 antigen (Rh-related antigen, integrin-associated signal transducer) Gene_symbol_2_NCBI_Entrez 1 1 7 3 up 1 0 1/0 3 1 7 3.00 3.00 CD47 antigen CD47 3 3.00 up FTC FA 3 4 publication 15475448 3 6 143 984 CDC2L1 cell division cycle 2-like 1 (PITSLRE proteins) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 -2.4 down 1 0 0/1 -2.4 1 16 -2.40 -2.40 M37712 M37712 P58/GTA (galactosyltransferase associated protein kinase) CDC2L1 -2.4 -2.40 down no 0.0035 PTC Norm 8 8 suppl. materials 11752453 2 2 72 989 SEPT7 septin 7 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 3.36 up 1 0 1/0 3.36 1 2 3.36 3.36 NM_001788 NM_001788 CDC10 cell division cycle 10 homologue CDC10 7.4 -7.40 down FCL Norm 1 1 publication 15785240 2 2 84 989 SEPT7 septin 7 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 3.36 up 1 0 1/0 3.36 1 2 3.36 3.36 NM_001788 NM_001788 Cell division cycle 10 homologue CDC10 3.36 3.36 up FCL Norm 1 1 publication 15785240 14 21 981 999 CDH1 cadherin 1, type 1, E-cadherin (epithelial) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 77 1.06 even 1 1 1/1 0.53 2 77 2.80 -1.74 H97778 H97778 E-cadherin 2.8 2.80 up PTC Norm 7 7 publication 15041723 16 24 1216 999 CDH1 cadherin 1, type 1, E-cadherin (epithelial) Gene_symbol_2_NCBI_Entrez 2 2 77 1.06 even 1 1 1/1 0.53 2 77 2.80 -1.74 CDH1 0.625954198 -1.60 down 0.04 PTC;FVPTC FA;HN 32 31 publication 15087409 16 24 1228 999 CDH1 cadherin 1, type 1, E-cadherin (epithelial) Gene_symbol_2_NCBI_Entrez 2 2 77 1.06 even 1 1 1/1 0.53 2 77 2.80 -1.74 CDH1 0.57615894 -1.74 down yes 0.001 PTC;FVPTC FA;HN 32 31 publication 15087409 24 33 1444 1001 CDH3 cadherin 3, type 1, P-cadherin (placental) Gene_symbol_2_NCBI_Entrez 2 2 87 89.82 up 2 0 2/0 44.91 2 87 48.84 40.98 Cadherin 3, type 1, P-cadherin (placental) CDH3 5.61 48.84 up PTC Norm 16 16 publication 15735049 25 34 1545 1001 CDH3 cadherin 3, type 1, P-cadherin (placental) affy_probe_2_Entrez 2 2 87 89.82 up 2 0 2/0 44.91 2 87 48.84 40.98 203256_at 203256_at cadherin 3, type 1, P-cadherin (placental) CDH3 40.978 40.98 up 1.95563E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 2 4 104 1006 CDH8 cadherin 8, type 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -4.2 down 1 0 0/1 -4.2 1 2 -4.20 -4.20 NM_001796 NM_001796 Cadherin 8, type 2 CDH8 4.2 -4.20 down yes PCL Norm 1 1 publication 15785240 25 34 1773 1014 CDH16 cadherin 16, KSP-cadherin affy_probe_2_Entrez 1 1 55 -9.33 down 1 0 0/1 -9.33 1 55 -9.33 -9.33 206517_at 206517_at cadherin 16, KSP-cadherin CDH16 -9.334 -9.33 down 3.20661E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 14 21 993 1015 CDH17 cadherin 17, LI cadherin (liver-intestine) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 2 up 1 0 1/0 2 1 14 2.00 2.00 AA088861 AA088861 LI-cadherin 2 2.00 up PTC Norm 7 7 publication 15041723 25 34 1635 1039 CDR2 cerebellar degeneration-related protein 2, 62kDa affy_probe_2_Entrez 1 1 55 -2 down 1 0 0/1 -2 1 55 -2.00 -2.00 209501_at 209501_at cerebellar degeneration-related protein 2, 62kDa CDR2 -2.004 -2.00 down 0.000976225 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 870 1054 CEBPG CCAAT/enhancer binding protein (C/EBP), gamma clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 U20240 U20240 CCAAT/enhancer binding protein (C/EBP), CEBPG up FTC FA 9 10 publication 12738736 24 33 1479 1075 CTSC cathepsin C Gene_symbol_2_NCBI_Entrez 1 1 32 4.72 up 1 0 1/0 4.72 1 32 4.72 4.72 Cathepsin C CTSC 2.24 4.72 up PTC Norm 16 16 publication 15735049 11 18 786 1087 CEACAM7 carcinoembryonic antigen-related cell adhesion molecule 7 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 33 3.23 even 1 1 1/1 3.23 1 2 3.23 3.23 L31792 L31792 Carcinoembryonic antigen (CGM2) down ACL;ATC Norm 21 10 publication 15613457 2 2 85 1087 CEACAM7 carcinoembryonic antigen-related cell adhesion molecule 7 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 33 3.23 even 1 1 1/1 3.23 1 2 3.23 3.23 NM_006890 NM_006890 Carcinoembryonic antigen-related cell adhesion molecule 7 CEACAM7 3.23 3.23 up FCL Norm 1 1 publication 15785240 14 21 991 1107 CHD3 chromodomain helicase DNA binding protein 3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 2 up 1 0 1/0 2 1 14 2.00 2.00 AA778077 AA778077 Chromodomain helicase DNA binding protein 3 2 2.00 up PTC Norm 7 7 publication 15041723 25 34 1727 1113 CHGA chromogranin A (parathyroid secretory protein 1) affy_probe_2_Entrez 1 1 55 -4.02 down 1 0 0/1 -4.02 1 55 -4.02 -4.02 204697_s_at 204697_s_at chromogranin A (parathyroid secretory protein 1) CHGA -4.017 -4.02 down 0.013328833 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1445 1116 CHI3L1 chitinase 3-like 1 (cartilage glycoprotein-39) Gene_symbol_2_NCBI_Entrez 2 2 48 49.56 up 2 0 2/0 24.78 2 48 27.70 21.86 Chitinase 3-like 1 (cartilage glycoprotein-39) CHI3L1 4.45 21.86 up PTC Norm 16 16 publication 15735049 3 6 114 1116 CHI3L1 chitinase 3-like 1 (cartilage glycoprotein-39) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 48 49.56 up 2 0 2/0 24.78 2 48 27.70 21.86 Y08374 Y08374 Cartilage GP-39 CHI3L1 27.7 27.70 up yes 0.002 PTC Norm 8 8 suppl. materials 11752453 18 31 1324 1152 CKB creatine kinase, brain clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -3.1 down 1 0 0/1 -3.1 1 59 -3.10 -3.10 X15334 X15334 Creatine kinase B CKBB 3.1 -3.10 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 2 3 95 1191 CLU clusterin (complement lysis inhibitor, SP-40,40, sulfated glycoprotein 2, testosterone-repressed prostate message 2, apolipoprotein J) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 4 -2.5 down 1 0 0/1 -2.5 1 4 -2.50 -2.50 NM_001831 NM_001831 Clusterin CLU 2.5 -2.50 down FCL;PCL;UCL Norm 3 1 publication 15785240 17 26 1266 1277 COL1A1 collagen, type I, alpha 1 tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 ACCAAAAACC ACCAAAAACC up FTC FA 1 1 publication 11076659 10 16 712 1293 COL6A3 collagen, type VI, alpha 3 affy_probe_2_Entrez 1 1 14 8.54 up 1 0 1/0 8.54 1 14 8.54 8.54 38077_at 38077_at Collagen, type VI, alpha 3 COL6A3 8.54 8.54 up no PTC GT 8 6 publication 15515157 24 33 1482 1296 COL8A2 collagen, type VIII, alpha 2 Gene_symbol_2_NCBI_Entrez 1 1 32 3.97 up 1 0 1/0 3.97 1 32 3.97 3.97 Collagen, type VIII, alpha2 COL8A2 1.99 3.97 up PTC Norm 16 16 publication 15735049 10 16 746 1299 COL9A3 collagen, type IX, alpha 3 affy_probe_2_Entrez 3 3 128 -41.92 down 3 0 0/3 -13.9733333333333 3 128 -4.50 -27.39 36455_at 36455_at Collagen, type IX, alpha 3 COL9A3 -10.03 -10.03 down yes PTC GT 8 6 publication 15515157 18 31 1307 1299 COL9A3 collagen, type IX, alpha 3 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 128 -41.92 down 3 0 0/3 -13.9733333333333 3 128 -4.50 -27.39 L41162 L41162 Collagen alpha 3 type IX (COL9A3) EDM3 4.5 -4.50 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1784 1299 COL9A3 collagen, type IX, alpha 3 affy_probe_2_Entrez 3 3 128 -41.92 down 3 0 0/3 -13.9733333333333 3 128 -4.50 -27.39 204724_s_at 204724_s_at collagen, type IX, alpha 3 COL9A3 -27.386 -27.39 down 0.002882418 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1471 1305 COL13A1 collagen, type XIII, alpha 1 Gene_symbol_2_NCBI_Entrez 1 1 32 5.46 up 1 0 1/0 5.46 1 32 5.46 5.46 Collagen, type XIII, alpha 1 COL13A1 2.45 5.46 up PTC Norm 16 16 publication 15735049 13 20 926 1306 COL15A1 collagen, type XV, alpha 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 L25286 L25286 Collagen, type XV, 1 COL15A1 down FTC FA 9 10 publication 12738736 24 33 1454 1311 COMP cartilage oligomeric matrix protein Gene_symbol_2_NCBI_Entrez 1 1 32 14.27 up 1 0 1/0 14.27 1 32 14.27 14.27 Cartilage oligomeric matrix protein COMP 3.835 14.27 up PTC Norm 16 16 publication 15735049 9 14 667 1363 CPE carboxypeptidase E affy_probe_2_Entrez 1 1 24 3.72 up 1 0 1/0 3.72 1 24 3.72 3.72 201117_s_at 201117_s_at carboxypeptidase E -3.72 3.72 up 0.000008 FA FTC 12 12 provided by authors 15713710 10 17 754 1381 CRABP1 cellular retinoic acid binding protein 1 affy_probe_2_Entrez 4 4 146 -46.19 down 4 0 0/4 -11.5475 4 146 -2.20 -24.45 542_at 542_at Cellular retinoic acid binding protein 1 CRABP1 -11.84 -11.84 down yes yes PTC Norm 8 8 publication 15515157 18 31 1376 1381 CRABP1 cellular retinoic acid binding protein 1 clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 146 -46.19 down 4 0 0/4 -11.5475 4 146 -2.20 -24.45 S74445 S74445 Cellular retinoic acid-binding protein I CRABPI 2.2 -2.20 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1782 1381 CRABP1 cellular retinoic acid binding protein 1 affy_probe_2_Entrez 4 4 146 -46.19 down 4 0 0/4 -11.5475 4 146 -2.20 -24.45 205350_at 205350_at cellular retinoic acid binding protein 1 CRABP1 -24.447 -24.45 down 0.00016996 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 160 1381 CRABP1 cellular retinoic acid binding protein 1 clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 146 -46.19 down 4 0 0/4 -11.5475 4 146 -2.20 -24.45 S74445 S74445 Cellular retinoic acid-binding protein CRABP1 -7.7 -7.70 down no 0.01 PTC Norm 8 8 suppl. materials 11752453 2 4 97 1387 CREBBP CREB binding protein (Rubinstein-Taybi syndrome) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -10.2 down 1 0 0/1 -10.2 1 2 -10.20 -10.20 NM_004380 NM_004380 CREB binding protein CREBBP 10.2 -10.20 down PCL Norm 1 1 publication 15785240 13 20 924 1390 CREM cAMP responsive element modulator clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 S68271 S68271 cAMP-responsive element modulator CREM down FTC FA 9 10 publication 12738736 9 14 606 1410 CRYAB crystallin, alpha B affy_probe_2_Entrez 1 1 24 -4.63 down 1 0 0/1 -4.63 1 24 -4.63 -4.63 209283_at 209283_at crystallin, alpha B 4.63 -4.63 down 0.006704 FA FTC 12 12 provided by authors 15713710 19 32 1407 1429 CRYZ crystallin, zeta (quinone reductase) tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 ACTGTATTGG ACTGTATTGG quinone reductase (crystallin Z) up 0.0245 FVPTC Norm 1 1 publication 14715705 14 21 975 1464 CSPG4 chondroitin sulfate proteoglycan 4 (melanoma-associated) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 3.1 up 1 0 1/0 3.1 1 14 3.10 3.10 R53541 R53541 Melanoma-associated chondroitin sulfate proteoglycan 3.1 3.10 up PTC Norm 7 7 publication 15041723 18 31 1384 1466 CSRP2 cysteine and glycine-rich protein 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2.1 down 1 0 0/1 -2.1 1 59 -2.10 -2.10 U57646 U57646 Cysteine and glycine-rich protein 2 CSRP2 2.1 -2.10 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 3 6 120 1474 CST6 cystatin E/M clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 9 up 1 0 1/0 9 1 16 9.00 9.00 W68521 W68521 Cystatin E/M CST6 9 9.00 up no 0.003 PTC Norm 8 8 suppl. materials 11752453 24 33 1536 1491 CTH cystathionase (cystathionine gamma-lyase) Gene_symbol_2_NCBI_Entrez 1 1 32 -2.58 down 1 0 0/1 -2.58 1 32 -2.58 -2.58 Cystathionase (cystathionine gamma-lyase) CTH -1.365 -2.58 down PTC Norm 16 16 publication 15735049 18 31 1345 1512 CTSH cathepsin H clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 2.5 up 1 0 1/0 2.5 1 59 2.50 2.50 X16832 X16832 Preprocathepsin H CPSB 2.5 2.50 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 2 4 101 1514 CTSL cathepsin L clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -6.1 down 1 0 0/1 -6.1 1 2 -6.10 -6.10 NM_001912 NM_001912 Cathepsin L CTSL 6.1 -6.10 down PCL Norm 1 1 publication 15785240 2 2 59 1522 CTSZ cathepsin Z clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -13.6 down 1 0 0/1 -13.6 1 2 -13.60 -13.60 NM_001336 NM_001336 Cathepsin Z CTSZ 13.6 -13.60 down FCL Norm 1 1 publication 15785240 10 16 734 1525 CXADR coxsackie virus and adenovirus receptor affy_probe_2_Entrez 1 1 14 -3.33 down 1 0 0/1 -3.33 1 14 -3.33 -3.33 37534_at 37534_at Coxsackievirus and adenovirus receptor CXADR -3.33 -3.33 down yes PTC GT 8 6 publication 15515157 12 19 843 1536 CYBB cytochrome b-245, beta polypeptide (chronic granulomatous disease) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 21 7.7 up 1 0 1/0 7.7 1 21 7.70 7.70 X04011 X04011 CGD 7.7 7.70 up PTC Norm 18 3 publication 12538453 9 14 615 1538 CYLC1 cylicin, basic protein of sperm head cytoskeleton 1 affy_probe_2_Entrez 1 1 24 -2.93 down 1 0 0/1 -2.93 1 24 -2.93 -2.93 216778_s_at 216778_s_at cylicin, basic protein of sperm head cytoskeleton 1 2.93 -2.93 down 0.000612 FA FTC 12 12 provided by authors 15713710 18 31 1301 1545 CYP1B1 cytochrome P450, family 1, subfamily B, polypeptide 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 6 up 1 0 1/0 6 1 59 6.00 6.00 U03688 U03688 Dioxin-inducible cytochrome P450 GLC3A 6 6.00 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 2 3 92 1634 DCN decorin clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 4 -3 down 1 0 0/1 -3 1 4 -3.00 -3.00 NM_001920 NM_001920 Decorin DCN 3 -3.00 down yes FCL;PCL;UCL Norm 3 1 publication 15785240 3 6 152 1645 AKR1C1 aldo-keto reductase family 1, member C1 (dihydrodiol dehydrogenase 1; 20-alpha (3-alpha)-hydroxysteroid dehydrogenase) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 -3.5 down 1 0 0/1 -3.5 1 16 -3.50 -3.50 U05861 U05861 Hepatic dihydrodiol dehydrogenase AKR1C2 -3.5 -3.50 down no 0.0015 PTC Norm 8 8 suppl. materials 11752453 12 19 860 1649 DDIT3 DNA-damage-inducible transcript 3 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 43 -3.85 up 2 1 2/1 -3.85 1 21 -3.85 -3.85 S40706 S40706 Growth arrest and DNA damage-inducible protein GADD153 (DDIT3) 0.26 -3.85 down yes PTC Norm 18 3 publication 12538453 13 20 875 1649 DDIT3 DNA-damage-inducible transcript 3 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 43 -3.85 up 2 1 2/1 -3.85 1 21 -3.85 -3.85 S62138 S62138 DNA damage-inducible transcript 3 DDIT3 up FTC FA 9 10 publication 12738736 5 10 380 1649 DDIT3 DNA-damage-inducible transcript 3 tag_2_refseq_or_mgc_2_Entrez 3 3 43 -3.85 up 2 1 2/1 -3.85 1 21 -3.85 -3.85 AACAATTGGG AACAATTGGG DDIT3 up yes FTC FA;Norm 1 2 publication 15085203 25 34 1764 1675 DF D component of complement (adipsin) affy_probe_2_Entrez 1 1 55 -7 down 1 0 0/1 -7 1 55 -7.00 -7.00 205382_s_at 205382_s_at D component of complement (adipsin) DF -6.998 -7.00 down 0.000843024 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 923 1733 DIO1 deiodinase, iodothyronine, type I clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 94 -7.5 down 3 0 0/3 -3.75 2 75 -2.30 -5.20 S48220 S48220 5iodothyronine deiodinase down FTC FA 9 10 publication 12738736 18 31 1363 1733 DIO1 deiodinase, iodothyronine, type I clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 94 -7.5 down 3 0 0/3 -3.75 2 75 -2.30 -5.20 S48220 S48220 Type I 5iodothyronine deiodinase TXDI1 2.3 -2.30 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 3 6 155 1733 DIO1 deiodinase, iodothyronine, type I clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 94 -7.5 down 3 0 0/3 -3.75 2 75 -2.30 -5.20 S48220 S48220 Type I 5 iodothyronine deiodinase DIO1 -5.2 -5.20 down no 0.005 PTC Norm 8 8 suppl. materials 11752453 16 24 1246 1734 DIO2 deiodinase, iodothyronine, type II Gene_symbol_2_NCBI_Entrez 2 2 79 -4.99 down 2 0 0/2 -2.495 2 79 -2.20 -2.79 DIO2 0.358974359 -2.79 down 0.02 PTC;FVPTC FA;HN 32 31 publication 15087409 3 6 139 1734 DIO2 deiodinase, iodothyronine, type II clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 79 -4.99 down 2 0 0/2 -2.495 2 79 -2.20 -2.79 AF093774 AF093774 Type 2 iodothyronine deiodinase DIO2 -2.2 -2.20 down no 0.0022 PTC Norm 8 8 suppl. materials 11752453 25 34 1636 1740 DLG2 discs, large homolog 2, chapsyn-110 (Drosophila) affy_probe_2_Entrez 1 1 55 -2.01 down 1 0 0/1 -2.01 1 55 -2.01 -2.01 206253_at 206253_at discs, large homolog 2, chapsyn-110 (Drosophila) DLG2 -2.010 -2.01 down 0.000857183 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 12 19 854 1741 DLG3 discs, large homolog 3 (neuroendocrine-dlg, Drosophila) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 21 -2.08 down 1 0 0/1 -2.08 1 21 -2.08 -2.08 U49089 U49089 Neuroendocrine-DLG, tumor suppressor protein interacting with the adenomatous polyposis coli protein (DLG3) 0.48 -2.08 down PTC Norm 18 3 publication 12538453 5 10 386 1777 DNASE2 deoxyribonuclease II, lysosomal tag_2_refseq_or_mgc_2_Entrez 1 1 3 0 up 1 0 1/0 0 0 0 0 0 AGCTGAGCTA AGCTGAGCTA DNASE2 up no FTC FA;Norm 1 2 publication 15085203 13 20 876 1796 DOK1 docking protein 1, 62kDa (downstream of tyrosine kinase 1) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 AF035299 AF035299 Docking protein 1 (downstream of tyrosine kinase 1) DOK1 up FTC FA 9 10 publication 12738736 24 33 1443 1803 DPP4 dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing protein 2) Gene_symbol_2_NCBI_Entrez 3 3 103 138.58 up 3 0 3/0 46.1933333333333 3 103 115.76 8.20 Dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing protein 2) DPP4 6.855 115.76 up PTC Norm 16 16 publication 15735049 25 34 1548 1803 DPP4 dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing protein 2) affy_probe_2_Entrez 3 3 103 138.58 up 3 0 3/0 46.1933333333333 3 103 115.76 8.20 203717_at 203717_at dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing protein 2) DPP4 14.840 14.84 up 0.000763244 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1549 1803 DPP4 dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing protein 2) affy_probe_2_Entrez 3 3 103 138.58 up 3 0 3/0 46.1933333333333 3 103 115.76 8.20 211478_s_at 211478_s_at dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing protein 2) DPP4 14.622 14.62 up 0.002319596 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 123 1803 DPP4 dipeptidylpeptidase 4 (CD26, adenosine deaminase complexing protein 2) clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 103 138.58 up 3 0 3/0 46.1933333333333 3 103 115.76 8.20 X60708 X60708 Liver dipeptidyl peptidase IV DPP4 8.2 8.20 up no 0.0005 PTC Norm 8 8 suppl. materials 11752453 25 34 1757 1804 DPP6 dipeptidylpeptidase 6 affy_probe_2_Entrez 1 1 55 -6.24 down 1 0 0/1 -6.24 1 55 -6.24 -6.24 207789_s_at 207789_s_at dipeptidylpeptidase 6 DPP6 -6.244 -6.24 down 9.05227E-10 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1772 1805 DPT dermatopontin affy_probe_2_Entrez 2 2 71 -19.84 down 2 0 0/2 -9.92 2 71 -5.50 -14.34 207977_s_at 207977_s_at dermatopontin DPT -8.765 -8.76 down 9.01594E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1774 1805 DPT dermatopontin affy_probe_2_Entrez 2 2 71 -19.84 down 2 0 0/2 -9.92 2 71 -5.50 -14.34 213068_at 213068_at dermatopontin DPT -9.365 -9.36 down 7.87215E-07 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1780 1805 DPT dermatopontin affy_probe_2_Entrez 2 2 71 -19.84 down 2 0 0/2 -9.92 2 71 -5.50 -14.34 213071_at 213071_at dermatopontin DPT -14.338 -14.34 down 1.24888E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 157 1805 DPT dermatopontin clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 71 -19.84 down 2 0 0/2 -9.92 2 71 -5.50 -14.34 Z22865 Z22865 Dermatopontin DPT -5.5 -5.50 down no 0.0003 PTC Norm 8 8 suppl. materials 11752453 9 14 656 1806 DPYD dihydropyrimidine dehydrogenase affy_probe_2_Entrez 1 1 24 3.33 up 1 0 1/0 3.33 1 24 3.33 3.33 204646_at 204646_at dihydropyrimidine dehydrogenase -3.33 3.33 up 0.000767 FA FTC 12 12 provided by authors 15713710 14 21 972 1819 DRG2 developmentally regulated GTP binding protein 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 4.3 up 1 0 1/0 4.3 1 14 4.30 4.30 AA456291 AA456291 GTP-binding protein 4.3 4.30 up PTC Norm 7 7 publication 15041723 15 22 1061 1843 DUSP1 dual specificity phosphatase 1 Gene_symbol_2_NCBI_Entrez 2 2 23 -12.4 down 2 0 0/2 -6.2 2 23 -2.40 -10.00 Dual specificity phosphatase 1 DUSP1 0.1 -10.00 down FTC FA 3 4 publication 15475448 3 6 142 1843 DUSP1 dual specificity phosphatase 1 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 23 -12.4 down 2 0 0/2 -6.2 2 23 -2.40 -10.00 X68277 X68277 CL 100 mRNA for protein tyrosine phosphatase DUSP1 -2.4 -2.40 down no 0.0058 PTC Norm 8 8 suppl. materials 11752453 18 31 1308 1846 DUSP4 dual specificity phosphatase 4 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 114 9.06 up 2 0 2/0 4.53 2 114 4.86 4.20 U48807 U48807 MAP kinase phosphatase MKP-2 4.2 4.20 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1570 1846 DUSP4 dual specificity phosphatase 4 affy_probe_2_Entrez 2 2 114 9.06 up 2 0 2/0 4.53 2 114 4.86 4.20 204015_s_at 204015_s_at dual specificity phosphatase 4 DUSP4 5.873 5.87 up 5.22167E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1579 1846 DUSP4 dual specificity phosphatase 4 affy_probe_2_Entrez 2 2 114 9.06 up 2 0 2/0 4.53 2 114 4.86 4.20 204014_at 204014_at dual specificity phosphatase 4 DUSP4 4.861 4.86 up 0.001878589 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 15 22 1053 1847 DUSP5 dual specificity phosphatase 5 Gene_symbol_2_NCBI_Entrez 3 3 129 4.32 up 2 1 2/1 1.44 3 129 4.05 -3.33 Dual specificity phosphatase 5 DUSP5 0.3 -3.33 down yes FTC FA 3 4 publication 15475448 16 24 1203 1847 DUSP5 dual specificity phosphatase 5 Gene_symbol_2_NCBI_Entrez 3 3 129 4.32 up 2 1 2/1 1.44 3 129 4.05 -3.33 DUSP5 4.051546392 4.05 up 0.01 PTC;FVPTC FA;HN 32 31 publication 15087409 18 31 1312 1847 DUSP5 dual specificity phosphatase 5 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 129 4.32 up 2 1 2/1 1.44 3 129 4.05 -3.33 U15932 U15932 Dual-specificity protein phosphatase HVH3 3.6 3.60 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1486 1848 DUSP6 dual specificity phosphatase 6 Gene_symbol_2_NCBI_Entrez 3 3 72 13.5 up 3 0 3/0 4.5 3 72 5.22 3.68 Dual specificity phosphatase 6 DUSP6 1.88 3.68 up PTC Norm 16 16 publication 15735049 3 6 132 1848 DUSP6 dual specificity phosphatase 6 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 72 13.5 up 3 0 3/0 4.5 3 72 5.22 3.68 AB013382 AB013382 Dual specificity phosphatase 6 DUSP6 4.6 4.60 up no 0.0001 PTC Norm 8 8 suppl. materials 11752453 9 14 668 1848 DUSP6 dual specificity phosphatase 6 affy_probe_2_Entrez 3 3 72 13.5 up 3 0 3/0 4.5 3 72 5.22 3.68 208891_at 208891_at dual specificity phosphatase 6 -3.72 3.72 up 0.000007 FA FTC 12 12 provided by authors 15713710 9 14 694 1848 DUSP6 dual specificity phosphatase 6 affy_probe_2_Entrez 3 3 72 13.5 up 3 0 3/0 4.5 3 72 5.22 3.68 208892_s_at 208892_s_at dual specificity phosphatase 6 -5.22 5.22 up 0.000084 FA FTC 12 12 provided by authors 15713710 19 32 1404 1893 ECM1 extracellular matrix protein 1 tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 ACTGCCCGCT ACTGCCCGCT extracellular matrix protein 1 (ECM1) up 0.0007 FVPTC Norm 1 1 publication 14715705 24 33 1495 1955 EGFL5 EGF-like-domain, multiple 5 Gene_symbol_2_NCBI_Entrez 1 1 32 2.66 up 1 0 1/0 2.66 1 32 2.66 2.66 Epidermal growth factor-like-domain, multiple 5 EGFL5 1.41 2.66 up PTC Norm 16 16 publication 15735049 25 34 1744 1958 EGR1 early growth response 1 affy_probe_2_Entrez 1 1 55 -5.09 down 1 0 0/1 -5.09 1 55 -5.09 -5.09 201693_s_at 201693_s_at early growth response 1 EGR1 -5.088 -5.09 down 0.004189334 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 928 1959 EGR2 early growth response 2 (Krox-20 homolog, Drosophila) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 J04076 J04076 Early growth response 2 EGR2 down FTC FA 9 10 publication 12738736 2 5 106 1965 EIF2S1 eukaryotic translation initiation factor 2, subunit 1 alpha, 35kDa clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -7.8 down 1 0 0/1 -7.8 1 2 -7.80 -7.80 NM_004094 NM_004094 Eukaryotic translation initiation factor 2, subunit 1 EIF2S1 7.8 -7.80 down UCL Norm 1 1 publication 15785240 25 34 1643 1983 EIF5 eukaryotic translation initiation factor 5 affy_probe_2_Entrez 1 1 55 -2.1 down 1 0 0/1 -2.1 1 55 -2.10 -2.10 208707_at 208707_at eukaryotic translation initiation factor 5 EIF5 -2.104 -2.10 down 0.003511325 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 16 24 1207 1999 ELF3 E74-like factor 3 (ets domain transcription factor, epithelial-specific ) Gene_symbol_2_NCBI_Entrez 1 1 63 1.77 up 1 0 1/0 1.77 1 63 1.77 1.77 ELF3 1.768292683 1.77 up 0.04 PTC;FVPTC FA;HN 32 31 publication 15087409 25 34 1691 2047 EPHB1 EPH receptor B1 affy_probe_2_Entrez 1 1 55 -2.95 down 1 0 0/1 -2.95 1 55 -2.95 -2.95 210753_s_at 210753_s_at --- --- -2.950 -2.95 down 2.50857E-07 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 18 31 1381 2059 EPS8 epidermal growth factor receptor pathway substrate 8 clone_accession_2_NCBI_rna_accession_2_Entrez 5 5 186 15.73 up 5 0 5/0 3.146 5 186 3.80 2.10 U12535 U12535 Epidermal growth factor receptor kinase substrate Eps8 2.1 2.10 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1488 2059 EPS8 epidermal growth factor receptor pathway substrate 8 Gene_symbol_2_NCBI_Entrez 5 5 186 15.73 up 5 0 5/0 3.146 5 186 3.80 2.10 Epidermal growth factor receptor pathway substrate 8 EPS8 1.6 3.03 up PTC Norm 16 16 publication 15735049 25 34 1590 2059 EPS8 epidermal growth factor receptor pathway substrate 8 affy_probe_2_Entrez 5 5 186 15.73 up 5 0 5/0 3.146 5 186 3.80 2.10 202609_at 202609_at epidermal growth factor receptor pathway substrate 8 EPS8 3.784 3.78 up 8.47516E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 136 2059 EPS8 epidermal growth factor receptor pathway substrate 8 clone_accession_2_NCBI_rna_accession_2_Entrez 5 5 186 15.73 up 5 0 5/0 3.146 5 186 3.80 2.10 U12535 U12535 Epidermal growth factor receptor kinase substrate 8 EPS8 3.8 3.80 up no 0.0001 PTC Norm 8 8 suppl. materials 11752453 9 14 633 2059 EPS8 epidermal growth factor receptor pathway substrate 8 affy_probe_2_Entrez 5 5 186 15.73 up 5 0 5/0 3.146 5 186 3.80 2.10 202609_at 202609_at epidermal growth factor receptor pathway substrate 8 -3.02 3.02 up 0.002265 FA FTC 12 12 provided by authors 15713710 13 20 900 2063 NR2F6 nuclear receptor subfamily 2, group F, member 6 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 X12794 X12794 Nuclear receptor subfamily 2, group F, member 6 NR2F6 up FTC FA 9 10 publication 12738736 18 31 1377 2065 ERBB3 v-erb-b2 erythroblastic leukemia viral oncogene homolog 3 (avian) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 2.1 up 1 0 1/0 2.1 1 59 2.10 2.10 M34309 M34309 HER3 protein precursor HER3 2.1 2.10 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 14 21 985 2071 ERCC3 excision repair cross-complementing rodent repair deficiency, complementation group 3 (xeroderma pigmentosum group B complementing) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 2.4 up 1 0 1/0 2.4 1 14 2.40 2.40 H20856 H20856 DNA repair helicase ERCC3 2.4 2.40 up PTC Norm 7 7 publication 15041723 25 34 1642 2104 ESRRG estrogen-related receptor gamma affy_probe_2_Entrez 1 1 55 -2.1 down 1 0 0/1 -2.1 1 55 -2.10 -2.10 209966_x_at 209966_x_at estrogen-related receptor gamma ESRRG -2.095 -2.10 down 0.000180269 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1585 2118 ETV4 ets variant gene 4 (E1A enhancer binding protein, E1AF) affy_probe_2_Entrez 1 1 55 4.23 up 1 0 1/0 4.23 1 55 4.23 4.23 211603_s_at 211603_s_at ets variant gene 4 (E1A enhancer binding protein, E1AF) /// ets variant gene 4 (E1A enhancer binding protein, E1AF) ETV4 4.226 4.23 up 0.008957754 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1489 2119 ETV5 ets variant gene 5 (ets-related molecule) Gene_symbol_2_NCBI_Entrez 3 3 111 10.81 up 3 0 3/0 3.60333333333333 3 111 4.38 2.98 Ets variant gene 5 (ets-related molecule) ETV5 1.575 2.98 up PTC Norm 16 16 publication 15735049 25 34 1582 2119 ETV5 ets variant gene 5 (ets-related molecule) affy_probe_2_Entrez 3 3 111 10.81 up 3 0 3/0 3.60333333333333 3 111 4.38 2.98 203349_s_at 203349_s_at ets variant gene 5 (ets-related molecule) ETV5 4.377 4.38 up 8.84969E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 642 2119 ETV5 ets variant gene 5 (ets-related molecule) affy_probe_2_Entrez 3 3 111 10.81 up 3 0 3/0 3.60333333333333 3 111 4.38 2.98 203348_s_at 203348_s_at ets variant gene 5 (ets-related molecule) -3.12 3.12 up 0.001774 FA FTC 12 12 provided by authors 15713710 9 14 659 2119 ETV5 ets variant gene 5 (ets-related molecule) affy_probe_2_Entrez 3 3 111 10.81 up 3 0 3/0 3.60333333333333 3 111 4.38 2.98 203349_s_at 203349_s_at ets variant gene 5 (ets-related molecule) -3.45 3.45 up 0.002668 FA FTC 12 12 provided by authors 15713710 15 22 1034 2132 EXT2 exostoses (multiple) 2 Gene_symbol_2_NCBI_Entrez 1 1 7 -2 down 1 0 0/1 -2 1 7 -2.00 -2.00 Exostose 2 EXT2 0.5 -2.00 down FTC FA 3 4 publication 15475448 11 18 807 2134 EXTL1 exostoses (multiple)-like 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U67191 U67191 Multiple exostosis-like protein (EXTL) down ACL;ATC Norm 21 10 publication 15613457 18 31 1305 2167 FABP4 fatty acid binding protein 4, adipocyte clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 130 -25.66 down 3 0 0/3 -8.55333333333333 3 130 -4.90 -15.36 AA128249 AA128249 Fatty acid-binding protein, human FABP4 4.9 -4.90 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1781 2167 FABP4 fatty acid binding protein 4, adipocyte affy_probe_2_Entrez 3 3 130 -25.66 down 3 0 0/3 -8.55333333333333 3 130 -4.90 -15.36 203980_at 203980_at fatty acid binding protein 4, adipocyte FABP4 -15.359 -15.36 down 0.010575236 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 156 2167 FABP4 fatty acid binding protein 4, adipocyte clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 130 -25.66 down 3 0 0/3 -8.55333333333333 3 130 -4.90 -15.36 AA128249 AA128249 Fatty acid binding protein 4 FABP4 -5.4 -5.40 down no 0.002 PTC Norm 8 8 suppl. materials 11752453 25 34 1743 2192 FBLN1 fibulin 1 affy_probe_2_Entrez 1 1 55 -5.06 down 1 0 0/1 -5.06 1 55 -5.06 -5.06 202995_s_at 202995_s_at fibulin 1 FBLN1 -5.058 -5.06 down 0.014030905 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 933 2200 FBN1 fibrillin 1 (Marfan syndrome) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 X63556 X63556 Fibrillin 1 FBN1 down FTC FA 9 10 publication 12738736 12 19 844 2207 FCER1G Fc fragment of IgE, high affinity I, receptor for; gamma polypeptide clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 21 7.1 up 1 0 1/0 7.1 1 21 7.10 7.10 M33195 M33195 FCER1G 7.1 7.10 up PTC Norm 18 3 publication 12538453 11 18 802 2217 FCGRT Fc fragment of IgG, receptor, transporter, alpha clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 109 -2.8 down 3 0 0/3 -2.8 1 59 -2.80 -2.80 U12255 U12255 IgG Fc receptor hFcRn (FCGRT) down ACL;ATC Norm 21 10 publication 15613457 13 20 932 2217 FCGRT Fc fragment of IgG, receptor, transporter, alpha clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 109 -2.8 down 3 0 0/3 -2.8 1 59 -2.80 -2.80 U12255 U12255 Fc fragment of IgG, receptor, transporter FCGRT down FTC FA 9 10 publication 12738736 18 31 1333 2217 FCGRT Fc fragment of IgG, receptor, transporter, alpha clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 109 -2.8 down 3 0 0/3 -2.8 1 59 -2.80 -2.80 U12255 U12255 Human IgG Fc receptor FCGRT 2.8 -2.80 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1521 2222 FDFT1 farnesyl-diphosphate farnesyltransferase 1 Gene_symbol_2_NCBI_Entrez 1 1 32 -1.44 down 1 0 0/1 -1.44 1 32 -1.44 -1.44 Farnesyl-diphosphate farnesyltransferase 1 FDFT1 -0.525 -1.44 down PTC Norm 16 16 publication 15735049 11 18 824 2242 FES feline sarcoma oncogene clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 X06292 X06292 c-fes/fps proto-oncogene (FES) down yes ACL;ATC Norm 21 10 publication 15613457 9 14 609 2258 FGF13 fibroblast growth factor 13 affy_probe_2_Entrez 1 1 24 -3.85 down 1 0 0/1 -3.85 1 24 -3.85 -3.85 205110_s_at 205110_s_at fibroblast growth factor 13 3.85 -3.85 down 0.002058 FA FTC 12 12 provided by authors 15713710 14 21 1009 2260 FGFR1 fibroblast growth factor receptor 1 (fms-related tyrosine kinase 2, Pfeiffer syndrome) Gene_symbol_2_NCBI_Entrez 1 1 14 0 up 1 0 1/0 0 0 0 0 0 bFGF receptor FGFR1 up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 18 31 1346 2263 FGFR2 fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2.1 down 1 0 0/1 -2.1 1 59 -2.10 -2.10 Z71929 Z71929 Fibroblast growth factor receptor 2 FGFR2 2.5 -2.50 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 18 31 1390 2263 FGFR2 fibroblast growth factor receptor 2 (bacteria-expressed kinase, keratinocyte growth factor receptor, craniofacial dysostosis 1, Crouzon syndrome, Pfeiffer syndrome, Jackson-Weiss syndrome) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2.1 down 1 0 0/1 -2.1 1 59 -2.10 -2.10 M87770 M87770 Fibroblast growth factor receptor K-sam-I 2.1 -2.10 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 14 21 1010 2264 FGFR4 fibroblast growth factor receptor 4 Gene_symbol_2_NCBI_Entrez 1 1 14 0 up 1 0 1/0 0 0 0 0 0 FGF 4 receptor FGFR4 up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 18 31 1388 2273 FHL1 four and a half LIM domains 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2.1 down 1 0 0/1 -2.1 1 59 -2.10 -2.10 AF063002 AF063002 Skeletal and cardiac muscle SLIM isoform SLIM1 2.1 -2.10 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1516 2314 FLII flightless I homolog (Drosophila) Gene_symbol_2_NCBI_Entrez 1 1 32 1.45 up 1 0 1/0 1.45 1 32 1.45 1.45 Flightless I homologue (Drosophila) FLII 0.54 1.45 up PTC Norm 16 16 publication 15735049 25 34 1645 2326 FMO1 flavin containing monooxygenase 1 affy_probe_2_Entrez 1 1 55 -2.12 down 1 0 0/1 -2.12 1 55 -2.12 -2.12 205666_at 205666_at flavin containing monooxygenase 1 FMO1 -2.121 -2.12 down 0.004172401 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1738 2331 FMOD fibromodulin affy_probe_2_Entrez 1 1 55 -4.82 down 1 0 0/1 -4.82 1 55 -4.82 -4.82 202709_at 202709_at fibromodulin FMOD -4.817 -4.82 down 1.09927E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 12 19 847 2335 FN1 fibronectin 1 clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 128 30.69 up 4 0 4/0 7.6725 4 128 10.30 5.20 X02761 X02761 FN 6 6.00 up yes yes PTC Norm 18 3 publication 12538453 18 31 1302 2335 FN1 fibronectin 1 clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 128 30.69 up 4 0 4/0 7.6725 4 128 10.30 5.20 M10905 M10905 Fibronectin FN1 5.2 5.20 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1462 2335 FN1 fibronectin 1 Gene_symbol_2_NCBI_Entrez 4 4 128 30.69 up 4 0 4/0 7.6725 4 128 10.30 5.20 Fibronectin 1 FN1 3.2 9.19 up PTC Norm 16 16 publication 15735049 3 6 119 2335 FN1 fibronectin 1 clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 128 30.69 up 4 0 4/0 7.6725 4 128 10.30 5.20 X02761 X02761 Fibronectin 1 FN1 10.3 10.30 up yes 0.0002 PTC Norm 8 8 suppl. materials 11752453 3 6 153 2354 FOSB FBJ murine osteosarcoma viral oncogene homolog B clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 -4 down 1 0 0/1 -4 1 16 -4.00 -4.00 L49169 L49169 FOSB FOSB -4 -4.00 down yes 0.0047 PTC Norm 8 8 suppl. materials 11752453 13 20 880 2358 FPRL1 formyl peptide receptor-like 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 M84562 M84562 Formyl peptide receptor-like 1 FPRL1 up FTC FA 9 10 publication 12738736 11 18 767 2526 FUT4 fucosyltransferase 4 (alpha (1,3) fucosyltransferase, myeloid-specific) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 M58596 M58596 ELAM-1 ligand fucosyltransferase (ELFT) up ACL;ATC Norm 21 10 publication 15613457 25 34 1566 2582 GALE UDP-galactose-4-epimerase affy_probe_2_Entrez 1 1 55 7.01 up 1 0 1/0 7.01 1 55 7.01 7.01 202528_at 202528_at galactose-4-epimerase, UDP- GALE 7.006 7.01 up 2.90326E-07 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 12 19 851 2617 GARS glycyl-tRNA synthetase clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 21 2.4 up 1 0 1/0 2.4 1 21 2.40 2.40 D30658 D30658 GARS 2.4 2.40 up PTC Norm 18 3 publication 12538453 3 6 147 2619 GAS1 growth arrest-specific 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 -2.9 down 1 0 0/1 -2.9 1 16 -2.90 -2.90 L13698 L13698 Gas1 GAS1 -2.9 -2.90 down yes 0.0185 PTC Norm 8 8 suppl. materials 11752453 24 33 1538 2628 GATM glycine amidinotransferase (L-arginine:glycine amidinotransferase) Gene_symbol_2_NCBI_Entrez 1 1 32 -3.33 down 1 0 0/1 -3.33 1 32 -3.33 -3.33 Glycine amidinotransferase (L-arginine:glycine amidinotransferase) GATM -1.735 -3.33 down PTC Norm 16 16 publication 15735049 11 18 756 2665 GDI2 GDP dissociation inhibitor 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 NM_001494 NM_001494 GD12 GDP dissociation inhibitor 2 up yes ACL;ATC Norm 21 10 publication 15613457 25 34 1717 2690 GHR growth hormone receptor affy_probe_2_Entrez 1 1 55 -3.6 down 1 0 0/1 -3.6 1 55 -3.60 -3.60 205498_at 205498_at growth hormone receptor GHR -3.605 -3.60 down 1.27617E-12 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 936 2697 GJA1 gap junction protein, alpha 1, 43kDa (connexin 43) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 -2.4 down 2 0 0/2 -2.4 1 59 -2.40 -2.40 X52947 X52947 Gap junction protein, 1, 43 kDa (connexin 43) GJA1 down FTC FA 9 10 publication 12738736 18 31 1357 2697 GJA1 gap junction protein, alpha 1, 43kDa (connexin 43) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 -2.4 down 2 0 0/2 -2.4 1 59 -2.40 -2.40 X52947 X52947 Connexin 43, cardiac gap junction protein CX43 2.4 -2.40 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1464 2707 GJB3 gap junction protein, beta 3, 31kDa (connexin 31) Gene_symbol_2_NCBI_Entrez 1 1 32 7.94 up 1 0 1/0 7.94 1 32 7.94 7.94 Gap junction protein, beta-3, 31 kDa (connexin 31) GJB3 2.99 7.94 up PTC Norm 16 16 publication 15735049 25 34 1700 2719 GPC3 glypican 3 affy_probe_2_Entrez 2 2 71 -6.65 down 2 0 0/2 -3.325 2 71 -3.15 -3.50 209220_at 209220_at glypican 3 GPC3 -3.145 -3.15 down 9.19624E-09 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 151 2719 GPC3 glypican 3 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 71 -6.65 down 2 0 0/2 -3.325 2 71 -3.15 -3.50 U50410 U50410 Heparan sulphate proteoglycan (OCI5) GPC3 -3.5 -3.50 down no 0.0053 PTC Norm 8 8 suppl. materials 11752453 11 18 806 2766 GMPR guanosine monophosphate reductase clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 M24470 M24470 Glucose-6-phosphate dehydrogenase down ACL;ATC Norm 21 10 publication 15613457 9 14 620 2776 GNAQ guanine nucleotide binding protein (G protein), q polypeptide affy_probe_2_Entrez 1 1 24 2.73 up 1 0 1/0 2.73 1 24 2.73 2.73 202615_at 202615_at Homo sapiens mRNA; cDNA DKFZp686D0521 (from clone DKFZp686D0521) -2.73 2.73 up 0.000003 FA FTC 12 12 provided by authors 15713710 15 22 1039 2804 GOLGB1 golgi autoantigen, golgin subfamily b, macrogolgin (with transmembrane signal), 1 Gene_symbol_2_NCBI_Entrez 1 1 7 -2 down 1 0 0/1 -2 1 7 -2.00 -2.00 Golgi autoantigen GOLGB1 0.5 -2.00 down FTC FA 3 4 publication 15475448 9 14 612 2805 GOT1 glutamic-oxaloacetic transaminase 1, soluble (aspartate aminotransferase 1) affy_probe_2_Entrez 1 1 24 -3.31 down 1 0 0/1 -3.31 1 24 -3.31 -3.31 208813_at 208813_at glutamic-oxaloacetic transaminase 1, soluble (aspartate aminotransferase 1) 3.31 -3.31 down 0.000833 FA FTC 12 12 provided by authors 15713710 24 33 1487 2810 SFN stratifin Gene_symbol_2_NCBI_Entrez 1 1 32 3.15 up 1 0 1/0 3.15 1 32 3.15 3.15 Stratifin SFN 1.655 3.15 up PTC Norm 16 16 publication 15735049 13 20 882 2817 GPC1 glypican 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 X54232 X54232 Glypican 1 CGPC1 up FTC FA 9 10 publication 12738736 25 34 1740 2823 GPM6A glycoprotein M6A affy_probe_2_Entrez 1 1 55 -7.34 down 1 0 0/1 -7.34 1 55 -7.34 -7.34 209470_s_at 209470_s_at glycoprotein M6A GPM6A -4.897 -4.90 down 4.17246E-07 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1767 2823 GPM6A glycoprotein M6A affy_probe_2_Entrez 1 1 55 -7.34 down 1 0 0/1 -7.34 1 55 -7.34 -7.34 209469_at 209469_at glycoprotein M6A GPM6A -7.337 -7.34 down 3.32241E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 15 22 1029 2896 GRN granulin Gene_symbol_2_NCBI_Entrez 1 1 7 2 up 1 0 1/0 2 1 7 2.00 2.00 Granulin GRN 2 2.00 up FTC FA 3 4 publication 15475448 13 20 937 2934 GSN gelsolin (amyloidosis, Finnish type) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 X04412 X04412 Gelsolin GSN down FTC FA 9 10 publication 12738736 2 3 90 2962 GTF2F1 general transcription factor IIF, polypeptide 1, 74kDa clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 4 4.1 up 1 0 1/0 4.1 1 4 4.10 4.10 NM_002096 NM_002096 General transcription factor IIF, polypeptide 1, 74 kd GTF2F1 4.1 4.10 up FCL;PCL;UCL Norm 3 1 publication 15785240 16 24 1208 2966 GTF2H2 general transcription factor IIH, polypeptide 2, 44kDa Gene_symbol_2_NCBI_Entrez 1 1 63 -1.46 down 1 0 0/1 -1.46 1 63 -1.46 -1.46 GTF2H2 0.683333333 -1.46 down 0.04 PTC;FVPTC FA;HN 32 31 publication 15087409 16 24 1206 2987 GUK1 guanylate kinase 1 Gene_symbol_2_NCBI_Entrez 1 1 63 1.79 up 1 0 1/0 1.79 1 63 1.79 1.79 GUK1 1.793103448 1.79 up 0.02 PTC;FVPTC FA;HN 32 31 publication 15087409 14 21 989 3014 H2AFX H2A histone family, member X clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 2.2 up 1 0 1/0 2.2 1 14 2.20 2.20 H95392 H95392 Histone H2A.X 2.2 2.20 up PTC Norm 7 7 publication 15041723 14 21 987 3021 H3F3B H3 histone, family 3B (H3.3B) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 16 -5.3 even 1 1 1/1 -2.65 2 16 2.30 -7.60 AA608514 AA608514 Histone H3.3 2.3 2.30 up PTC Norm 7 7 publication 15041723 2 5 107 3021 H3F3B H3 histone, family 3B (H3.3B) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 16 -5.3 even 1 1 1/1 -2.65 2 16 2.30 -7.60 NM_002107 NM_002107 H3 histone, family 3A H3F3A 7.6 -7.60 down UCL Norm 1 1 publication 15785240 12 19 856 3040 HBA2 hemoglobin, alpha 2 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 69 -10.5 down 3 0 0/3 -3.5 3 69 -2.38 -4.72 V00491 V00491 Hemoglobin, alpha-chain (HBA1) 0.42 -2.38 down PTC Norm 18 3 publication 12538453 24 33 1542 3040 HBA2 hemoglobin, alpha 2 Gene_symbol_2_NCBI_Entrez 3 3 69 -10.5 down 3 0 0/3 -3.5 3 69 -2.38 -4.72 Hemoglobin, alpha2 HBA2 -2.24 -4.72 down PTC Norm 16 16 publication 15735049 3 6 150 3040 HBA2 hemoglobin, alpha 2 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 69 -10.5 down 3 0 0/3 -3.5 3 69 -2.38 -4.72 J00153 J00153 Alpha globin HBA -3.4 -3.40 down no 0.0076 PTC Norm 8 8 suppl. materials 11752453 11 18 822 3043 HBB hemoglobin, beta clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 118 -15.16 down 3 0 0/3 -7.58 2 87 -3.77 -11.39 AF117710 AF117710 HBB hemoglobin, b down ACL;ATC Norm 21 10 publication 15613457 24 33 1539 3043 HBB hemoglobin, beta Gene_symbol_2_NCBI_Entrez 3 3 118 -15.16 down 3 0 0/3 -7.58 2 87 -3.77 -11.39 Hemoglobin, beta HBB -1.915 -3.77 down PTC Norm 16 16 publication 15735049 25 34 1768 3043 HBB hemoglobin, beta affy_probe_2_Entrez 3 3 118 -15.16 down 3 0 0/3 -7.58 2 87 -3.77 -11.39 211696_x_at 211696_x_at hemoglobin, beta /// hemoglobin, beta HBB -7.645 -7.64 down 0.039837845 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1775 3043 HBB hemoglobin, beta affy_probe_2_Entrez 3 3 118 -15.16 down 3 0 0/3 -7.58 2 87 -3.77 -11.39 217232_x_at 217232_x_at --- --- -9.853 -9.85 down 0.033878047 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1777 3043 HBB hemoglobin, beta affy_probe_2_Entrez 3 3 118 -15.16 down 3 0 0/3 -7.58 2 87 -3.77 -11.39 209116_x_at 209116_x_at hemoglobin, beta HBB -11.392 -11.39 down 0.039581121 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1708 3045 HBD hemoglobin, delta affy_probe_2_Entrez 1 1 55 -3.37 down 1 0 0/1 -3.37 1 55 -3.37 -3.37 206834_at 206834_at hemoglobin, delta HBD -3.371 -3.37 down 0.001258285 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 2 2 63 3066 HDAC2 histone deacetylase 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -10 down 1 0 0/1 -10 1 2 -10.00 -10.00 NM_001527 NM_001527 Histone deacetylase 2 HDAC2 10 -10.00 down FCL Norm 1 1 publication 15785240 18 31 1339 3081 HGD homogentisate 1,2-dioxygenase (homogentisate oxidase) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 75 -7.3 down 2 0 0/2 -3.65 2 75 -2.70 -4.60 AF000573 AF000573 Homogentisate 1,2-dioxygenase HGO 2.7 -2.70 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 3 6 154 3081 HGD homogentisate 1,2-dioxygenase (homogentisate oxidase) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 75 -7.3 down 2 0 0/2 -3.65 2 75 -2.70 -4.60 AF000573 AF000573 Homogentisate 1,2-dioxygenase HGD -4.6 -4.60 down no 0.003 PTC Norm 8 8 suppl. materials 11752453 12 19 845 3091 HIF1A hypoxia-inducible factor 1, alpha subunit (basic helix-loop-helix transcription factor) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 21 6.6 up 1 0 1/0 6.6 1 21 6.60 6.60 U22431 U22431 HIF-1 6.6 6.60 up PTC Norm 18 3 publication 12538453 2 5 108 3094 HINT1 histidine triad nucleotide binding protein 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -6.8 down 1 0 0/1 -6.8 1 2 -6.80 -6.80 NM_005340 NM_005340 HIstidine triad nucleotide binding protein 1 HINT1 6.8 -6.80 down UCL Norm 1 1 publication 15785240 25 34 1632 3096 HIVEP1 human immunodeficiency virus type I enhancer binding protein 1 affy_probe_2_Entrez 1 1 55 2.12 up 1 0 1/0 2.12 1 55 2.12 2.12 204512_at 204512_at human immunodeficiency virus type I enhancer binding protein 1 HIVEP1 2.117 2.12 up 0.001786449 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 2 2 74 3098 HK1 hexokinase 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -7 down 1 0 0/1 -7 1 2 -7.00 -7.00 NM_000188 NM_000188 Hexokinase 1 HK1 7 -7.00 down FCL Norm 1 1 publication 15785240 17 29 1292 3106 HLA-B major histocompatibility complex, class I, B tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 CTGACCTGTG CTGACCTGTG up PTC FA 1 1 publication 11076659 12 19 848 3115 HLA-DPB1 major histocompatibility complex, class II, DP beta 1 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 80 8.2 up 2 0 2/0 4.1 2 80 6.00 2.20 M83664 M83664 Major histocompatibility complex, class II, DP 1 (HLA-DPB1) 6 6.00 up PTC Norm 18 3 publication 12538453 18 31 1367 3115 HLA-DPB1 major histocompatibility complex, class II, DP beta 1 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 80 8.2 up 2 0 2/0 4.1 2 80 6.00 2.20 M83664 M83664 MHC class II lymphocyte antigen HLA-DP1B 2.2 2.20 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 18 31 1361 3119 HLA-DQB1 major histocompatibility complex, class II, DQ beta 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 2.3 up 1 0 1/0 2.3 1 59 2.30 2.30 M81141 M81141 MHC class II HLA-DQ-beta HLA-DQ-beta 2.3 2.30 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 10 16 713 3134 HLA-F major histocompatibility complex, class I, F affy_probe_2_Entrez 1 1 14 7.99 up 1 0 1/0 7.99 1 14 7.99 7.99 37420_i_at 37420_i_at Human leukocyte antigen F HLA-F 7.99 7.99 up yes PTC GT 8 6 publication 15515157 14 21 997 3162 HMOX1 heme oxygenase (decycling) 1 Gene_symbol_2_NCBI_Entrez 1 1 14 0 up 1 0 1/0 0 0 0 0 0 Heme oxygenase (decycling) 1 HMOX1 up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 14 21 984 3178 HNRPA1 heterogeneous nuclear ribonucleoprotein A1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 2.4 up 1 0 1/0 2.4 1 14 2.40 2.40 AA126911 AA126911 Heterogeneous nuclear ribonucleoprotein A1 2.4 2.40 up PTC Norm 7 7 publication 15041723 25 34 1634 3182 HNRPAB heterogeneous nuclear ribonucleoprotein A/B affy_probe_2_Entrez 1 1 55 2.03 up 1 0 1/0 2.03 1 55 2.03 2.03 201277_s_at 201277_s_at heterogeneous nuclear ribonucleoprotein A/B HNRPAB 2.026 2.03 up 0.000184196 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 11 18 771 3190 HNRPK heterogeneous nuclear ribonucleoprotein K clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 S74678 S74678 Heterogeneous nuclear ribonucleoprotein complex K up ACL;ATC Norm 21 10 publication 15613457 11 18 762 3192 HNRPU heterogeneous nuclear ribonucleoprotein U (scaffold attachment factor A) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 AF068846 AF068846 Scaffold attachment factor A (SAF-A) up ACL;ATC Norm 21 10 publication 15613457 24 33 1519 3281 HSBP1 heat shock factor binding protein 1 Gene_symbol_2_NCBI_Entrez 1 1 32 -1.43 down 1 0 0/1 -1.43 1 32 -1.43 -1.43 Heat shock factor binding protein 1 HSBP1 -0.52 -1.43 down PTC Norm 16 16 publication 15735049 18 31 1353 3293 HSD17B3 hydroxysteroid (17-beta) dehydrogenase 3 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 114 -4.44 down 2 0 0/2 -2.22 2 114 -2.04 -2.40 U05659 U05659 17-beta-hydroxysteroid dehydrogenase type 3 EDH17B3 2.4 -2.40 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1638 3293 HSD17B3 hydroxysteroid (17-beta) dehydrogenase 3 affy_probe_2_Entrez 2 2 114 -4.44 down 2 0 0/2 -2.22 2 114 -2.04 -2.40 206985_at 206985_at hydroxysteroid (17-beta) dehydrogenase 3 HSD17B3 -2.037 -2.04 down 0.001096937 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 16 24 1222 3295 HSD17B4 hydroxysteroid (17-beta) dehydrogenase 4 Gene_symbol_2_NCBI_Entrez 1 1 63 -1.65 down 1 0 0/1 -1.65 1 63 -1.65 -1.65 HSD17B4 0.606896552 -1.65 down 0.03 PTC;FVPTC FA;HN 32 31 publication 15087409 11 18 760 3303 HSPA1A heat shock 70kDa protein 1A clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 AA706503 AA706503 IMAGE:1141693 50 similar to gb:X 16869 elongation factor 1-a 1 (eef1a1) up ACL;ATC Norm 21 10 publication 15613457 9 14 630 3309 HSPA5 heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) affy_probe_2_Entrez 1 1 24 2.96 up 1 0 1/0 2.96 1 24 2.96 2.96 211936_at 211936_at heat shock 70kDa protein 5 (glucose-regulated protein, 78kDa) -2.96 2.96 up 0.000005 FA FTC 12 12 provided by authors 15713710 11 18 765 3312 HSPA8 heat shock 70kDa protein 8 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 BC016660 BC016660 HSP A8 heat shock 70 kDa protein 8 up yes ACL;ATC Norm 21 10 publication 15613457 15 22 1043 3337 DNAJB1 DnaJ (Hsp40) homolog, subfamily B, member 1 Gene_symbol_2_NCBI_Entrez 1 1 7 -2.5 down 1 0 0/1 -2.5 1 7 -2.50 -2.50 DNAJ (Hsp40) homolog, subfamily B, member 1 DNAJB1 0.4 -2.50 down FTC FA 3 4 publication 15475448 13 20 884 3371 TNC tenascin C (hexabrachion) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 6.6 up 2 0 2/0 6.6 1 59 6.60 6.60 X78565 X78565 Hexabrachion (tenascin-C) HXB up FTC FA 9 10 publication 12738736 18 31 1299 3371 TNC tenascin C (hexabrachion) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 6.6 up 2 0 2/0 6.6 1 59 6.60 6.60 X78565 X78565 Tenascin-C TNC 6.6 6.60 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 10 16 724 3397 ID1 inhibitor of DNA binding 1, dominant negative helix-loop-helix protein affy_probe_2_Entrez 2 2 73 -5.61 down 2 0 0/2 -2.805 2 73 -2.40 -3.21 36617_at 36617_at Inhibitor of DNA binding 1, ID1 -2.51 -2.51 down yes PTC GT 8 6 publication 15515157 10 16 732 3397 ID1 inhibitor of DNA binding 1, dominant negative helix-loop-helix protein affy_probe_2_Entrez 2 2 73 -5.61 down 2 0 0/2 -2.805 2 73 -2.40 -3.21 36618_g_at 36618_g_at Inhibitor of DNA binding 1, ID1 -3.21 -3.21 down yes PTC GT 8 6 publication 15515157 18 31 1355 3397 ID1 inhibitor of DNA binding 1, dominant negative helix-loop-helix protein clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 73 -5.61 down 2 0 0/2 -2.805 2 73 -2.40 -3.21 X77956 X77956 Human helix-loop-helix Id1protein Id-1 2.4 -2.40 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 13 20 944 3400 ID4 inhibitor of DNA binding 4, dominant negative helix-loop-helix protein clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 89 -7.29 down 3 0 0/3 -3.645 2 70 -2.29 -5.00 AL022726 AL022726 Inhibitor of DNA binding 4 ID4 down FTC FA 9 10 publication 12738736 15 22 1060 3400 ID4 inhibitor of DNA binding 4, dominant negative helix-loop-helix protein Gene_symbol_2_NCBI_Entrez 3 3 89 -7.29 down 3 0 0/3 -3.645 2 70 -2.29 -5.00 Inhibitor of DNA binding 4 ID4 0.2 -5.00 down FTC FA 3 4 publication 15475448 16 24 1245 3400 ID4 inhibitor of DNA binding 4, dominant negative helix-loop-helix protein Gene_symbol_2_NCBI_Entrez 3 3 89 -7.29 down 3 0 0/3 -3.645 2 70 -2.29 -5.00 ID4 0.436363636 -2.29 down 0.01 PTC;FVPTC FA;HN 32 31 publication 15087409 11 18 775 3420 IDH3B isocitrate dehydrogenase 3 (NAD+) beta clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 U49283 U49283 NAD+-specific isocitrate dehydrogenase b subunit precursor (IDH3B) up ACL;ATC Norm 21 10 publication 15613457 11 18 799 3421 IDH3G isocitrate dehydrogenase 3 (NAD+) gamma clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U69268 U69268 NAD (H)-specific isocitrate dehydrogenase g subunit (IDH3G) down ACL;ATC Norm 21 10 publication 15613457 16 24 1232 3422 IDI1 isopentenyl-diphosphate delta isomerase 1 Gene_symbol_2_NCBI_Entrez 1 1 63 -1.85 down 1 0 0/1 -1.85 1 63 -1.85 -1.85 IDI1 0.540145985 -1.85 down 0.01 PTC;FVPTC FA;HN 32 31 publication 15087409 19 32 1406 3423 IDS iduronate 2-sulfatase (Hunter syndrome) tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 AGGACAAATA AGGACAAATA iduronate 2-sulfatase up 0.0245 FVPTC Norm 1 1 publication 14715705 14 21 1011 3480 IGF1R insulin-like growth factor 1 receptor Gene_symbol_2_NCBI_Entrez 1 1 14 0 up 1 0 1/0 0 0 0 0 0 Insulin-like growth factor 1 receptor IGF1R up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 25 34 1615 3482 IGF2R insulin-like growth factor 2 receptor affy_probe_2_Entrez 1 1 55 2.5 up 1 0 1/0 2.5 1 55 2.50 2.50 201393_s_at 201393_s_at insulin-like growth factor 2 receptor IGF2R 2.500 2.50 up 0.020340043 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 888 3486 IGFBP3 insulin-like growth factor binding protein 3 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 2.8 up 2 0 2/0 2.8 1 59 2.80 2.80 M35878 M35878 Insulin-like growth factor binding protein 3 IGFBP3 up FTC FA 9 10 publication 12738736 13 20 889 3486 IGFBP3 insulin-like growth factor binding protein 3 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 2.8 up 2 0 2/0 2.8 1 59 2.80 2.80 M35878 M35878 Insulin-like growth factor binding protein 3 IGFBP3 up FTC FA 9 10 publication 12738736 18 31 1330 3486 IGFBP3 insulin-like growth factor binding protein 3 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 2.8 up 2 0 2/0 2.8 1 59 2.80 2.80 M35878 M35878 Insulin-like growth factor-binding protein-3 precursor IGFBP3 2.8 2.80 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 10 16 715 3488 IGFBP5 insulin-like growth factor binding protein 5 affy_probe_2_Entrez 1 1 14 5.96 up 1 0 1/0 5.96 1 14 5.96 5.96 38650_at 38650_at Insulin-like growth factor binding protein 5 IGFBP5 5.96 5.96 up no PTC GT 8 6 publication 15515157 13 20 947 3490 IGFBP7 insulin-like growth factor binding protein 7 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 L19182 L19182 Insulin-like growth factor binding protein 7 IGFBP7 down FTC FA 9 10 publication 12738736 12 19 858 3491 CYR61 cysteine-rich, angiogenic inducer, 61 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 28 -23.23 down 2 0 0/2 -11.615 2 28 -3.23 -20.00 AF031385 AF031385 Cystein-rich protein 61 (CYR61) 0.31 -3.23 down PTC Norm 18 3 publication 12538453 15 22 1063 3491 CYR61 cysteine-rich, angiogenic inducer, 61 Gene_symbol_2_NCBI_Entrez 2 2 28 -23.23 down 2 0 0/2 -11.615 2 28 -3.23 -20.00 Cysteine-rich, angiogenic inducer, 61 CYR61 0.05 -20.00 down yes FTC FA 3 4 publication 15475448 13 20 943 3500 IGHG1 immunoglobulin heavy constant gamma 1 (G1m marker) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 Y14737 Y14737 Immunoglobulin heavy constant 3 marker IGHG3 down FTC FA 9 10 publication 12738736 24 33 1450 3547 IGSF1 immunoglobulin superfamily, member 1 Gene_symbol_2_NCBI_Entrez 1 1 32 19.03 up 1 0 1/0 19.03 1 32 19.03 19.03 Immunoglobulin superfamily, member 1 IGSF1 4.25 19.03 up PTC Norm 16 16 publication 15735049 13 20 948 3590 IL11RA interleukin 11 receptor, alpha clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 U32324 U32324 Interleukin 11 receptor, IL11RA down FTC FA 9 10 publication 12738736 24 33 1515 3597 IL13RA1 interleukin 13 receptor, alpha 1 Gene_symbol_2_NCBI_Entrez 2 2 87 3.8 up 2 0 2/0 1.9 2 87 2.32 1.48 Interleukin 13 receptor, alpha1 IL13RA1 0.565 1.48 up PTC Norm 16 16 publication 15735049 25 34 1621 3597 IL13RA1 interleukin 13 receptor, alpha 1 affy_probe_2_Entrez 2 2 87 3.8 up 2 0 2/0 1.9 2 87 2.32 1.48 201888_s_at 201888_s_at interleukin 13 receptor, alpha 1 IL13RA1 2.318 2.32 up 0.02057311 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 18 31 1399 3613 IMPA2 inositol(myo)-1(or 4)-monophosphatase 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2 down 1 0 0/1 -2 1 59 -2.00 -2.00 AF014398 AF014398 Myo-inositol monophosphatase 2 IMPA2 2 -2.00 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 14 21 1017 3631 INPP4A inositol polyphosphate-4-phosphatase, type I, 107kDa Gene_symbol_2_NCBI_Synonym_2_Entrez 2 2 69 2.14 up 2 0 2/0 2.14 1 55 2.14 2.14 Inositol polyphosphate 4-phosphatase INPP4 up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 25 34 1629 3631 INPP4A inositol polyphosphate-4-phosphatase, type I, 107kDa affy_probe_2_Entrez 2 2 69 2.14 up 2 0 2/0 2.14 1 55 2.14 2.14 204552_at 204552_at inositol polyphosphate-4-phosphatase, type I, 107kDa INPP4A 2.142 2.14 up 0.001980641 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 14 21 1013 3636 INPPL1 inositol polyphosphate phosphatase-like 1 Gene_symbol_2_NCBI_Entrez 1 1 14 0 up 1 0 1/0 0 0 0 0 0 Inositol polyphosphate phosphatase-like protein 1 INPPL1 up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 18 31 1323 3662 IRF4 interferon regulatory factor 4 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 3.2 up 1 0 1/0 3.2 1 59 3.20 3.20 U52682 U52682 Human lymphocyte specific interferon regulatory factor LSIRF 3.2 3.20 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 18 31 1395 3667 IRS1 insulin receptor substrate 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2 down 1 0 0/1 -2 1 59 -2.00 -2.00 S62539 S62539 Insulin receptor substrate-1 IRS-1 2 -2.00 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 5 10 388 3703 ITM1 integral membrane protein 1 tag_2_refseq_or_mgc_2_Entrez 1 1 3 0 up 1 0 1/0 0 0 0 0 0 GCTTTACTTT GCTTTACTTT ITM1 up yes FTC FA;Norm 1 2 publication 15085203 13 20 945 3708 ITPR1 inositol 1,4,5-triphosphate receptor, type 1 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 94 -5.2 down 3 0 0/3 -2.6 2 75 -2.50 -2.70 D26070 D26070 Inositol 1, 4, 5-triphosphate receptor, type 1 ITPR1 down FTC FA 9 10 publication 12738736 13 20 946 3708 ITPR1 inositol 1,4,5-triphosphate receptor, type 1 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 94 -5.2 down 3 0 0/3 -2.6 2 75 -2.50 -2.70 D26070 D26070 Inositol 1, 4, 5-triphosphate receptor, type 1 ITPR1 down FTC FA 9 10 publication 12738736 18 31 1347 3708 ITPR1 inositol 1,4,5-triphosphate receptor, type 1 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 94 -5.2 down 3 0 0/3 -2.6 2 75 -2.50 -2.70 D26070 D26070 Type 1 inositol 1,4,5-trisphosphate receptor InsP3R1 2.5 -2.50 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 3 6 145 3708 ITPR1 inositol 1,4,5-triphosphate receptor, type 1 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 94 -5.2 down 3 0 0/3 -2.6 2 75 -2.50 -2.70 D26070 D26070 Type 1 inositol 1,4,5-trisphosphate receptor ITPR1 -2.7 -2.70 down yes 0.0013 PTC Norm 8 8 suppl. materials 11752453 13 20 966 3725 JUN v-jun sarcoma virus 17 oncogene homolog (avian) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 J04111 J04111 v-Jun avian sarcoma virus 17 oncogene homolog JUN down FTC FA 9 10 publication 12738736 25 34 1559 3759 KCNJ2 potassium inwardly-rectifying channel, subfamily J, member 2 affy_probe_2_Entrez 1 1 55 9.17 up 1 0 1/0 9.17 1 55 9.17 9.17 206765_at 206765_at potassium inwardly-rectifying channel, subfamily J, member 2 KCNJ2 9.173 9.17 up 0.018440032 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1659 3769 KCNJ13 potassium inwardly-rectifying channel, subfamily J, member 13 affy_probe_2_Entrez 1 1 55 -2.41 down 1 0 0/1 -2.41 1 55 -2.41 -2.41 210179_at 210179_at potassium inwardly-rectifying channel, subfamily J, member 13 KCNJ13 -2.408 -2.41 down 0.000155458 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 18 31 1304 3783 KCNN4 potassium intermediate/small conductance calcium-activated channel, subfamily N, member 4 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 4.9 up 1 0 1/0 4.9 1 59 4.90 4.90 AF022797 AF022797 Intermediate conductance calcium-activated potassium channel hSK4 4.9 4.90 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 16 24 1248 3815 KIT v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog Gene_symbol_2_NCBI_Entrez 2 2 118 -15.7 down 2 0 0/2 -7.85 2 118 -3.16 -12.54 KIT 0.316666667 -3.16 down yes 0.0001 PTC;FVPTC FA;HN 32 31 publication 15087409 25 34 1779 3815 KIT v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog affy_probe_2_Entrez 2 2 118 -15.7 down 2 0 0/2 -7.85 2 118 -3.16 -12.54 205051_s_at 205051_s_at v-kit Hardy-Zuckerman 4 feline sarcoma viral oncogene homolog KIT -12.543 -12.54 down 0.000130559 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1625 3838 KPNA2 karyopherin alpha 2 (RAG cohort 1, importin alpha 1) affy_probe_2_Entrez 1 1 55 2.27 up 1 0 1/0 2.27 1 55 2.27 2.27 211762_s_at 211762_s_at karyopherin alpha 2 (RAG cohort 1, importin alpha 1) /// karyopherin alpha 2 (RAG cohort 1, importin alpha 1) KPNA2 2.267 2.27 up 0.02115598 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 15 22 1057 3856 KRT8 keratin 8 Gene_symbol_2_NCBI_Entrez 1 1 7 -5 down 1 0 0/1 -5 1 7 -5.00 -5.00 Keratin 8 KRT8 0.2 -5.00 down FTC FA 3 4 publication 15475448 18 31 1310 3880 KRT19 keratin 19 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 107 19.65 up 3 0 3/0 6.55 3 107 9.35 4.00 Y00503 Y00503 Keratin 19 KRT19 4 4.00 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1461 3880 KRT19 keratin 19 Gene_symbol_2_NCBI_Entrez 3 3 107 19.65 up 3 0 3/0 6.55 3 107 9.35 4.00 Keratin 19 KRT19 3.225 9.35 up PTC Norm 16 16 publication 15735049 3 6 129 3880 KRT19 keratin 19 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 107 19.65 up 3 0 3/0 6.55 3 107 9.35 4.00 Y00503 Y00503 Keratin 19 KRT19 6.3 6.30 up no 0.01 PTC Norm 8 8 suppl. materials 11752453 25 34 1669 3908 LAMA2 laminin, alpha 2 (merosin, congenital muscular dystrophy) affy_probe_2_Entrez 1 1 55 -2.56 down 1 0 0/1 -2.56 1 55 -2.56 -2.56 216840_s_at 216840_s_at laminin, alpha 2 (merosin, congenital muscular dystrophy) LAMA2 -2.558 -2.56 down 0.040376953 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 18 31 1383 3912 LAMB1 laminin, beta 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2.1 down 1 0 0/1 -2.1 1 59 -2.10 -2.10 M61916 M61916 Human laminin B1 chain LAMB1 2.1 -2.10 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1457 3914 LAMB3 laminin, beta 3 Gene_symbol_2_NCBI_Entrez 1 1 32 12.95 up 1 0 1/0 12.95 1 32 12.95 12.95 Laminin, beta3 LAMB3 3.695 12.95 up PTC Norm 16 16 publication 15735049 11 18 793 3915 LAMC1 laminin, gamma 1 (formerly LAMB2) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 J03202 J03202 Laminin B2 chain down ACL;ATC Norm 21 10 publication 15613457 11 18 766 3925 STMN1 stathmin 1/oncoprotein 18 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 X53305 X53305 Stathmin up yes yes ACL;ATC Norm 21 10 publication 15613457 24 33 1467 3934 LCN2 lipocalin 2 (oncogene 24p3) Gene_symbol_2_NCBI_Entrez 1 1 32 6.96 up 1 0 1/0 6.96 1 32 6.96 6.96 Lipocalin 2 (oncogene 24p3) LCN2 2.8 6.96 up PTC Norm 16 16 publication 15735049 11 18 769 3939 LDHA lactate dehydrogenase A clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 52 6.3 up 2 0 2/0 6.3 1 21 6.30 6.30 NM_005566 NM_005566 Lactate dehydrogenase-A (LDH-A, EC 1.1.1.27) up yes ACL;ATC Norm 21 10 publication 15613457 12 19 846 3939 LDHA lactate dehydrogenase A clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 52 6.3 up 2 0 2/0 6.3 1 21 6.30 6.30 X02152 X02152 LDH-A 6.3 6.30 up PTC Norm 18 3 publication 12538453 11 18 784 3945 LDHB lactate dehydrogenase B clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 Y00711 Y00711 Lactate dehydrogenase B (LDH-B) up yes ACL;ATC Norm 21 10 publication 15613457 18 31 1313 3958 LGALS3 lectin, galactoside-binding, soluble, 3 (galectin 3) clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 107 11.1 up 3 0 3/0 3.7 3 107 3.80 3.50 AB006780 AB006780 Galectin-3 GALBP 3.5 3.50 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1484 3958 LGALS3 lectin, galactoside-binding, soluble, 3 (galectin 3) Gene_symbol_2_NCBI_Entrez 3 3 107 11.1 up 3 0 3/0 3.7 3 107 3.80 3.50 Lectin, galactoside-binding, soluble, 3 (galectin 3) LGALS3 1.925 3.80 up PTC Norm 16 16 publication 15735049 3 6 135 3958 LGALS3 lectin, galactoside-binding, soluble, 3 (galectin 3) clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 107 11.1 up 3 0 3/0 3.7 3 107 3.80 3.50 AB006780 AB006780 Galectin-3 LGALS3 3.8 3.80 up no 0.0001 PTC Norm 8 8 suppl. materials 11752453 2 5 113 3960 LGALS4 lectin, galactoside-binding, soluble, 4 (galectin 4) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 2.73 up 1 0 1/0 2.73 1 2 2.73 2.73 NM_006149 NM_006149 Lectin, galactoside-binding, soluble, 4 (galectin 4) LGALS4 2.73 2.73 up UCL Norm 1 1 publication 15785240 13 20 895 4015 LOX lysyl oxidase clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 2.2 up 2 0 2/0 2.2 1 59 2.20 2.20 L16895 L16895 Lysyl oxidase LOX up FTC FA 9 10 publication 12738736 18 31 1366 4015 LOX lysyl oxidase clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 2.2 up 2 0 2/0 2.2 1 59 2.20 2.20 L16895 L16895 Lysyl oxidase LOX 2.2 2.20 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 18 31 1300 4038 LRP4 low density lipoprotein receptor-related protein 4 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 146 43.42 up 3 0 3/0 14.4733333333333 3 146 19.43 6.40 AB011540 AB011540 Similar to LDL receptor-like protein; tSXV motif MEGF7 6.4 6.40 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1449 4038 LRP4 low density lipoprotein receptor-related protein 4 Gene_symbol_2_NCBI_Entrez 3 3 146 43.42 up 3 0 3/0 14.4733333333333 3 146 19.43 6.40 Low density lipoprotein receptor-related protein 4 LRP4 4.28 19.43 up PTC Norm 16 16 publication 15735049 25 34 1547 4038 LRP4 low density lipoprotein receptor-related protein 4 affy_probe_2_Entrez 3 3 146 43.42 up 3 0 3/0 14.4733333333333 3 146 19.43 6.40 212850_s_at 212850_s_at low density lipoprotein receptor-related protein 4 LRP4 17.590 17.59 up 4.36232E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 14 21 967 4067 LYN v-yes-1 Yamaguchi sarcoma viral related oncogene homolog clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 62 up 1 0 1/0 62 1 14 62.00 62.00 R83837 R83837 V-yes-1 Yamaguchi sarcoma viral related oncogene 62 62.00 up PTC Norm 7 7 publication 15041723 3 6 121 4068 SH2D1A SH2 domain protein 1A, Duncan's disease (lymphoproliferative syndrome) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 8.7 up 1 0 1/0 8.7 1 16 8.70 8.70 AL022718 AL022718 Odz (odd Oz/ten-m, Drosophila ) 1 ODZ1 8.7 8.70 up yes 0.0001 PTC Norm 8 8 suppl. materials 11752453 18 31 1296 4070 TACSTD2 tumor-associated calcium signal transducer 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 9.6 up 1 0 1/0 9.6 1 59 9.60 9.60 J04152 J04152 GA733-1 protein precursor TROP2 9.6 9.60 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1656 4086 SMAD1 SMAD, mothers against DPP homolog 1 (Drosophila) affy_probe_2_Entrez 1 1 55 -2.24 down 1 0 0/1 -2.24 1 55 -2.24 -2.24 210993_s_at 210993_s_at SMAD, mothers against DPP homolog 1 (Drosophila) SMAD1 -2.242 -2.24 down 0.002998803 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 12 19 857 4089 SMAD4 SMAD, mothers against DPP homolog 4 (Drosophila) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 21 -3.03 down 1 0 0/1 -3.03 1 21 -3.03 -3.03 U44378 U44378 Homozygous deletion target in pancreatic carcinoma (DPC4/SMAD4) 0.33 -3.03 down PTC Norm 18 3 publication 12538453 2 4 100 4090 SMAD5 SMAD, mothers against DPP homolog 5 (Drosophila) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -7 down 1 0 0/1 -7 1 2 -7.00 -7.00 NM_005903 NM_005903 MAD, mothers against decapentaplegic homologue 5 MADH5 7 -7.00 down PCL Norm 1 1 publication 15785240 13 20 899 4099 MAG myelin associated glycoprotein clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 M29273 M29273 Myelin-associated glycoprotein MAG up FTC FA 9 10 publication 12738736 13 20 896 4118 MAL mal, T-cell differentiation protein clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 X76220 X76220 Mal, T-cell differentiation protein MAL up FTC FA 9 10 publication 12738736 19 32 1412 4123 MAN2C1 mannosidase, alpha, class 2C, member 1 tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 AGGCCCACAA AGGCCCACAA mannosidase, alpha2C up 0.0029 FVPTC Norm 1 1 publication 14715705 18 31 1343 4147 MATN2 matrilin 2 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 114 -9.66 down 2 0 0/2 -4.83 2 114 -2.60 -7.06 U69263 U69263 Matrilin-2 precursor MATN2 2.6 -2.60 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1765 4147 MATN2 matrilin 2 affy_probe_2_Entrez 2 2 114 -9.66 down 2 0 0/2 -4.83 2 114 -2.60 -7.06 202350_s_at 202350_s_at matrilin 2 MATN2 -7.062 -7.06 down 0.002361334 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 621 4154 MBNL1 muscleblind-like (Drosophila) affy_probe_2_Entrez 1 1 24 2.74 up 1 0 1/0 2.74 1 24 2.74 2.74 201151_s_at 201151_s_at muscleblind-like (Drosophila) -2.74 2.74 up 0.000005 FA FTC 12 12 provided by authors 15713710 15 22 1024 4176 MCM7 MCM7 minichromosome maintenance deficient 7 (S. cerevisiae) Gene_symbol_2_NCBI_Entrez 1 1 7 3 up 1 0 1/0 3 1 7 3.00 3.00 Minichromosome maintenance deficient (S. cerevisiae)7 MCM7 3 3.00 up FTC FA 3 4 publication 15475448 15 22 1032 4212 MEIS2 Meis1, myeloid ecotropic viral integration site 1 homolog 2 (mouse) Gene_symbol_2_NCBI_Entrez 1 1 7 2 up 1 0 1/0 2 1 7 2.00 2.00 Meis (mouse) homolog 2 MEIS2 2 2.00 up FTC FA 3 4 publication 15475448 3 6 141 4223 MEOX2 mesenchyme homeo box 2 (growth arrest-specific homeo box) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 -2.4 down 1 0 0/1 -2.4 1 16 -2.40 -2.40 AI743406 AI743406 Growth arrest-specific homeo box MEOX2 -2.4 -2.40 down no 0.0082 PTC Norm 8 8 suppl. materials 11752453 12 19 861 4233 MET met proto-oncogene (hepatocyte growth factor receptor) clone_accession_2_NCBI_rna_accession_2_Entrez 6 6 202 18.18 up 6 0 6/0 4.545 4 162 6.60 2.60 J02958 J02958 Hepatocyte growth factor receptor (c-MET) up yes PTC Norm 18 3 publication 12538453 13 20 897 4233 MET met proto-oncogene (hepatocyte growth factor receptor) clone_accession_2_NCBI_rna_accession_2_Entrez 6 6 202 18.18 up 6 0 6/0 4.545 4 162 6.60 2.60 J02958 J02958 Met proto-oncogene (hepatocyte growth factor receptor) MET up yes FTC FA 9 10 publication 12738736 18 31 1341 4233 MET met proto-oncogene (hepatocyte growth factor receptor) clone_accession_2_NCBI_rna_accession_2_Entrez 6 6 202 18.18 up 6 0 6/0 4.545 4 162 6.60 2.60 J02958 J02958 MET proto-oncogene protein HGFR 2.6 2.60 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1493 4233 MET met proto-oncogene (hepatocyte growth factor receptor) Gene_symbol_2_NCBI_Entrez 6 6 202 18.18 up 6 0 6/0 4.545 4 162 6.60 2.60 Met proto-oncogene (hepatocyte growth factor receptor) MET 1.47 2.77 up PTC Norm 16 16 publication 15735049 25 34 1569 4233 MET met proto-oncogene (hepatocyte growth factor receptor) affy_probe_2_Entrez 6 6 202 18.18 up 6 0 6/0 4.545 4 162 6.60 2.60 203510_at 203510_at met proto-oncogene (hepatocyte growth factor receptor) MET 6.213 6.21 up 0.011209368 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 127 4233 MET met proto-oncogene (hepatocyte growth factor receptor) Gene_symbol_2_NCBI_Entrez 6 6 202 18.18 up 6 0 6/0 4.545 4 162 6.60 2.60 Met protooncogene MET 6.6 6.60 up no 0.0001 PTC Norm 8 8 suppl. materials 11752453 18 31 1342 4240 MFGE8 milk fat globule-EGF factor 8 protein clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 2.6 up 1 0 1/0 2.6 1 59 2.60 2.60 U58516 U58516 Breast epithelial antigen 46 BA46 2.6 2.60 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1531 4291 MLF1 myeloid leukemia factor 1 Gene_symbol_2_NCBI_Entrez 2 2 87 -4.99 down 2 0 0/2 -2.495 2 87 -2.20 -2.79 Myeloid leukemia factor 1 MLF1 -1.135 -2.20 down PTC Norm 16 16 publication 15735049 25 34 1679 4291 MLF1 myeloid leukemia factor 1 affy_probe_2_Entrez 2 2 87 -4.99 down 2 0 0/2 -2.495 2 87 -2.20 -2.79 204783_at 204783_at myeloid leukemia factor 1 MLF1 -2.748 -2.75 down 0.018119122 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1681 4291 MLF1 myeloid leukemia factor 1 affy_probe_2_Entrez 2 2 87 -4.99 down 2 0 0/2 -2.495 2 87 -2.20 -2.79 204784_s_at 204784_s_at myeloid leukemia factor 1 MLF1 -2.787 -2.79 down 0.008676001 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1666 4300 MLLT3 myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 affy_probe_2_Entrez 1 1 55 -2.51 down 1 0 0/1 -2.51 1 55 -2.51 -2.51 204917_s_at 204917_s_at myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila); translocated to, 3 MLLT3 -2.510 -2.51 down 0.043508956 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 12 19 862 4320 MMP11 matrix metalloproteinase 11 (stromelysin 3) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 21 0 up 1 0 1/0 0 0 0 0 0 X57766 X57766 MMP-11 up yes PTC Norm 18 3 publication 12538453 2 2 77 4324 MMP15 matrix metalloproteinase 15 (membrane-inserted) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 6.5 up 1 0 1/0 6.5 1 2 6.50 6.50 NM_002428 NM_002428 Matrix metalloproteinase 15 MMP15 6.5 6.50 up FCL Norm 1 1 publication 15785240 11 18 798 4329 ALDH6A1 aldehyde dehydrogenase 6 family, member A1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 M93405 M93405 Methylmalonate semialdehyde dehydrogenase (M M SDH) down ACL;ATC Norm 21 10 publication 15613457 18 31 1297 4435 CITED1 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 1 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 107 56.21 up 3 0 3/0 18.7366666666667 3 107 26.90 7.90 U65092 U65092 Melanocyte-specific gene MSG1 7.9 7.90 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1446 4435 CITED1 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 1 Gene_symbol_2_NCBI_Entrez 3 3 107 56.21 up 3 0 3/0 18.7366666666667 3 107 26.90 7.90 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxyl-terminal domain, 1 CITED1 4.42 21.41 up PTC Norm 16 16 publication 15735049 3 6 115 4435 CITED1 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 1 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 107 56.21 up 3 0 3/0 18.7366666666667 3 107 26.90 7.90 U65092 U65092 Cbp/p300-interacting transactivator 1 CITED1 26.9 26.90 up yes 0.0005 PTC Norm 8 8 suppl. materials 11752453 10 16 723 4489 MT1A metallothionein 1A (functional) affy_probe_2_Entrez 2 2 73 -4.59 down 2 0 0/2 -2.295 2 73 -2.20 -2.39 31623_f_at 31623_f_at Metallothionein A MT1A -2.39 -2.39 down yes PTC GT 8 6 publication 15515157 18 31 1349 4489 MT1A metallothionein 1A (functional) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 73 -4.59 down 2 0 0/2 -2.295 2 73 -2.20 -2.39 K01383 K01383 Human metallothionein-I-A MT1A 2.5 -2.50 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 18 31 1374 4489 MT1A metallothionein 1A (functional) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 73 -4.59 down 2 0 0/2 -2.295 2 73 -2.20 -2.39 M13485 M13485 Metallothionein I-B MT1B 2.2 -2.20 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 10 16 722 4493 MT1E metallothionein 1E (functional) affy_probe_2_Entrez 2 2 73 -4.29 down 2 0 0/2 -2.145 2 73 -2.00 -2.29 36130_f_at 36130_f_at Similar to RNA helicase-related protein MT1E -2.29 -2.29 down yes PTC GT 8 6 publication 15515157 18 31 1394 4493 MT1E metallothionein 1E (functional) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 73 -4.29 down 2 0 0/2 -2.145 2 73 -2.00 -2.29 R92331 R92331 Human metallothionein-le gene MT1E 2 -2.00 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 10 16 730 4494 MT1F metallothionein 1F (functional) affy_probe_2_Entrez 3 3 92 -5.71 down 3 0 0/3 -2.855 2 73 -2.80 -2.91 31622_f_at 31622_f_at Metallothionein 1F MT1F -2.91 -2.91 down yes PTC GT 8 6 publication 15515157 13 20 953 4494 MT1F metallothionein 1F (functional) clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 92 -5.71 down 3 0 0/3 -2.855 2 73 -2.80 -2.91 M10943 M10943 Metallothionein 1 F (functional) MT1F down FTC FA 9 10 publication 12738736 18 31 1332 4494 MT1F metallothionein 1F (functional) clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 92 -5.71 down 3 0 0/3 -2.855 2 73 -2.80 -2.91 M10943 M10943 Human metallothionein-lf MT1F 2.8 -2.80 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 10 16 742 4495 MT1G metallothionein 1G affy_probe_2_Entrez 3 3 89 -16.65 down 3 0 0/3 -5.55 3 89 -2.30 -8.60 926_at 926_at Metallothionein IG MT-IG -5.75 -5.75 down yes PTC GT 8 6 publication 15515157 18 31 1364 4495 MT1G metallothionein 1G clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 89 -16.65 down 3 0 0/3 -5.55 3 89 -2.30 -8.60 J03910 J03910 Metallothionein-IG MT1G 2.3 -2.30 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 3 6 162 4495 MT1G metallothionein 1G clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 89 -16.65 down 3 0 0/3 -5.55 3 89 -2.30 -8.60 J03910 J03910 Metallothionein-IG MT1G -8.6 -8.60 down no 0.0023 PTC Norm 8 8 suppl. materials 11752453 10 16 726 4496 MT1H metallothionein 1H affy_probe_2_Entrez 1 1 14 -2.57 down 1 0 0/1 -2.57 1 14 -2.57 -2.57 39594_f_at 39594_f_at Metallothionein 1H MT1H -2.57 -2.57 down yes PTC GT 8 6 publication 15515157 18 31 1317 4501 MT1X metallothionein 1X clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -3.4 down 1 0 0/1 -3.4 1 59 -3.40 -3.40 AA224832 AA224832 Human metallothionein-1L MT1L 3.4 -3.40 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 11 18 819 4580 MTX1 metaxin 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 NM_002455 NM_002455 Metaxin 1 (MTX1) down ACL;ATC Norm 21 10 publication 15613457 24 33 1494 4628 MYH10 myosin, heavy polypeptide 10, non-muscle Gene_symbol_2_NCBI_Entrez 1 1 32 2.72 up 1 0 1/0 2.72 1 32 2.72 2.72 Myosin, heavy polypeptide 10, nonmuscle MYH10 1.445 2.72 up PTC Norm 16 16 publication 15735049 25 34 1563 4646 MYO6 myosin VI affy_probe_2_Entrez 1 1 55 7.87 up 1 0 1/0 7.87 1 55 7.87 7.87 210480_s_at 210480_s_at myosin VI MYO6 7.867 7.87 up 0.005460828 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1683 4653 MYOC myocilin, trabecular meshwork inducible glucocorticoid response affy_probe_2_Entrez 1 1 55 -2.86 down 1 0 0/1 -2.86 1 55 -2.86 -2.86 210155_at 210155_at myocilin, trabecular meshwork inducible glucocorticoid response MYOC -2.863 -2.86 down 0.000503961 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1749 4684 NCAM1 neural cell adhesion molecule 1 affy_probe_2_Entrez 1 1 55 -5.61 down 1 0 0/1 -5.61 1 55 -5.61 -5.61 212843_at 212843_at neural cell adhesion molecule 1 NCAM1 -5.608 -5.61 down 0.027099522 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 11 18 773 4735 SEPT2 septin 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 NM_004404 NM_004404 NEDD5: neural precursor cell expressed, developmentally down regulated 5 up ACL;ATC Norm 21 10 publication 15613457 18 31 1309 4753 NELL2 NEL-like 2 (chicken) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 4 up 1 0 1/0 4 1 59 4.00 4.00 D83018 D83018 Neuropilin 2 NRP2 4 4.00 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 15 22 1026 4771 NF2 neurofibromin 2 (bilateral acoustic neuroma) Gene_symbol_2_NCBI_Entrez 1 1 7 3 up 1 0 1/0 3 1 7 3.00 3.00 Neurofibromin 2 NF2 3 3.00 up FTC FA 3 4 publication 15475448 9 14 653 4781 NFIB nuclear factor I/B affy_probe_2_Entrez 1 1 24 3.29 up 1 0 1/0 3.29 1 24 3.29 3.29 213032_at 213032_at Homo sapiens mRNA; cDNA DKFZp564H1916 (from clone DKFZp564H1916) -3.29 3.29 up 0.000205 FA FTC 12 12 provided by authors 15713710 11 18 788 4839 NOL1 nucleolar protein 1, 120kDa clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 M32110 M32110 Proliferating-cell nucleolar protein P120 down ACL;ATC Norm 21 10 publication 15613457 11 18 817 4842 NOS1 nitric oxide synthase 1 (neuronal) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U17327 U17327 Neuronal nitric oxide synthase (NOS1) down ACL;ATC Norm 21 10 publication 15613457 25 34 1701 4856 NOV nephroblastoma overexpressed gene affy_probe_2_Entrez 1 1 55 -3.15 down 1 0 0/1 -3.15 1 55 -3.15 -3.15 214321_at 214321_at nephroblastoma overexpressed gene NOV -3.152 -3.15 down 0.026812738 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1483 4897 NRCAM neuronal cell adhesion molecule Gene_symbol_2_NCBI_Entrez 2 2 87 8.65 up 2 0 2/0 4.325 2 87 4.79 3.86 Neuronal cell adhesion molecule NRCAM 1.95 3.86 up PTC Norm 16 16 publication 15735049 25 34 1580 4897 NRCAM neuronal cell adhesion molecule affy_probe_2_Entrez 2 2 87 8.65 up 2 0 2/0 4.325 2 87 4.79 3.86 204105_s_at 204105_s_at neuronal cell adhesion molecule NRCAM 4.795 4.79 up 4.95381E-08 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 19 32 1402 4907 NT5E 5'-nucleotidase, ecto (CD73) tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 AGCCTGCTCA AGCCTGCTCA CD73 (5'nucleotidase) up 0.0245 FVPTC Norm 1 1 publication 14715705 14 21 973 4929 NR4A2 nuclear receptor subfamily 4, group A, member 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 3.6 up 1 0 1/0 3.6 1 14 3.60 3.60 AA598611 AA598611 Immediate-early response protein 3.6 3.60 up PTC Norm 7 7 publication 15041723 25 34 1741 4948 OCA2 oculocutaneous albinism II (pink-eye dilution homolog, mouse) affy_probe_2_Entrez 1 1 55 -4.99 down 1 0 0/1 -4.99 1 55 -4.99 -4.99 206498_at 206498_at oculocutaneous albinism II (pink-eye dilution homolog, mouse) OCA2 -4.995 -4.99 down 0.014316043 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 11 18 785 4953 ODC1 ornithine decarboxylase 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 M16650 M16650 Ornithine decarboxylase (ODC1) up ACL;ATC Norm 21 10 publication 15613457 25 34 1675 4969 OGN osteoglycin (osteoinductive factor, mimecan) affy_probe_2_Entrez 1 1 55 -2.68 down 1 0 0/1 -2.68 1 55 -2.68 -2.68 218730_s_at 218730_s_at osteoglycin (osteoinductive factor, mimecan) OGN -2.683 -2.68 down 0.023495586 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 956 4982 TNFRSF11B tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 -2.4 down 2 0 0/2 -2.4 1 59 -2.40 -2.40 AB008822 AB008822 Tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) TNFRSF11B down FTC FA 9 10 publication 12738736 18 31 1356 4982 TNFRSF11B tumor necrosis factor receptor superfamily, member 11b (osteoprotegerin) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 -2.4 down 2 0 0/2 -2.4 1 59 -2.40 -2.40 AB008822 AB008822 Osteoclastogenesis inhibitory factor OCIF 2.4 -2.40 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 14 21 986 5036 PA2G4 proliferation-associated 2G4, 38kDa clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 2.4 up 1 0 1/0 2.4 1 14 2.40 2.40 AA488332 AA488332 Cell cycle protein p38-2G4 2.4 2.40 up PTC Norm 7 7 publication 15041723 11 18 805 5037 PBP prostatic binding protein clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 X75252 X75252 Phosphatidylethanolamine-binding protein (PBP) down yes ACL;ATC Norm 21 10 publication 15613457 15 22 1045 5046 PCSK6 proprotein convertase subtilisin/kexin type 6 Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 7 -2.5 down 1 0 0/1 -2.5 1 7 -2.50 -2.50 Paired basic amino acid cleaving system 4 PACE4 0.4 -2.50 down FTC FA 3 4 publication 15475448 16 24 1220 5052 PRDX1 peroxiredoxin 1 Gene_symbol_2_NCBI_Entrez 1 1 63 -1.62 down 1 0 0/1 -1.62 1 63 -1.62 -1.62 PRDX1 0.617647059 -1.62 down 0.02 PTC;FVPTC FA;HN 32 31 publication 15087409 2 2 80 5058 PAK1 p21/Cdc42/Rac1-activated kinase 1 (STE20 homolog, yeast) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 4.71 up 1 0 1/0 4.71 1 2 4.71 4.71 NM_002576 NM_002576 P21/Cdc42/Rac1-activated kinase 1 PAK1 4.71 4.71 up FCL Norm 1 1 publication 15785240 24 33 1512 5066 PAM peptidylglycine alpha-amidating monooxygenase Gene_symbol_2_NCBI_Entrez 1 1 32 1.69 up 1 0 1/0 1.69 1 32 1.69 1.69 Peptidylglycine alpha-amidating monooxygenase PAM 0.755 1.69 up PTC Norm 16 16 publication 15735049 9 14 698 5090 PBX3 pre-B-cell leukemia transcription factor 3 affy_probe_2_Entrez 1 1 24 7.88 up 1 0 1/0 7.88 1 24 7.88 7.88 204082_at 204082_at pre-B-cell leukemia transcription factor 3 -7.88 7.88 up 0.0097 FA FTC 12 12 provided by authors 15713710 5 10 383 5126 PCSK2 proprotein convertase subtilisin/kexin type 2 tag_2_refseq_or_mgc_2_Entrez 1 1 3 0 up 1 0 1/0 0 0 0 0 0 TTGTAAATTA TTGTAAATTA PCSK2 up no FTC FA;Norm 1 2 publication 15085203 13 20 902 5127 PCTK1 PCTAIRE protein kinase 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 X66363 X66363 PCTAIRE protein kinase 1 PCTK1 up FTC FA 9 10 publication 12738736 13 20 903 5127 PCTK1 PCTAIRE protein kinase 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 X66363 X66363 PCTAIRE protein kinase 1 PTCK1 up FTC FA 9 10 publication 12738736 14 21 992 5154 PDGFA platelet-derived growth factor alpha polypeptide clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 2 up 1 0 1/0 2 1 14 2.00 2.00 AA701502 AA701502 Platelet-derived growth factor PDGF-A 2 2.00 up PTC Norm 7 7 publication 15041723 13 20 879 5167 ENPP1 ectonucleotide pyrophosphatase/phosphodiesterase 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 D12485 D12485 Ectonucleotide pyrophosphatase/phosphodiesterase 1 ENPP1 up FTC FA 9 10 publication 12738736 13 20 877 5168 ENPP2 ectonucleotide pyrophosphatase/phosphodiesterase 2 (autotaxin) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 L35594 L35594 Ectonucleotide pyrophosphatase/phosphodiesterase 2 (autotaxin) ENPP2 up yes FTC FA 9 10 publication 12738736 13 20 878 5168 ENPP2 ectonucleotide pyrophosphatase/phosphodiesterase 2 (autotaxin) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 L35594 L35594 Ectonucleotide pyrophosphatase/phosphodiesterase 2 (autotaxin) ENPP2 up yes FTC FA 9 10 publication 12738736 18 31 1365 5172 SLC26A4 solute carrier family 26, member 4 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2.3 down 1 0 0/1 -2.3 1 59 -2.30 -2.30 AF030880 AF030880 Pedrin PDS 2.3 -2.30 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 18 31 1386 5222 PGA5 pepsinogen 5, group I (pepsinogen A) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2.1 down 1 0 0/1 -2.1 1 59 -2.10 -2.10 J00287 J00287 Pepsinogen PEP 2.1 -2.10 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 14 21 1004 5228 PGF placental growth factor, vascular endothelial growth factor-related protein Gene_symbol_2_NCBI_Entrez 1 1 14 0 up 1 0 1/0 0 0 0 0 0 placental growth factor PGF up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 10 16 709 5265 SERPINA1 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 affy_probe_2_Entrez 5 6 192 95.04 up 6 0 6/0 15.84 6 192 27.64 5.00 36781_at 36781_at Serine (or cysteine) proteinase inhibitor SERPIN-A1 16.51 16.51 up yes PTC GT 8 6 publication 15515157 10 17 747 5265 SERPINA1 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 affy_probe_2_Entrez 5 6 192 95.04 up 6 0 6/0 15.84 6 192 27.64 5.00 36781_at 36781_at Serine (or cysteine) proteinase inhibitor, clade A SERPIN-A1 11.35 11.35 up yes yes PTC Norm 8 8 publication 15515157 18 31 1303 5265 SERPINA1 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 clone_accession_2_NCBI_rna_accession_2_Entrez 5 6 192 95.04 up 6 0 6/0 15.84 6 192 27.64 5.00 X01683 X01683 Alpha 1-antitrypsin AAT 5 5.00 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1447 5265 SERPINA1 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 Gene_symbol_2_NCBI_Entrez 5 6 192 95.04 up 6 0 6/0 15.84 6 192 27.64 5.00 Serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 SERPINA1 4.395 21.04 up PTC Norm 16 16 publication 15735049 25 34 1546 5265 SERPINA1 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 affy_probe_2_Entrez 5 6 192 95.04 up 6 0 6/0 15.84 6 192 27.64 5.00 202833_s_at 202833_s_at serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 SERPINA1 27.636 27.64 up 0.009800013 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 117 5265 SERPINA1 serine (or cysteine) proteinase inhibitor, clade A (alpha-1 antiproteinase, antitrypsin), member 1 clone_accession_2_NCBI_rna_accession_2_Entrez 5 6 192 95.04 up 6 0 6/0 15.84 6 192 27.64 5.00 X01683 X01683 Alpha 1-antitrypsin SERPINA1 13.5 13.50 up no 0.002 PTC Norm 8 8 suppl. materials 11752453 18 31 1359 5270 SERPINE2 serine (or cysteine) proteinase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 2.3 up 1 0 1/0 2.3 1 59 2.30 2.30 AI743134 AI743134 Glial-derived nexin precursor PN-1 2.3 2.30 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 12 19 859 5310 PKD1 polycystic kidney disease 1 (autosomal dominant) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 21 -3.57 down 1 0 0/1 -3.57 1 21 -3.57 -3.57 U24497 U24497 Autosomal dominant PKD1 0.28 -3.57 down PTC Norm 18 3 publication 12538453 13 20 909 5315 PKM2 pyruvate kinase, muscle clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 M26252 M26252 Pyruvate kinase, muscle PKM2 up FTC FA 9 10 publication 12738736 18 31 1393 5328 PLAU plasminogen activator, urokinase clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 91 7.9 up 2 0 2/0 3.95 2 91 5.90 2.00 X02419 X02419 Urokinase-type plasminogen activator uPA 2 2.00 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1469 5328 PLAU plasminogen activator, urokinase Gene_symbol_2_NCBI_Entrez 2 2 91 7.9 up 2 0 2/0 3.95 2 91 5.90 2.00 Plasminogen activator, urokinase PLAU 2.56 5.90 up PTC Norm 16 16 publication 15735049 13 20 904 5332 PLCB4 phospholipase C, beta 4 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 L41349 L41349 Phospholipase C, 4 PLCB4 up FTC FA 9 10 publication 12738736 25 34 1668 5348 FXYD1 FXYD domain containing ion transport regulator 1 (phospholemman) affy_probe_2_Entrez 1 1 55 -2.55 down 1 0 0/1 -2.55 1 55 -2.55 -2.55 205384_at 205384_at FXYD domain containing ion transport regulator 1 (phospholemman) FXYD1 -2.546 -2.55 down 6.07053E-07 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 695 5376 PMP22 peripheral myelin protein 22 affy_probe_2_Entrez 1 1 24 5.37 up 1 0 1/0 5.37 1 24 5.37 5.37 210139_s_at 210139_s_at peripheral myelin protein 22 -5.37 5.37 up 0.001508 FA FTC 12 12 provided by authors 15713710 13 20 905 5442 POLRMT polymerase (RNA) mitochondrial (DNA directed) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 U75370 U75370 Polymerase (RNA) mitochondrial (DNA directed) POLRMT up FTC FA 9 10 publication 12738736 2 5 112 5479 PPIB peptidylprolyl isomerase B (cyclophilin B) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -6.6 down 1 0 0/1 -6.6 1 2 -6.60 -6.60 NM_000942 NM_000942 Peptidylprolyl isomerase B (cyclophilin B) PPIB 6.6 -6.60 down UCL Norm 1 1 publication 15785240 19 32 1403 5480 PPIC peptidylprolyl isomerase C (cyclophilin C) tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 ACCGTCCACT ACCGTCCACT cyclophilin C up 0.0245 FVPTC Norm 1 1 publication 14715705 2 5 109 5524 PPP2R4 protein phosphatase 2A, regulatory subunit B' (PR 53) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -6.8 down 1 0 0/1 -6.8 1 2 -6.80 -6.80 NM_021131 NM_021131 Protein phosphatase 2, regulatory subunit “B” 53 PPP2R4 6.8 -6.80 down UCL Norm 1 1 publication 15785240 14 21 990 5529 PPP2R5E protein phosphatase 2, regulatory subunit B (B56), epsilon isoform clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 2.1 up 1 0 1/0 2.1 1 14 2.10 2.10 R53787 R53787 Protein phosphatase 2A B56-epsilon (PP2A) 2.1 2.10 up PTC Norm 7 7 publication 15041723 11 18 825 5536 PPP5C protein phosphatase 5, catalytic subunit clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U25174 U25174 Serine-threonine phosphatase (PP5) down ACL;ATC Norm 21 10 publication 15613457 15 22 1052 5567 PRKACB protein kinase, cAMP-dependent, catalytic, beta Gene_symbol_2_NCBI_Entrez 1 1 7 -3.33 down 1 0 0/1 -3.33 1 7 -3.33 -3.33 Protein kinase-cyclic AMP-dependent catalytic PRKACB 0.3 -3.33 down FTC FA 3 4 publication 15475448 15 22 1044 5569 PKIA protein kinase (cAMP-dependent, catalytic) inhibitor alpha Gene_symbol_2_NCBI_Entrez 1 1 7 -2.5 down 1 0 0/1 -2.5 1 7 -2.50 -2.50 Protein kinase (cyclic amp-dependent, catalytic) inhibitor PKIA 0.4 -2.50 down FTC FA 3 4 publication 15475448 9 14 631 5583 PRKCH protein kinase C, eta affy_probe_2_Entrez 1 1 24 2.98 up 1 0 1/0 2.98 1 24 2.98 2.98 218764_at 218764_at hypothetical protein MGC5363 -2.98 2.98 up 0.000271 FA FTC 12 12 provided by authors 15713710 25 34 1658 5588 PRKCQ protein kinase C, theta affy_probe_2_Entrez 1 1 55 -2.96 down 1 0 0/1 -2.96 1 55 -2.96 -2.96 210039_s_at 210039_s_at protein kinase C, theta PRKCQ -2.367 -2.37 down 0.000919797 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1692 5588 PRKCQ protein kinase C, theta affy_probe_2_Entrez 1 1 55 -2.96 down 1 0 0/1 -2.96 1 55 -2.96 -2.96 210038_at 210038_at protein kinase C, theta PRKCQ -2.956 -2.96 down 0.000320748 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 16 24 1242 5596 MAPK4 mitogen-activated protein kinase 4 Gene_symbol_2_NCBI_Entrez 1 1 63 -2.2 down 1 0 0/1 -2.2 1 63 -2.20 -2.20 MAPK4 0.454545455 -2.20 down 0.01 PTC;FVPTC FA;HN 32 31 publication 15087409 9 14 634 5606 MAP2K3 mitogen-activated protein kinase kinase 3 affy_probe_2_Entrez 1 1 24 3.02 up 1 0 1/0 3.02 1 24 3.02 3.02 207667_s_at 207667_s_at mitogen-activated protein kinase kinase 3 -3.02 3.02 up 0.000008 FA FTC 12 12 provided by authors 15713710 10 16 737 5610 EIF2AK2 eukaryotic translation initiation factor 2-alpha kinase 2 affy_probe_2_Entrez 1 1 14 -4.24 down 1 0 0/1 -4.24 1 14 -4.24 -4.24 1008_f_at 1008_f_at Human interferon-inducible kinase PRKR -4.24 -4.24 down yes PTC GT 8 6 publication 15515157 13 20 907 5627 PROS1 protein S (alpha) clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 149 17.29 up 4 0 4/0 5.76333333333333 3 130 7.39 3.40 M15036 M15036 Protein S (alpha) PROS1 up FTC FA 9 10 publication 12738736 18 31 1315 5627 PROS1 protein S (alpha) clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 149 17.29 up 4 0 4/0 5.76333333333333 3 130 7.39 3.40 M15036 M15036 S plasma protein PROS 3.4 3.40 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1564 5627 PROS1 protein S (alpha) affy_probe_2_Entrez 4 4 149 17.29 up 4 0 4/0 5.76333333333333 3 130 7.39 3.40 207808_s_at 207808_s_at --- --- 7.388 7.39 up 3.67179E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 128 5627 PROS1 protein S (alpha) clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 149 17.29 up 4 0 4/0 5.76333333333333 3 130 7.39 3.40 M15036 M15036 Vitamin K-dependent plasma protein S PROS1 6.5 6.50 up no 0.001 PTC Norm 8 8 suppl. materials 11752453 25 34 1637 5629 PROX1 prospero-related homeobox 1 affy_probe_2_Entrez 1 1 55 -2.02 down 1 0 0/1 -2.02 1 55 -2.02 -2.02 207401_at 207401_at prospero-related homeobox 1 PROX1 -2.024 -2.02 down 0.000209821 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1735 5649 RELN reelin affy_probe_2_Entrez 1 1 55 -4.65 down 1 0 0/1 -4.65 1 55 -4.65 -4.65 205923_at 205923_at reelin RELN -4.649 -4.65 down 1.89052E-10 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 2 2 67 5655 KLK10 kallikrein 10 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -8.8 down 1 0 0/1 -8.8 1 2 -8.80 -8.80 NM_002776 NM_002776 Kallikrein 10 KLK10 8.8 -8.80 down FCL Norm 1 1 publication 15785240 15 22 1027 5676 PSG7 pregnancy specific beta-1-glycoprotein 7 Gene_symbol_2_NCBI_Entrez 1 1 7 3 up 1 0 1/0 3 1 7 3.00 3.00 Pregnancy specific beta-1-glycoprotein 7 PSG7 3 3.00 up FTC FA 3 4 publication 15475448 11 18 778 5694 PSMB6 proteasome (prosome, macropain) subunit, beta type, 6 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 D29012 D29012 PSMB6, proteasome subunit Y up yes ACL;ATC Norm 21 10 publication 15613457 11 18 826 5700 PSMC1 proteasome (prosome, macropain) 26S subunit, ATPase, 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 NM_002802 NM_002802 PSMC1 proteasome 26S subunit, ATPase, 1 down ACL;ATC Norm 21 10 publication 15613457 11 18 827 5708 PSMD2 proteasome (prosome, macropain) 26S subunit, non-ATPase, 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 D78151 D78151 26S proteasome subunit p97 down ACL;ATC Norm 21 10 publication 15613457 14 21 1020 5723 PSPH phosphoserine phosphatase Gene_symbol_2_NCBI_Entrez 1 1 14 0 up 1 0 1/0 0 0 0 0 0 L-3-Phosphoserine-phosphatase PSPH up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 11 18 821 5763 PTMS parathymosin clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 M24398 M24398 Parathymosin down ACL;ATC Norm 21 10 publication 15613457 2 4 105 5774 PTPN3 protein tyrosine phosphatase, non-receptor type 3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 3.19 up 1 0 1/0 3.19 1 2 3.19 3.19 NM_002829 NM_002829 Protein tyrosine phosphatase nonreceptor 3 PTPN3 3.19 3.19 up PCL Norm 1 1 publication 15785240 12 19 852 5802 PTPRS protein tyrosine phosphatase, receptor type, S clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 21 -2.04 down 1 0 0/1 -2.04 1 21 -2.04 -2.04 U35234 U35234 Protein tyrosine phosphatase (PTPRS) 0.49 -2.04 down PTC Norm 18 3 publication 12538453 25 34 1574 5873 RAB27A RAB27A, member RAS oncogene family affy_probe_2_Entrez 2 2 79 7.91 up 2 0 2/0 3.955 2 79 3.98 3.93 210951_x_at 210951_x_at RAB27A, member RAS oncogene family RAB27A 5.588 5.59 up 3.30059E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1584 5873 RAB27A RAB27A, member RAS oncogene family affy_probe_2_Entrez 2 2 79 7.91 up 2 0 2/0 3.955 2 79 3.98 3.93 209514_s_at 209514_s_at RAB27A, member RAS oncogene family RAB27A 4.243 4.24 up 8.57809E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1587 5873 RAB27A RAB27A, member RAS oncogene family affy_probe_2_Entrez 2 2 79 7.91 up 2 0 2/0 3.955 2 79 3.98 3.93 209515_s_at 209515_s_at RAB27A, member RAS oncogene family RAB27A 3.984 3.98 up 0.00340633 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 679 5873 RAB27A RAB27A, member RAS oncogene family affy_probe_2_Entrez 2 2 79 7.91 up 2 0 2/0 3.955 2 79 3.98 3.93 209515_s_at 209515_s_at RAB27A, member RAS oncogene family -3.93 3.93 up 0.005235 FA FTC 12 12 provided by authors 15713710 25 34 1592 5887 RAD23B RAD23 homolog B (S. cerevisiae) affy_probe_2_Entrez 1 1 55 2.37 up 1 0 1/0 2.37 1 55 2.37 2.37 201222_s_at 201222_s_at RAD23 homolog B (S. cerevisiae) RAD23B 3.495 3.49 up 0.013912466 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1619 5887 RAD23B RAD23 homolog B (S. cerevisiae) affy_probe_2_Entrez 1 1 55 2.37 up 1 0 1/0 2.37 1 55 2.37 2.37 201223_s_at 201223_s_at RAD23 homolog B (S. cerevisiae) RAD23B 2.371 2.37 up 0.043653268 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1730 5909 RAP1GA1 RAP1, GTPase activating protein 1 affy_probe_2_Entrez 1 1 55 -4.42 down 1 0 0/1 -4.42 1 55 -4.42 -4.42 203911_at 203911_at RAP1, GTPase activating protein 1 RAP1GA1 -4.423 -4.42 down 0.039001953 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 15 22 1022 5911 RAP2A RAP2A, member of RAS oncogene family Gene_symbol_2_NCBI_Entrez 1 1 7 4 up 1 0 1/0 4 1 7 4.00 4.00 RAP2A RAP2A 4 4.00 up FTC FA 3 4 publication 15475448 11 18 780 5914 RARA retinoic acid receptor, alpha clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 35 10.4 up 2 0 2/0 10.4 1 4 10.40 10.40 M26697 M26697 hB23 gene for B23 nucleophosmin up yes ACL;ATC Norm 21 10 publication 15613457 2 3 88 5914 RARA retinoic acid receptor, alpha clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 35 10.4 up 2 0 2/0 10.4 1 4 10.40 10.40 NM_002520 NM_002520 Nucleophosmin 1 NPM1 10.4 10.40 up yes FCL;PCL;UCL Norm 3 1 publication 15785240 25 34 1620 5921 RASA1 RAS p21 protein activator (GTPase activating protein) 1 affy_probe_2_Entrez 1 1 55 2.21 up 1 0 1/0 2.21 1 55 2.21 2.21 210621_s_at 210621_s_at RAS p21 protein activator (GTPase activating protein) 1 RASA1 2.370 2.37 up 0.029326205 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1626 5921 RASA1 RAS p21 protein activator (GTPase activating protein) 1 affy_probe_2_Entrez 1 1 55 2.21 up 1 0 1/0 2.21 1 55 2.21 2.21 202677_at 202677_at RAS p21 protein activator (GTPase activating protein) 1 RASA1 2.215 2.21 up 0.041850157 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 910 5947 RBP1 retinol binding protein 1, cellular clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 M11433 M11433 Retinol-binding protein 1, cellular RBP1 up FTC FA 9 10 publication 12738736 9 14 644 5955 RCN2 reticulocalbin 2, EF-hand calcium binding domain affy_probe_2_Entrez 1 1 24 3.14 up 1 0 1/0 3.14 1 24 3.14 3.14 201485_s_at 201485_s_at reticulocalbin 2, EF-hand calcium binding domain -3.14 3.14 up 0.00262 FA FTC 12 12 provided by authors 15713710 14 21 1000 5966 REL v-rel reticuloendotheliosis viral oncogene homolog (avian) Gene_symbol_2_NCBI_Entrez 1 1 14 0 up 1 0 1/0 0 0 0 0 0 V-rel avian reticuloendotheliosis viral oncogene REL up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 14 21 982 6000 RGS7 regulator of G-protein signalling 7 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 2.7 up 1 0 1/0 2.7 1 14 2.70 2.70 H24326 H24326 Regulator of G-protein signaling (RGS7) 2.7 2.70 up PTC Norm 7 7 publication 15041723 18 31 1397 6004 RGS16 regulator of G-protein signalling 16 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 130 -12.05 down 3 0 0/3 -4.01666666666667 3 130 -2.00 -6.75 U70426 U70426 Homo sapiens A28-RGS14p A28-RGS14 2 -2.00 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1748 6004 RGS16 regulator of G-protein signalling 16 affy_probe_2_Entrez 3 3 130 -12.05 down 3 0 0/3 -4.01666666666667 3 130 -2.00 -6.75 209325_s_at 209325_s_at regulator of G-protein signalling 16 RGS16 -5.588 -5.59 down 1.12702E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1760 6004 RGS16 regulator of G-protein signalling 16 affy_probe_2_Entrez 3 3 130 -12.05 down 3 0 0/3 -4.01666666666667 3 130 -2.00 -6.75 209324_s_at 209324_s_at regulator of G-protein signalling 16 RGS16 -6.745 -6.75 down 2.04741E-09 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 148 6004 RGS16 regulator of G-protein signalling 16 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 130 -12.05 down 3 0 0/3 -4.01666666666667 3 130 -2.00 -6.75 U70426 U70426 A28-RGS14p RGS16 -3.3 -3.30 down no 0.0059 PTC Norm 8 8 suppl. materials 11752453 2 2 73 6009 RHEB Ras homolog enriched in brain clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -7.4 down 1 0 0/1 -7.4 1 2 -7.40 -7.40 NM_005614 NM_005614 Ras homologue enriched in brain RHEB2 7.4 -7.40 down FCL Norm 1 1 publication 15785240 13 20 958 6035 RNASE1 ribonuclease, RNase A family, 1 (pancreatic) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 -2.2 down 2 0 0/2 -2.2 1 59 -2.20 -2.20 D26129 D26129 Ribonuclease Rnase A family 1 (pancreatic) RNASE1 down FTC FA 9 10 publication 12738736 18 31 1375 6035 RNASE1 ribonuclease, RNase A family, 1 (pancreatic) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 -2.2 down 2 0 0/2 -2.2 1 59 -2.20 -2.20 D26129 D26129 Ribonuclease A RNase A 2.2 -2.20 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 11 18 757 6133 RPL9 ribosomal protein L9 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 U09953 U09953 Ribosomal protein L9 up ACL;ATC Norm 21 10 publication 15613457 11 18 828 6137 RPL13 ribosomal protein L13 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 X64707 X64707 BBC1 down ACL;ATC Norm 21 10 publication 15613457 11 18 764 6188 RPS3 ribosomal protein S3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 X55715 X55715 Hums3 mRNA for 40S ribosomal protein s3 up ACL;ATC Norm 21 10 publication 15613457 11 18 776 6188 RPS3 ribosomal protein S3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 X55715 X55715 Hums3 mRNA for 40S ribosomal protein s3 up ACL;ATC Norm 21 10 publication 15613457 24 33 1459 6258 RXRG retinoid X receptor, gamma Gene_symbol_2_NCBI_Entrez 2 2 87 17.25 up 2 0 2/0 8.625 2 87 11.55 5.70 Retinoid X receptor gamma RXRG 3.53 11.55 up PTC Norm 16 16 publication 15735049 25 34 1573 6258 RXRG retinoid X receptor, gamma affy_probe_2_Entrez 2 2 87 17.25 up 2 0 2/0 8.625 2 87 11.55 5.70 205954_at 205954_at retinoid X receptor, gamma RXRG 5.701 5.70 up 0.007459523 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1690 6262 RYR2 ryanodine receptor 2 (cardiac) affy_probe_2_Entrez 1 1 55 -3.74 down 1 0 0/1 -3.74 1 55 -3.74 -3.74 207557_s_at 207557_s_at ryanodine receptor 2 (cardiac) RYR2 -2.936 -2.94 down 0.000836639 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1722 6262 RYR2 ryanodine receptor 2 (cardiac) affy_probe_2_Entrez 1 1 55 -3.74 down 1 0 0/1 -3.74 1 55 -3.74 -3.74 214044_at 214044_at ryanodine receptor 2 (cardiac) RYR2 -3.743 -3.74 down 3.18078E-10 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1510 6277 S100A6 S100 calcium binding protein A6 (calcyclin) Gene_symbol_2_NCBI_Entrez 1 1 32 1.93 up 1 0 1/0 1.93 1 32 1.93 1.93 S100 calcium binding protein A6 (calcyclin) S100A6 0.945 1.93 up PTC Norm 16 16 publication 15735049 24 33 1498 6282 S100A11 S100 calcium binding protein A11 (calgizzarin) Gene_symbol_2_NCBI_Entrez 1 1 32 2.52 up 1 0 1/0 2.52 1 32 2.52 2.52 S100 calcium binding protein A11 (calgizzarin) S100A11 1.335 2.52 up PTC Norm 16 16 publication 15735049 9 14 675 6310 ATXN1 ataxin 1 affy_probe_2_Entrez 1 1 24 3.83 up 1 0 1/0 3.83 1 24 3.83 3.83 203231_s_at 203231_s_at spinocerebellar ataxia 1 (olivopontocerebellar ataxia 1, autosomal dominant, ataxin 1) -3.83 3.83 up 0.000002 FA FTC 12 12 provided by authors 15713710 14 21 988 6314 ATXN7 ataxin 7 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 2.2 up 1 0 1/0 2.2 1 14 2.20 2.20 AA704255 AA704255 Spinocerebellar ataxia 7 2.2 2.20 up PTC Norm 7 7 publication 15041723 18 31 1392 6337 SCNN1A sodium channel, nonvoltage-gated 1 alpha clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 83 -2 even 1 1 1/1 -1 2 83 2.00 -4 X76180 X76180 Lung amiloride sensitive Nachannel ENaCa 2 2.00 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 9 14 608 6337 SCNN1A sodium channel, nonvoltage-gated 1 alpha affy_probe_2_Entrez 2 2 83 -2 even 1 1 1/1 -1 2 83 2.00 -4 203453_at 203453_at sodium channel, nonvoltage-gated 1 alpha 4 -4 down 0.006097 FA FTC 12 12 provided by authors 15713710 18 31 1354 6355 CCL8 chemokine (C-C motif) ligand 8 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2.4 down 1 0 0/1 -2.4 1 59 -2.40 -2.40 Y16645 Y16645 Monocyte chemotactic protein-2 MCP-2 2.4 -2.40 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1535 6359 CCL15 chemokine (C-C motif) ligand 15 Gene_symbol_2_NCBI_Entrez 1 1 32 -2.47 down 1 0 0/1 -2.47 1 32 -2.47 -2.47 Chemokine (C-C motif) ligand 15 CCL15 -1.305 -2.47 down PTC Norm 16 16 publication 15735049 25 34 1776 6366 CCL21 chemokine (C-C motif) ligand 21 affy_probe_2_Entrez 2 2 71 -28.97 down 2 0 0/2 -14.485 2 71 -11.37 -17.60 204606_at 204606_at chemokine (C-C motif) ligand 21 CCL21 -11.370 -11.37 down 0.001106354 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 164 6366 CCL21 chemokine (C-C motif) ligand 21 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 71 -28.97 down 2 0 0/2 -14.485 2 71 -11.37 -17.60 AB002409 AB002409 Small inducible cytokine subfamily, member 21 SCYA21 -17.6 -17.60 down no 0.02 PTC Norm 8 8 suppl. materials 11752453 9 14 648 6383 SDC2 syndecan 2 (heparan sulfate proteoglycan 1, cell surface-associated, fibroglycan) affy_probe_2_Entrez 1 1 24 3.81 up 1 0 1/0 3.81 1 24 3.81 3.81 212154_at 212154_at syndecan 2 (heparan sulfate proteoglycan 1, cell surface-associated, fibroglycan) -3.17 3.17 up 0.000212 FA FTC 12 12 provided by authors 15713710 9 14 673 6383 SDC2 syndecan 2 (heparan sulfate proteoglycan 1, cell surface-associated, fibroglycan) affy_probe_2_Entrez 1 1 24 3.81 up 1 0 1/0 3.81 1 24 3.81 3.81 212157_at 212157_at syndecan 2 (heparan sulfate proteoglycan 1, cell surface-associated, fibroglycan) -3.81 3.81 up 0.000043 FA FTC 12 12 provided by authors 15713710 18 31 1360 6385 SDC4 syndecan 4 (amphiglycan, ryudocan) clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 130 9.97 up 3 0 3/0 3.32333333333333 3 130 4.17 2.30 D79206 D79206 Ryudocan core protein SYND4 2.3 2.30 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1586 6385 SDC4 syndecan 4 (amphiglycan, ryudocan) affy_probe_2_Entrez 3 3 130 9.97 up 3 0 3/0 3.32333333333333 3 130 4.17 2.30 202071_at 202071_at syndecan 4 (amphiglycan, ryudocan) SDC4 4.168 4.17 up 0.036184849 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 137 6385 SDC4 syndecan 4 (amphiglycan, ryudocan) clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 130 9.97 up 3 0 3/0 3.32333333333333 3 130 4.17 2.30 D79206 D79206 Ryudocan core protein SDC4 3.5 3.50 up no 0.0003 PTC Norm 8 8 suppl. materials 11752453 13 20 959 6414 SEPP1 selenoprotein P, plasma, 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 Z11793 Z11793 Selenoprotein P, plasma 1 SEPP1 down FTC FA 9 10 publication 12738736 11 18 789 6432 SFRS7 splicing factor, arginine/serine-rich 7, 35kDa clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 45 2.5 even 1 1 1/1 2.5 1 14 2.50 2.50 NM_006276 NM_006276 Splicing factor, arginine/serine-rich 7 (SFRS7) down ACL;ATC Norm 21 10 publication 15613457 14 21 983 6432 SFRS7 splicing factor, arginine/serine-rich 7, 35kDa clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 45 2.5 even 1 1 1/1 2.5 1 14 2.50 2.50 H54020 H54020 Splicing factor (9G8) 2.5 2.50 up PTC Norm 7 7 publication 15041723 3 6 118 6439 SFTPB surfactant, pulmonary-associated protein B clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 12.5 up 1 0 1/0 12.5 1 16 12.50 12.50 J02761 J02761 Surfactant, pulmonary-associated protein B SFTPB 12.5 12.50 up no 0.03 PTC Norm 8 8 suppl. materials 11752453 9 14 671 6446 SGK serum/glucocorticoid regulated kinase affy_probe_2_Entrez 1 1 24 3.74 up 1 0 1/0 3.74 1 24 3.74 3.74 201739_at 201739_at serum/glucocorticoid regulated kinase -3.74 3.74 up 0.002867 FA FTC 12 12 provided by authors 15713710 18 31 1336 6447 SGNE1 secretory granule, neuroendocrine protein 1 (7B2 protein) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 2.7 up 1 0 1/0 2.7 1 59 2.70 2.70 Y00757 Y00757 Polypeptide 7B2 precursor SGNE1 2.7 2.70 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 11 18 818 6462 SHBG sex hormone-binding globulin clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 X05403 X05403 Sex hormone-binding globulin (SHBG) down ACL;ATC Norm 21 10 publication 15613457 9 14 691 6503 SLA Src-like-adaptor affy_probe_2_Entrez 1 1 24 4.93 up 1 0 1/0 4.93 1 24 4.93 4.93 214977_at 214977_at Homo sapiens cDNA FLJ13790 fis, clone THYRO1000026 -4.93 4.93 up 0.004454 FA FTC 12 12 provided by authors 15713710 15 22 1037 6505 SLC1A1 solute carrier family 1 (neuronal/epithelial high affinity glutamate transporter, system Xag), member 1 Gene_symbol_2_NCBI_Entrez 1 1 7 -2 down 1 0 0/1 -2 1 7 -2.00 -2.00 Solute carrier family 1 1 SLC1A1 0.5 -2.00 down FTC FA 3 4 publication 15475448 24 33 1474 6585 SLIT1 slit homolog 1 (Drosophila) Gene_symbol_2_NCBI_Entrez 1 1 32 5.21 up 1 0 1/0 5.21 1 32 5.21 5.21 Slit homologue 1 (Drosophila) SLIT1 2.38 5.21 up PTC Norm 16 16 publication 15735049 18 31 1321 6590 SLPI secretory leukocyte protease inhibitor (antileukoproteinase) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 91 9.72 up 2 0 2/0 4.86 2 91 6.52 3.20 X04470 X04470 Antileukoprotease ALP 3.2 3.20 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1468 6590 SLPI secretory leukocyte protease inhibitor (antileukoproteinase) Gene_symbol_2_NCBI_Entrez 2 2 91 9.72 up 2 0 2/0 4.86 2 91 6.52 3.20 Secretory leukocyte protease inhibitor (antileukoproteinase) SLPI 2.705 6.52 up PTC Norm 16 16 publication 15735049 25 34 1588 6597 SMARCA4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 affy_probe_2_Entrez 1 1 55 2.17 up 1 0 1/0 2.17 1 55 2.17 2.17 215714_s_at 215714_s_at SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 SMARCA4 3.978 3.98 up 0.007393916 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1627 6597 SMARCA4 SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 affy_probe_2_Entrez 1 1 55 2.17 up 1 0 1/0 2.17 1 55 2.17 2.17 208794_s_at 208794_s_at SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 4 SMARCA4 2.171 2.17 up 0.044864178 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1673 6640 SNTA1 syntrophin, alpha 1 (dystrophin-associated protein A1, 59kDa, acidic component) affy_probe_2_Entrez 1 1 55 -2.63 down 1 0 0/1 -2.63 1 55 -2.63 -2.63 203516_at 203516_at syntrophin, alpha 1 (dystrophin-associated protein A1, 59kDa, acidic component) SNTA1 -2.630 -2.63 down 8.3961E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1597 6642 SNX1 sorting nexin 1 affy_probe_2_Entrez 1 1 55 3.29 up 1 0 1/0 3.29 1 55 3.29 3.29 214531_s_at 214531_s_at sorting nexin 1 SNX1 3.290 3.29 up 7.87124E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 922 6652 SORD sorbitol dehydrogenase clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 L29254 L29254 Sorbitol dehydrogenase SORD down FTC FA 9 10 publication 12738736 14 21 969 6668 SP2 Sp2 transcription factor clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 34 up 1 0 1/0 34 1 14 34.00 34.00 T81103 T81103 Sp2 transcription factor 34 34.00 up PTC Norm 7 7 publication 15041723 13 20 911 6692 SPINT1 serine protease inhibitor, Kunitz type 1 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 74 4.45 up 2 0 2/0 4.45 1 55 4.45 4.45 AB000095 AB000095 Serine protease inhibitor, Kunitz type 1 SPINT1 up FTC FA 9 10 publication 12738736 25 34 1581 6692 SPINT1 serine protease inhibitor, Kunitz type 1 affy_probe_2_Entrez 2 2 74 4.45 up 2 0 2/0 4.45 1 55 4.45 4.45 202826_at 202826_at serine protease inhibitor, Kunitz type 1 SPINT1 4.450 4.45 up 1.08009E-10 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 18 31 1351 6696 SPP1 secreted phosphoprotein 1 (osteopontin, bone sialoprotein I, early T-lymphocyte activation 1) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 2.4 up 1 0 1/0 2.4 1 59 2.40 2.40 J04765 J04765 Osteopontin precursor OPN 2.4 2.40 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 13 20 961 6722 SRF serum response factor (c-fos serum response element-binding transcription factor) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 74 -2.87 down 2 0 0/2 -2.87 1 55 -2.87 -2.87 J03161 J03161 Serum response factor (c-fos serum response element-binding transcription factor) SRF down FTC FA 9 10 publication 12738736 25 34 1684 6722 SRF serum response factor (c-fos serum response element-binding transcription factor) affy_probe_2_Entrez 2 2 74 -2.87 down 2 0 0/2 -2.87 1 55 -2.87 -2.87 202401_s_at 202401_s_at serum response factor (c-fos serum response element-binding transcription factor) SRF -2.865 -2.87 down 0.003713672 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 881 6756 SSX1 synovial sarcoma, X breakpoint 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 S79325 S79325 Fusion gene up FTC FA 9 10 publication 12738736 24 33 1511 6768 ST14 suppression of tumorigenicity 14 (colon carcinoma, matriptase, epithin) Gene_symbol_2_NCBI_Entrez 1 1 32 1.82 up 1 0 1/0 1.82 1 32 1.82 1.82 Suppression of tumorigenicity 14 (colon carcinoma, matriptase, epithin) ST14 0.86 1.82 up PTC Norm 16 16 publication 15735049 13 20 912 6778 STAT6 signal transducer and activator of transcription 6, interleukin-4 induced clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 U16031 U16031 Signal transducer and activator of transcription 6, interleukin-4 induced STAT6 up FTC FA 9 10 publication 12738736 3 6 146 6781 STC1 stanniocalcin 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 -2.8 down 1 0 0/1 -2.8 1 16 -2.80 -2.80 U25997 U25997 Stanniocalcin precursor (STC) STC1 -2.8 -2.80 down no 0.022 PTC Norm 8 8 suppl. materials 11752453 11 18 797 6818 SULT1A3 sulfotransferase family, cytosolic, 1A, phenol-preferring, member 3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 L25275 L25275 Estrogen sulfotransferase (SULTIA3) down ACL;ATC Norm 21 10 publication 15613457 18 31 1348 6834 SURF1 surfeit 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2.5 down 1 0 0/1 -2.5 1 59 -2.50 -2.50 Z35093 Z35093 SURF-1 SURF1 2.5 -2.50 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 10 16 721 6925 TCF4 transcription factor 4 affy_probe_2_Entrez 2 2 38 0.59 even 1 1 1/1 0.295 2 38 2.88 -2.29 32872_at 32872_at cDNA DKFZp564I083 -2.29 -2.29 down yes PTC GT 8 6 publication 15515157 9 14 628 6925 TCF4 transcription factor 4 affy_probe_2_Entrez 2 2 38 0.59 even 1 1 1/1 0.295 2 38 2.88 -2.29 213891_s_at 213891_s_at Homo sapiens cDNA FLJ11918 fis, clone HEMBB1000272 -2.88 2.88 up 0.000001 FA FTC 12 12 provided by authors 15713710 13 20 962 6993 TCTEL1 t-complex-associated-testis-expressed 1-like 1 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 -2.1 down 2 0 0/2 -2.1 1 59 -2.10 -2.10 D50663 D50663 T-complex-associated-testis-expressed 1-like 1 TCTEL1 down FTC FA 9 10 publication 12738736 18 31 1385 6993 TCTEL1 t-complex-associated-testis-expressed 1-like 1 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 -2.1 down 2 0 0/2 -2.1 1 59 -2.10 -2.10 D50663 D50663 T-complex-associated-testis-expressed 1-like 1 TCTEL1 2.1 -2.10 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1649 7004 TEAD4 TEA domain family member 4 affy_probe_2_Entrez 1 1 55 -2.19 down 1 0 0/1 -2.19 1 55 -2.19 -2.19 41037_at 41037_at TEA domain family member 4 TEAD4 -2.185 -2.19 down 0.000195038 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 10 17 752 7033 TFF3 trefoil factor 3 (intestinal) affy_probe_2_Entrez 6 6 196 -88.17 down 6 0 0/6 -22.0425 4 146 -3.80 -63.55 31477_at 31477_at Trefoil factor 3 (intestinal) TFF3 -6.81 -6.81 down yes yes PTC Norm 8 8 publication 15515157 10 17 753 7033 TFF3 trefoil factor 3 (intestinal) affy_probe_2_Entrez 6 6 196 -88.17 down 6 0 0/6 -22.0425 4 146 -3.80 -63.55 37897_s_at 37897_s_at Trefoil factor 3 (intestinal) TFF3 -8.52 -8.52 down yes yes PTC Norm 8 8 publication 15515157 11 18 816 7033 TFF3 trefoil factor 3 (intestinal) clone_accession_2_NCBI_rna_accession_2_Entrez 6 6 196 -88.17 down 6 0 0/6 -22.0425 4 146 -3.80 -63.55 L15203 L15203 Secretory protein (P1.B) down ACL;ATC Norm 21 10 publication 15613457 13 20 964 7033 TFF3 trefoil factor 3 (intestinal) clone_accession_2_NCBI_rna_accession_2_Entrez 6 6 196 -88.17 down 6 0 0/6 -22.0425 4 146 -3.80 -63.55 AI985964 AI985964 Trefoil factor 3 (intestinal) TFF3 down FTC FA 9 10 publication 12738736 13 20 965 7033 TFF3 trefoil factor 3 (intestinal) clone_accession_2_NCBI_rna_accession_2_Entrez 6 6 196 -88.17 down 6 0 0/6 -22.0425 4 146 -3.80 -63.55 L08044 L08044 Trefoil factor 3 (intestinal) TFF3 down FTC FA 9 10 publication 12738736 18 31 1298 7033 TFF3 trefoil factor 3 (intestinal) clone_accession_2_NCBI_rna_accession_2_Entrez 6 6 196 -88.17 down 6 0 0/6 -22.0425 4 146 -3.80 -63.55 AI985964 AI985964 Intestinal Trefoil Factor, precursor TFF3 7.6 -7.60 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 18 31 1311 7033 TFF3 trefoil factor 3 (intestinal) clone_accession_2_NCBI_rna_accession_2_Entrez 6 6 196 -88.17 down 6 0 0/6 -22.0425 4 146 -3.80 -63.55 L08044 L08044 Human intestinal trefoil factor TFF3 3.8 -3.80 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1785 7033 TFF3 trefoil factor 3 (intestinal) affy_probe_2_Entrez 6 6 196 -88.17 down 6 0 0/6 -22.0425 4 146 -3.80 -63.55 204623_at 204623_at trefoil factor 3 (intestinal) TFF3 -63.550 -63.55 down 9.36533E-11 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 163 7033 TFF3 trefoil factor 3 (intestinal) clone_accession_2_NCBI_rna_accession_2_Entrez 6 6 196 -88.17 down 6 0 0/6 -22.0425 4 146 -3.80 -63.55 L08044 L08044 Intestinal trefoil factor TFF3 -12.3 -12.30 down yes 0.004 PTC Norm 8 8 suppl. materials 11752453 25 34 1651 7035 TFPI tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) affy_probe_2_Entrez 1 1 55 -2.22 down 1 0 0/1 -2.22 1 55 -2.22 -2.22 210664_s_at 210664_s_at tissue factor pathway inhibitor (lipoprotein-associated coagulation inhibitor) TFPI -2.221 -2.22 down 1.48179E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 15 22 1047 7037 TFRC transferrin receptor (p90, CD71) Gene_symbol_2_NCBI_Entrez 1 1 7 -2.5 down 1 0 0/1 -2.5 1 7 -2.50 -2.50 Transferrin receptor TFRC 0.4 -2.50 down FTC FA 3 4 publication 15475448 11 18 801 7038 TG thyroglobulin clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 X05615 X05615 Thyroglobulin (TG) down yes ACL;ATC Norm 21 10 publication 15613457 13 20 916 7039 TGFA transforming growth factor, alpha clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 165 18.55 up 4 0 4/0 6.18333333333333 3 146 7.91 3.20 X70340 X70340 Transforming growth factor, TGFA up FTC FA 9 10 publication 12738736 18 31 1322 7039 TGFA transforming growth factor, alpha clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 165 18.55 up 4 0 4/0 6.18333333333333 3 146 7.91 3.20 X70340 X70340 Transforming growth factor alpha TGFA 3.2 3.20 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1465 7039 TGFA transforming growth factor, alpha Gene_symbol_2_NCBI_Entrez 4 4 165 18.55 up 4 0 4/0 6.18333333333333 3 146 7.91 3.20 Transforming growth factor, alpha TGFA 2.895 7.44 up PTC Norm 16 16 publication 15735049 25 34 1562 7039 TGFA transforming growth factor, alpha affy_probe_2_Entrez 4 4 165 18.55 up 4 0 4/0 6.18333333333333 3 146 7.91 3.20 205016_at 205016_at transforming growth factor, alpha TGFA 7.907 7.91 up 7.0336E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 2 5 111 7046 TGFBR1 transforming growth factor, beta receptor I (activin A receptor type II-like kinase, 53kDa) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -6.6 down 1 0 0/1 -6.6 1 2 -6.60 -6.60 NM_004612 NM_004612 Transforming growth factor, beta receptor I TGFBR1 6.6 -6.60 down UCL Norm 1 1 publication 15785240 13 20 963 7048 TGFBR2 transforming growth factor, beta receptor II (70/80kDa) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 -2.2 down 2 0 0/2 -2.2 1 59 -2.20 -2.20 D50683 D50683 Transforming growth factor, receptor II TGFBR2 down yes FTC FA 9 10 publication 12738736 18 31 1370 7048 TGFBR2 transforming growth factor, beta receptor II (70/80kDa) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 -2.2 down 2 0 0/2 -2.2 1 59 -2.20 -2.20 D50683 D50683 Transforming growth factor-beta II receptor alpha TGF-beta IIRa 2.2 -2.20 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 10 16 711 7076 TIMP1 tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor) affy_probe_2_Entrez 4 5 142 26.89 up 5 0 5/0 5.378 5 142 10.31 3.20 1693_s_at 1693_s_at Tissue inhibitor of metalloproteinase 1 TIMP1 10.31 10.31 up yes yes PTC GT 8 6 publication 15515157 10 17 749 7076 TIMP1 tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor) affy_probe_2_Entrez 4 5 142 26.89 up 5 0 5/0 5.378 5 142 10.31 3.20 1693_s_at 1693_s_at Tissue inhibitor of metalloproteinase 1 TIMP1 5.17 5.17 up yes no PTC Norm 8 8 publication 15515157 12 19 850 7076 TIMP1 tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor) clone_accession_2_NCBI_rna_accession_2_Entrez 4 5 142 26.89 up 5 0 5/0 5.378 5 142 10.31 3.20 X03124 X03124 Erythroid potentiating activity (TIMP-1) 3.2 3.20 up yes yes PTC Norm 18 3 publication 12538453 18 31 1320 7076 TIMP1 tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor) clone_accession_2_NCBI_rna_accession_2_Entrez 4 5 142 26.89 up 5 0 5/0 5.378 5 142 10.31 3.20 D11139 D11139 Tissue inhibitor of metalloproteinases TIMP 3.2 3.20 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1475 7076 TIMP1 tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor) Gene_symbol_2_NCBI_Entrez 4 5 142 26.89 up 5 0 5/0 5.378 5 142 10.31 3.20 Tissue inhibitor of metalloproteinase 1 (erythroid potentiating activity, collagenase inhibitor) TIMP1 2.325 5.01 up PTC Norm 16 16 publication 15735049 24 33 1533 7091 TLE4 transducin-like enhancer of split 4 (E(sp1) homolog, Drosophila) Gene_symbol_2_NCBI_Entrez 1 1 32 -2.39 down 1 0 0/1 -2.39 1 32 -2.39 -2.39 Transducin-like enhancer of split 4 [E(sp1) homologue, Drosophila] TLE4 -1.26 -2.39 down PTC Norm 16 16 publication 15735049 14 21 978 7103 TSPAN8 tetraspanin 8 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 69 0.56 even 1 1 1/1 0.28 2 69 2.80 -2.24 AA045699 AA045699 Tumor-associated antigen CO-029 2.8 2.80 up PTC Norm 7 7 publication 15041723 25 34 1655 7103 TSPAN8 tetraspanin 8 affy_probe_2_Entrez 2 2 69 0.56 even 1 1 1/1 0.28 2 69 2.80 -2.24 203824_at 203824_at transmembrane 4 superfamily member 3 TM4SF3 -2.240 -2.24 down 0.024228004 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 18 31 1314 7122 CLDN5 claudin 5 (transmembrane protein deleted in velocardiofacial syndrome) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -3.5 down 1 0 0/1 -3.5 1 59 -3.50 -3.50 AF000959 AF000959 Deleted in Velo-Cardio-Facial Syndrome TMVCF 3.5 -3.50 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 18 31 1373 7123 CLEC3B C-type lectin domain family 3, member B clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2.2 down 1 0 0/1 -2.2 1 59 -2.20 -2.20 X64559 X64559 Tetranectin, a plasminogen-kringle 4 binding protein TN 2.2 -2.20 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1687 7148 TNXB tenascin XB affy_probe_2_Entrez 1 1 55 -3.85 down 1 0 0/1 -3.85 1 55 -3.85 -3.85 208609_s_at 208609_s_at tenascin XB /// tenascin XB TNXB -2.880 -2.88 down 0.046554302 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1723 7148 TNXB tenascin XB affy_probe_2_Entrez 1 1 55 -3.85 down 1 0 0/1 -3.85 1 55 -3.85 -3.85 206093_x_at 206093_x_at tenascin XB TNXB -3.852 -3.85 down 0.022672896 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 11 18 783 7156 TOP3A topoisomerase (DNA) III alpha clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 U43431 U43431 DNA topoisomerase III up ACL;ATC Norm 21 10 publication 15613457 10 16 744 7173 TPO thyroid peroxidase affy_probe_2_Entrez 4 4 91 -18.77 down 4 0 0/4 -6.25666666666667 3 89 -2.70 -8.60 35928_at 35928_at Thyroid peroxidase TPO -7.47 -7.47 down yes PTC GT 8 6 publication 15515157 18 31 1340 7173 TPO thyroid peroxidase clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 91 -18.77 down 4 0 0/4 -6.25666666666667 3 89 -2.70 -8.60 J02969 J02969 Thyroid peroxidase TPX 2.7 -2.70 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 19 32 1415 7173 TPO thyroid peroxidase tag_2_refseq_or_mgc_2_Entrez 4 4 91 -18.77 down 4 0 0/4 -6.25666666666667 3 89 -2.70 -8.60 GATGAATAAA GATGAATAAA thyroid peroxidase (TPO) down 0.0001 FVPTC Norm 1 1 publication 14715705 3 6 161 7173 TPO thyroid peroxidase clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 91 -18.77 down 4 0 0/4 -6.25666666666667 3 89 -2.70 -8.60 J02969 J02969 Thyroid peroxidase TPO -8.6 -8.60 down no 0.0022 PTC Norm 8 8 suppl. materials 11752453 17 26 1263 7178 TPT1 tumor protein, translationally-controlled 1 tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 down 1 0 0/1 0 0 0 0 0 TAGGTTGTCT TAGGTTGTCT down FTC FA 1 1 publication 11076659 11 18 832 7189 TRAF6 TNF receptor-associated factor 6 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U78798 U78798 TNF receptor associated factor 6 (TRAF6) down ACL;ATC Norm 21 10 publication 15613457 9 14 639 7253 TSHR thyroid stimulating hormone receptor affy_probe_2_Entrez 1 1 24 3.97 up 1 0 1/0 3.97 1 24 3.97 3.97 215443_at 215443_at thyroid stimulating hormone receptor -3.09 3.09 up 0.000044 FA FTC 12 12 provided by authors 15713710 9 14 680 7253 TSHR thyroid stimulating hormone receptor affy_probe_2_Entrez 1 1 24 3.97 up 1 0 1/0 3.97 1 24 3.97 3.97 215442_s_at 215442_s_at thyroid stimulating hormone receptor -3.97 3.97 up 0.000009 FA FTC 12 12 provided by authors 15713710 10 16 710 7262 PHLDA2 pleckstrin homology-like domain, family A, member 2 affy_probe_2_Entrez 3 3 89 24.06 up 3 0 3/0 8.02 3 89 15.96 2.50 31888_s_at 31888_s_at Tumor-suppressing subtransferable candidate 3 TSSC3 15.96 15.96 up yes yes PTC GT 8 6 publication 15515157 18 31 1344 7262 PHLDA2 pleckstrin homology-like domain, family A, member 2 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 89 24.06 up 3 0 3/0 8.02 3 89 15.96 2.50 AF001294 AF001294 Imprinted in Placenta and Liver IPL 2.5 2.50 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 3 6 130 7262 PHLDA2 pleckstrin homology-like domain, family A, member 2 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 89 24.06 up 3 0 3/0 8.02 3 89 15.96 2.50 AF001294 AF001294 Tumor suppressing subtransferable candidate 3 TSSC3 5.6 5.60 up no 0.0001 PTC Norm 8 8 suppl. materials 11752453 24 33 1513 7264 TSTA3 tissue specific transplantation antigen P35B Gene_symbol_2_NCBI_Entrez 1 1 32 1.6 up 1 0 1/0 1.6 1 32 1.60 1.60 Tissue specific transplantation antigen P35B TSTA3 0.68 1.60 up PTC Norm 16 16 publication 15735049 13 20 939 7290 HIRA HIR histone cell cycle regulation defective homolog A (S. cerevisiae) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 X89887 X89887 Histone cell cycle regulation-defective homolog A HIRA down FTC FA 9 10 publication 12738736 19 32 1422 7299 TYR tyrosinase (oculocutaneous albinism IA) tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 TTGGCTGGGC TTGGCTGGGC EST up 0.0015 FVPTC Norm 1 1 publication 14715705 18 31 1326 7301 TYRO3 TYRO3 protein tyrosine kinase clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 2.1 up 1 0 1/0 2.1 1 59 2.10 2.10 D17517 D17517 Sky RSE 3 3.00 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 18 31 1378 7301 TYRO3 TYRO3 protein tyrosine kinase clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 2.1 up 1 0 1/0 2.1 1 59 2.10 2.10 U18934 U18934 DTK receptor tyrosine kinase DTK 2.1 2.10 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 9 14 610 7306 TYRP1 tyrosinase-related protein 1 affy_probe_2_Entrez 1 1 24 -3.62 down 1 0 0/1 -3.62 1 24 -3.62 -3.62 205694_at 205694_at tyrosinase-related protein 1 3.62 -3.62 down 0.000555 FA FTC 12 12 provided by authors 15713710 2 2 87 7311 UBA52 ubiquitin A-52 residue ribosomal protein fusion product 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 2.86 up 1 0 1/0 2.86 1 2 2.86 2.86 NM_021009 NM_021009 Ubiquitin C UBC 2.86 2.86 up FCL Norm 1 1 publication 15785240 11 18 836 7318 UBE1L ubiquitin-activating enzyme E1-like clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 L13852 L13852 Ubiquitin-activating enzyme E1-related protein down ACL;ATC Norm 21 10 publication 15613457 15 22 1042 7335 UBE2V1 ubiquitin-conjugating enzyme E2 variant 1 Gene_symbol_2_NCBI_Entrez 1 1 7 -2.5 down 1 0 0/1 -2.5 1 7 -2.50 -2.50 Ubiquitin-conjugating enzyme E2 variant 1 UBE2V1 0.4 -2.50 down FTC FA 3 4 publication 15475448 11 18 835 7347 UCHL3 ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiolesterase) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 M30496 M30496 UCHL3 ubiquitin carboxyl-terminal esterase L3 (ubiquitin thiol esterase) down ACL;ATC Norm 21 10 publication 15613457 15 22 1062 7356 SCGB1A1 secretoglobin, family 1A, member 1 (uteroglobin) Gene_symbol_2_NCBI_Entrez 1 1 7 -10 down 1 0 0/1 -10 1 7 -10.00 -10.00 Secretoglobin SCGB1A1 0.1 -10.00 down FTC FA 3 4 publication 15475448 3 6 122 7378 UPP1 uridine phosphorylase 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 8.3 up 1 0 1/0 8.3 1 16 8.30 8.30 X90858 X90858 Uridine phosphorylase UP 8.3 8.30 up no 0.002 PTC Norm 8 8 suppl. materials 11752453 14 21 976 7410 VAV2 vav 2 oncogene clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 0 up 1 0 1/0 0 0 0 0 0 AA682337 AA682337 Vav 2 oncogene 3 3.00 up PTC Norm 7 7 publication 15041723 14 21 999 7410 VAV2 vav 2 oncogene Gene_symbol_2_NCBI_Entrez 1 1 14 0 up 1 0 1/0 0 0 0 0 0 vav 2 VAV2 up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 15 22 1049 7422 VEGF vascular endothelial growth factor Gene_symbol_2_NCBI_Entrez 1 1 7 -3.33 down 1 0 0/1 -3.33 1 7 -3.33 -3.33 Vascular endothelial growth factor VEGF 0.3 -3.33 down FTC FA 3 4 publication 15475448 14 21 1002 7423 VEGFB vascular endothelial growth factor B Gene_symbol_2_NCBI_Entrez 1 1 14 0 up 1 0 1/0 0 0 0 0 0 VEGF-B VEGFB up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 25 34 1663 7466 WFS1 Wolfram syndrome 1 (wolframin) affy_probe_2_Entrez 1 1 55 -2.48 down 1 0 0/1 -2.48 1 55 -2.48 -2.48 202908_at 202908_at Wolfram syndrome 1 (wolframin) WFS1 -2.476 -2.48 down 0.024879125 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1678 7481 WNT11 wingless-type MMTV integration site family, member 11 affy_probe_2_Entrez 1 1 55 -2.75 down 1 0 0/1 -2.75 1 55 -2.75 -2.75 206737_at 206737_at wingless-type MMTV integration site family, member 11 WNT11 -2.747 -2.75 down 9.50816E-08 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 16 24 1229 7507 XPA xeroderma pigmentosum, complementation group A Gene_symbol_2_NCBI_Entrez 1 1 63 -1.75 down 1 0 0/1 -1.75 1 63 -1.75 -1.75 XPA 0.572052402 -1.75 down 0.01 PTC;FVPTC FA;HN 32 31 publication 15087409 19 32 1410 7508 XPC xeroderma pigmentosum, complementation group C tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 CACGGAGGCG CACGGAGGCG xeroderma pigmentosum, group C up 0.0245 FVPTC Norm 1 1 publication 14715705 11 18 761 7534 YWHAZ tyrosine 3-monooxygenase/tryptophan 5-monooxygenase activation protein, zeta polypeptide clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 NM_003406 NM_003406 Tyrosine 3-mono-oxygenase/tryptophan 5-mono-oxygenase activation protein, . poly peptide up ACL;ATC Norm 21 10 publication 15613457 11 18 804 7535 ZAP70 zeta-chain (TCR) associated protein kinase 70kDa clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 L05148 L05148 Protein tyrosine kinase related mRNA sequence down ACL;ATC Norm 21 10 publication 15613457 15 22 1054 7543 ZFX zinc finger protein, X-linked Gene_symbol_2_NCBI_Entrez 1 1 7 -3.33 down 1 0 0/1 -3.33 1 7 -3.33 -3.33 Zinc finger protein, X-linked ZFX 0.3 -3.33 down FTC FA 3 4 publication 15475448 13 20 921 7644 ZNF91 zinc finger protein 91 (HPF7, HTF10) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 L11672 L11672 Zinc finger protein 91 (HPF7, HTF10) ZNF91 up FTC FA 9 10 publication 12738736 10 16 729 7707 ZNF148 zinc finger protein 148 (pHZ-52) affy_probe_2_Entrez 1 1 14 -9.07 down 1 0 0/1 -9.07 1 14 -9.07 -9.07 41465_at 41465_at Zinc finger protein 148 (pHZ-52) ZNF148 -2.9 -2.90 down yes PTC GT 8 6 publication 15515157 10 16 745 7707 ZNF148 zinc finger protein 148 (pHZ-52) affy_probe_2_Entrez 1 1 14 -9.07 down 1 0 0/1 -9.07 1 14 -9.07 -9.07 41466_s_at 41466_s_at Zinc finger protein 148 (pHZ-52) ZNF148 -9.07 -9.07 down yes PTC GT 8 6 publication 15515157 11 18 763 7846 TUBA3 tubulin, alpha 3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 H11622 H11622 IMAGE:47833 30 similar to gb:K00558 tubulin a-1 chain up ACL;ATC Norm 21 10 publication 15613457 15 22 1031 7874 USP7 ubiquitin specific protease 7 (herpes virus-associated) Gene_symbol_2_NCBI_Entrez 1 1 7 2 up 1 0 1/0 2 1 7 2.00 2.00 Ubiquitin specific protease 7 USP7 2 2.00 up FTC FA 3 4 publication 15475448 9 14 696 7881 KCNAB1 potassium voltage-gated channel, shaker-related subfamily, beta member 1 affy_probe_2_Entrez 1 1 24 6.61 up 1 0 1/0 6.61 1 24 6.61 6.61 210471_s_at 210471_s_at potassium voltage-gated channel, shaker-related subfamily, beta member 1 -5.48 5.48 up 0.000312 FA FTC 12 12 provided by authors 15713710 9 14 697 7881 KCNAB1 potassium voltage-gated channel, shaker-related subfamily, beta member 1 affy_probe_2_Entrez 1 1 24 6.61 up 1 0 1/0 6.61 1 24 6.61 6.61 210078_s_at 210078_s_at potassium voltage-gated channel, shaker-related subfamily, beta member 1 -6.61 6.61 up 0.000095 FA FTC 12 12 provided by authors 15713710 13 20 940 7922 SLC39A7 solute carrier family 39 (zinc transporter), member 7 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 AL031228 AL031228 HLA class II region-expressed gene KE4 HKE4 down FTC FA 9 10 publication 12738736 3 6 149 7932 OR2H2 olfactory receptor, family 2, subfamily H, member 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 -3.3 down 1 0 0/1 -3.3 1 16 -3.30 -3.30 AL031983 AL031983 Diubiquitin UBD -3.3 -3.30 down no 0.0115 PTC Norm 8 8 suppl. materials 11752453 14 21 970 7984 ARHGEF5 Rho guanine nucleotide exchange factor (GEF) 5 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 7.6 up 1 0 1/0 7.6 1 14 7.60 7.60 AA045822 AA045822 Guanine nucleotide regulatory protein (tim) 7.6 7.60 up PTC Norm 7 7 publication 15041723 24 33 1466 7991 TUSC3 tumor suppressor candidate 3 Gene_symbol_2_NCBI_Synonym_2_Entrez 3 3 103 17.52 up 3 0 3/0 5.84 3 103 7.70 2.43 Putative prostate cancer tumor suppressor N33 2.885 7.39 up PTC Norm 16 16 publication 15735049 25 34 1557 7991 TUSC3 tumor suppressor candidate 3 affy_probe_2_Entrez 3 3 103 17.52 up 3 0 3/0 5.84 3 103 7.70 2.43 213423_x_at 213423_x_at tumor suppressor candidate 3 TUSC3 9.579 9.58 up 3.13192E-08 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1567 7991 TUSC3 tumor suppressor candidate 3 affy_probe_2_Entrez 3 3 103 17.52 up 3 0 3/0 5.84 3 103 7.70 2.43 209228_x_at 209228_x_at tumor suppressor candidate 3 TUSC3 6.483 6.48 up 2.40645E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1618 7991 TUSC3 tumor suppressor candidate 3 affy_probe_2_Entrez 3 3 103 17.52 up 3 0 3/0 5.84 3 103 7.70 2.43 209227_at 209227_at tumor suppressor candidate 3 TUSC3 2.433 2.43 up 0.021654313 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 125 7991 TUSC3 tumor suppressor candidate 3 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 103 17.52 up 3 0 3/0 5.84 3 103 7.70 2.43 U42349 U42349 Putative prostate cancer tumor suppressor N33 7.7 7.70 up no 0.0001 PTC Norm 8 8 suppl. materials 11752453 25 34 1555 8091 HMGA2 high mobility group AT-hook 2 affy_probe_2_Entrez 1 1 55 10.33 up 1 0 1/0 10.33 1 55 10.33 10.33 208025_s_at 208025_s_at high mobility group AT-hook 2 /// high mobility group AT-hook 2 HMGA2 10.329 10.33 up 0.013091579 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 10 16 736 8364 HIST1H4C histone 1, H4c affy_probe_2_Entrez 2 2 69 -6.82 down 2 0 0/2 -3.41 2 69 -2.60 -4.22 39969_at 39969_at H4 histone family, member G H4FG -4.22 -4.22 down yes PTC GT 8 6 publication 15515157 25 34 1670 8364 HIST1H4C histone 1, H4c affy_probe_2_Entrez 2 2 69 -6.82 down 2 0 0/2 -3.41 2 69 -2.60 -4.22 205967_at 205967_at histone 1, H4f HIST1H4F -2.597 -2.60 down 0.011390558 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1729 8406 SRPX sushi-repeat-containing protein, X-linked affy_probe_2_Entrez 1 1 55 -4.28 down 1 0 0/1 -4.28 1 55 -4.28 -4.28 204955_at 204955_at sushi-repeat-containing protein, X-linked SRPX -4.282 -4.28 down 0.019937143 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 661 8418 CMAH cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMP-N-acetylneuraminate monooxygenase) affy_probe_2_Entrez 1 1 24 3.49 up 1 0 1/0 3.49 1 24 3.49 3.49 205518_s_at 205518_s_at cytidine monophosphate-N-acetylneuraminic acid hydroxylase (CMP-N-acetylneuraminate monooxygenase) -3.49 3.49 up 0.003132 FA FTC 12 12 provided by authors 15713710 11 18 803 8470 ARGBP2 Arg/Abl-interacting protein ArgBP2 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 86 -7.85 down 2 0 0/2 -7.85 1 55 -7.85 -7.85 AF049884 AF049884 Arg/Abl-interacting protein ArgBP2a (ArgBP2a) down ACL;ATC Norm 21 10 publication 15613457 25 34 1769 8470 ARGBP2 Arg/Abl-interacting protein ArgBP2 affy_probe_2_Entrez 2 2 86 -7.85 down 2 0 0/2 -7.85 1 55 -7.85 -7.85 204288_s_at 204288_s_at Arg/Abl-interacting protein ArgBP2 ARGBP2 -7.855 -7.85 down 0.045328617 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 635 8490 RGS5 regulator of G-protein signalling 5 affy_probe_2_Entrez 1 1 24 3.03 up 1 0 1/0 3.03 1 24 3.03 3.03 209071_s_at 209071_s_at regulator of G-protein signalling 5 -3.03 3.03 up 0.000001 FA FTC 12 12 provided by authors 15713710 14 21 971 8493 PPM1D protein phosphatase 1D magnesium-dependent, delta isoform clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 4.7 up 1 0 1/0 4.7 1 14 4.70 4.70 N33955 N33955 Protein phosphatase Wip1 4.7 4.70 up PTC Norm 7 7 publication 15041723 25 34 1617 8547 FCN3 ficolin (collagen/fibrinogen domain containing) 3 (Hakata antigen) affy_probe_2_Entrez 1 1 55 2.45 up 1 0 1/0 2.45 1 55 2.45 2.45 205866_at 205866_at --- --- 2.451 2.45 up 0.022158313 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 2 2 69 8554 PIAS1 protein inhibitor of activated STAT, 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -8 down 1 0 0/1 -8 1 2 -8.00 -8.00 NM_016166 NM_016166 Protein inhibitor of activated STAT, 1 PIAS1 8 -8.00 down FCL Norm 1 1 publication 15785240 10 16 717 8560 DEGS1 degenerative spermatocyte homolog 1, lipid desaturase (Drosophila) affy_probe_2_Entrez 1 1 14 5.24 up 1 0 1/0 5.24 1 14 5.24 5.24 33337_at 33337_at Degenerative spermatocyte lipid desaturase DEGS 5.24 5.24 up yes PTC GT 8 6 publication 15515157 16 24 1210 8562 DENR density-regulated protein Gene_symbol_2_NCBI_Entrez 1 1 63 -1.51 down 1 0 0/1 -1.51 1 63 -1.51 -1.51 DENR 0.662337662 -1.51 down 0.02 PTC;FVPTC FA;HN 32 31 publication 15087409 11 18 791 8570 KHSRP KH-type splicing regulatory protein (FUSE binding protein 2) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U94832 U94832 KH type splicing regulatory protein (KSRP) down ACL;ATC Norm 21 10 publication 15613457 3 6 116 8572 PDLIM4 PDZ and LIM domain 4 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 14.5 up 1 0 1/0 14.5 1 16 14.50 14.50 X93510 X93510 37-kDa LIM domain protein RIL 14.5 14.50 up no 0.003 PTC Norm 8 8 suppl. materials 11752453 9 14 652 8613 PPAP2B phosphatidic acid phosphatase type 2B affy_probe_2_Entrez 1 1 24 4.46 up 1 0 1/0 4.46 1 24 4.46 4.46 212230_at 212230_at phosphatidic acid phosphatase type 2B -3.28 3.28 up 0.000001 FA FTC 12 12 provided by authors 15713710 9 14 678 8613 PPAP2B phosphatidic acid phosphatase type 2B affy_probe_2_Entrez 1 1 24 4.46 up 1 0 1/0 4.46 1 24 4.46 4.46 212226_s_at 212226_s_at phosphatidic acid phosphatase type 2B -3.91 3.91 up 0 FA FTC 12 12 provided by authors 15713710 9 14 688 8613 PPAP2B phosphatidic acid phosphatase type 2B affy_probe_2_Entrez 1 1 24 4.46 up 1 0 1/0 4.46 1 24 4.46 4.46 209355_s_at 209355_s_at phosphatidic acid phosphatase type 2B -4.46 4.46 up 0.000001 FA FTC 12 12 provided by authors 15713710 16 24 1247 8630 HSD17B6 hydroxysteroid (17-beta) dehydrogenase 6 Gene_symbol_2_NCBI_Synonym_2_Entrez 2 2 122 -5.82 down 2 0 0/2 -2.91 2 122 -2.80 -3.02 RODH 0.330882353 -3.02 down 0.01 PTC;FVPTC FA;HN 32 31 publication 15087409 18 31 1331 8630 HSD17B6 hydroxysteroid (17-beta) dehydrogenase 6 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 122 -5.82 down 2 0 0/2 -2.91 2 122 -2.80 -3.02 U89281 U89281 Oxidative 3 alpha hydroxysteroid dehydrogenase RODH 2.8 -2.80 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1554 8714 ABCC3 ATP-binding cassette, sub-family C (CFTR/MRP), member 3 affy_probe_2_Entrez 1 1 55 7.08 up 1 0 1/0 7.08 1 55 7.08 7.08 208161_s_at 208161_s_at ATP-binding cassette, sub-family C (CFTR/MRP), member 3 ABCC3 10.353 10.35 up 0.000350203 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1565 8714 ABCC3 ATP-binding cassette, sub-family C (CFTR/MRP), member 3 affy_probe_2_Entrez 1 1 55 7.08 up 1 0 1/0 7.08 1 55 7.08 7.08 209641_s_at 209641_s_at ATP-binding cassette, sub-family C (CFTR/MRP), member 3 ABCC3 7.076 7.08 up 6.91482E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1601 8795 TNFRSF10B tumor necrosis factor receptor superfamily, member 10b affy_probe_2_Entrez 1 1 55 2.54 up 1 0 1/0 2.54 1 55 2.54 2.54 209294_x_at 209294_x_at tumor necrosis factor receptor superfamily, member 10b TNFRSF10B 3.130 3.13 up 0.0056309 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1612 8795 TNFRSF10B tumor necrosis factor receptor superfamily, member 10b affy_probe_2_Entrez 1 1 55 2.54 up 1 0 1/0 2.54 1 55 2.54 2.54 209295_at 209295_at tumor necrosis factor receptor superfamily, member 10b TNFRSF10B 2.544 2.54 up 0.000148339 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1453 8796 SCEL sciellin Gene_symbol_2_NCBI_Entrez 2 2 48 19.73 up 2 0 2/0 9.865 2 48 15.03 4.70 Sciellin SCEL 3.91 15.03 up PTC Norm 16 16 publication 15735049 3 6 131 8796 SCEL sciellin clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 48 19.73 up 2 0 2/0 9.865 2 48 15.03 4.70 AF045941 AF045941 Sciellin SCEL 4.7 4.70 up yes 0.0002 PTC Norm 8 8 suppl. materials 11752453 24 33 1507 8828 NRP2 neuropilin 2 Gene_symbol_2_NCBI_Entrez 1 1 32 2.04 up 1 0 1/0 2.04 1 32 2.04 2.04 Neuropilin 2 NRP2 1.03 2.04 up PTC Norm 16 16 publication 15735049 11 18 796 8841 HDAC3 histone deacetylase 3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U66914 U66914 Histone deacetylase 3 (HDAC3) down ACL;ATC Norm 21 10 publication 15613457 25 34 1737 8842 PROM1 prominin 1 affy_probe_2_Entrez 1 1 55 -4.76 down 1 0 0/1 -4.76 1 55 -4.76 -4.76 204304_s_at 204304_s_at prominin 1 PROM1 -4.758 -4.76 down 0.019298975 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 10 16 733 8857 FCGBP Fc fragment of IgG binding protein affy_probe_2_Entrez 3 4 108 -9.62 down 4 0 0/4 -3.20666666666667 3 89 -3.10 -3.30 39014_at 39014_at Fc fragment of IgG binding protein FCGBP -3.22 -3.22 down yes PTC GT 8 6 publication 15515157 10 17 751 8857 FCGBP Fc fragment of IgG binding protein affy_probe_2_Entrez 3 4 108 -9.62 down 4 0 0/4 -3.20666666666667 3 89 -3.10 -3.30 39014_at 39014_at Fc fragment of IgG binding protein FCGBP -3.3 -3.30 down no PTC Norm 8 8 publication 15515157 13 20 931 8857 FCGBP Fc fragment of IgG binding protein clone_accession_2_NCBI_rna_accession_2_Entrez 3 4 108 -9.62 down 4 0 0/4 -3.20666666666667 3 89 -3.10 -3.30 D84239 D84239 Fc fragment of IgG binding protein FCGBP down FTC FA 9 10 publication 12738736 18 31 1325 8857 FCGBP Fc fragment of IgG binding protein clone_accession_2_NCBI_rna_accession_2_Entrez 3 4 108 -9.62 down 4 0 0/4 -3.20666666666667 3 89 -3.10 -3.30 D84239 D84239 IgG Fc binding protein FC(GAMMA)BP 3.1 -3.10 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1602 8869 ST3GAL5 ST3 beta-galactoside alpha-2,3-sialyltransferase 5 affy_probe_2_Entrez 1 1 55 2.95 up 1 0 1/0 2.95 1 55 2.95 2.95 203217_s_at 203217_s_at sialyltransferase 9 (CMP-NeuAc:lactosylceramide alpha-2,3-sialyltransferase; GM3 synthase) SIAT9 2.955 2.95 up 0.014813632 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 18 31 1400 8892 EIF2B2 eukaryotic translation initiation factor 2B, subunit 2 beta, 39kDa clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 -2 down 1 0 0/1 -2 1 59 -2.00 -2.00 AF035280 AF035280 Translation initiation factor eIF-2B beta subunit EIF2B2 2 -2.00 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 13 20 930 8939 FUBP3 far upstream element (FUSE) binding protein 3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 U69127 U69127 Far upstream element (FUSE) binding protein 3 FUBP3 down FTC FA 9 10 publication 12738736 10 16 738 8942 KYNU kynureninase (L-kynurenine hydrolase) affy_probe_2_Entrez 1 1 14 -4.29 down 1 0 0/1 -4.29 1 14 -4.29 -4.29 38492_at 38492_at Kynureninase (L-kynurenine hydrolase) KYNU -4.29 -4.29 down yes PTC GT 8 6 publication 15515157 24 33 1490 8974 P4HA2 procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II Gene_symbol_2_NCBI_Entrez 3 3 103 11.27 up 3 0 3/0 3.75666666666667 3 103 4.50 2.93 Procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II P4HA2 1.55 2.93 up PTC Norm 16 16 publication 15735049 25 34 1589 8974 P4HA2 procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II affy_probe_2_Entrez 3 3 103 11.27 up 3 0 3/0 3.75666666666667 3 103 4.50 2.93 202733_at 202733_at procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II P4HA2 3.839 3.84 up 0.000172295 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 3 6 133 8974 P4HA2 procollagen-proline, 2-oxoglutarate 4-dioxygenase (proline 4-hydroxylase), alpha polypeptide II clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 103 11.27 up 3 0 3/0 3.75666666666667 3 103 4.50 2.93 U90441 U90441 Prolyl 4-hydroxylase alpha (II) subunit P4HA2 4.5 4.50 up no 0.0001 PTC Norm 8 8 suppl. materials 11752453 11 18 794 8985 PLOD3 procollagen-lysine, 2-oxoglutarate 5-dioxygenase 3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 AF046889 AF046889 lysylhydoxylase isoform 3 (PLOD3) down ACL;ATC Norm 21 10 publication 15613457 15 22 1055 8991 SELENBP1 selenium binding protein 1 Gene_symbol_2_NCBI_Entrez 2 2 66 -5.43 down 2 0 0/2 -2.715 2 66 -2.10 -3.33 Selenium binding protein 1 SELENBP1 0.3 -3.33 down FTC FA 3 4 publication 15475448 18 31 1387 8991 SELENBP1 selenium binding protein 1 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 66 -5.43 down 2 0 0/2 -2.715 2 66 -2.10 -3.33 U29091 U29091 Human selenium-binding protein HSBP 2.1 -2.10 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 11 18 772 8992 ATP6V0E ATPase, H+ transporting, lysosomal 9kDa, V0 subunit e clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 Y15286 Y15286 Vascular proton-ATPase subunit M9.2 up ACL;ATC Norm 21 10 publication 15613457 25 34 1652 9060 PAPSS2 3'-phosphoadenosine 5'-phosphosulfate synthase 2 affy_probe_2_Entrez 1 1 55 -6.95 down 1 0 0/1 -6.95 1 55 -6.95 -6.95 203059_s_at 203059_s_at 3'-phosphoadenosine 5'-phosphosulfate synthase 2 PAPSS2 -2.224 -2.22 down 0.007712264 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1762 9060 PAPSS2 3'-phosphoadenosine 5'-phosphosulfate synthase 2 affy_probe_2_Entrez 1 1 55 -6.95 down 1 0 0/1 -6.95 1 55 -6.95 -6.95 203058_s_at 203058_s_at 3'-phosphoadenosine 5'-phosphosulfate synthase 2 PAPSS2 -6.893 -6.89 down 6.01927E-14 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1763 9060 PAPSS2 3'-phosphoadenosine 5'-phosphosulfate synthase 2 affy_probe_2_Entrez 1 1 55 -6.95 down 1 0 0/1 -6.95 1 55 -6.95 -6.95 203060_s_at 203060_s_at 3'-phosphoadenosine 5'-phosphosulfate synthase 2 PAPSS2 -6.947 -6.95 down 6.02663E-07 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1476 9071 CLDN10 claudin 10 Gene_symbol_2_NCBI_Entrez 1 1 32 4.99 up 1 0 1/0 4.99 1 32 4.99 4.99 Claudin 10 CLDN10 2.32 4.99 up PTC Norm 16 16 publication 15735049 25 34 1553 9076 CLDN1 claudin 1 affy_probe_2_Entrez 1 1 55 10.75 up 1 0 1/0 10.75 1 55 10.75 10.75 218182_s_at 218182_s_at claudin 1 CLDN1 10.754 10.75 up 0.002431061 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1527 9110 MTMR4 myotubularin related protein 4 Gene_symbol_2_NCBI_Entrez 1 1 32 -1.83 down 1 0 0/1 -1.83 1 32 -1.83 -1.83 Myotubularin-related protein 4 MTMR4 -0.875 -1.83 down PTC Norm 16 16 publication 15735049 11 18 831 9138 ARHGEF1 Rho guanine nucleotide exchange factor (GEF) 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U64105 U64105 Guanine nucleotide exchange factor p115-RhoGEF (ARHGEF1) down ACL;ATC Norm 21 10 publication 15613457 16 24 1204 9144 SYNGR2 synaptogyrin 2 Gene_symbol_2_NCBI_Entrez 1 1 63 2.49 up 1 0 1/0 2.49 1 63 2.49 2.49 SYNGR2 2.493333333 2.49 up yes 0.01 PTC;FVPTC FA;HN 32 31 publication 15087409 25 34 1754 9162 DGKI diacylglycerol kinase, iota affy_probe_2_Entrez 1 1 55 -6.07 down 1 0 0/1 -6.07 1 55 -6.07 -6.07 206806_at 206806_at diacylglycerol kinase, iota DGKI -6.070 -6.07 down 8.56779E-08 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1524 9166 EBAG9 estrogen receptor binding site associated, antigen, 9 Gene_symbol_2_NCBI_Entrez 1 1 32 -1.57 down 1 0 0/1 -1.57 1 32 -1.57 -1.57 Estrogen receptor binding site associated antigen 9 EBAG9 -0.65 -1.57 down PTC Norm 16 16 publication 15735049 10 16 718 9168 TMSB10 thymosin, beta 10 affy_probe_2_Entrez 1 1 14 5.09 up 1 0 1/0 5.09 1 14 5.09 5.09 31481_s_at 31481_s_at Thymosin, beta 10 TMSB10 5.09 5.09 up yes PTC GT 8 6 publication 15515157 2 2 82 9201 DCAMKL1 doublecortin and CaM kinase-like 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 4.09 up 1 0 1/0 4.09 1 2 4.09 4.09 NM_004734 NM_004734 Double cortin and CaM kinase-like 1 DCAMKL1 4.09 4.09 up FCL Norm 1 1 publication 15785240 25 34 1694 9252 RPS6KA5 ribosomal protein S6 kinase, 90kDa, polypeptide 5 affy_probe_2_Entrez 1 1 55 -2.99 down 1 0 0/1 -2.99 1 55 -2.99 -2.99 204633_s_at 204633_s_at ribosomal protein S6 kinase, 90kDa, polypeptide 5 RPS6KA5 -2.992 -2.99 down 8.9986E-07 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 11 18 774 9349 RPL23 ribosomal protein L23 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 X55954 X55954 HL23 ribosomal protein homolog up ACL;ATC Norm 21 10 publication 15613457 16 24 1241 9352 TXNL1 thioredoxin-like 1 Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 63 -2.09 down 1 0 0/1 -2.09 1 63 -2.09 -2.09 TXNL 0.478991597 -2.09 down 0.01 PTC;FVPTC FA;HN 32 31 publication 15087409 9 14 627 9411 ARHGAP29 Rho GTPase activating protein 29 affy_probe_2_Entrez 1 1 24 2.86 up 1 0 1/0 2.86 1 24 2.86 2.86 203910_at 203910_at PTPL1-associated RhoGAP 1 -2.86 2.86 up 0.000011 FA FTC 12 12 provided by authors 15713710 13 20 935 9413 C9orf61 chromosome 9 open reading frame 61 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 102 1.32 down 2 1 1/2 0.66 2 83 3.42 -2.10 L27479 L27479 Friedriech ataxia region gene X123 X123 down FTC FA 9 10 publication 12738736 18 31 1382 9413 C9orf61 chromosome 9 open reading frame 61 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 102 1.32 down 2 1 1/2 0.66 2 83 3.42 -2.10 L27479 L27479 Human X123 X123 2.1 -2.10 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 9 14 658 9413 C9orf61 chromosome 9 open reading frame 61 affy_probe_2_Entrez 3 3 102 1.32 down 2 1 1/2 0.66 2 83 3.42 -2.10 213900_at 213900_at Friedreich ataxia region gene X123 -3.42 3.42 up 0.000211 FA FTC 12 12 provided by authors 15713710 18 31 1391 9435 CHST2 carbohydrate (N-acetylglucosamine-6-O) sulfotransferase 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 2 up 1 0 1/0 2 1 59 2.00 2.00 AB014679 AB014679 N-acetylglucosamine-6-O-sulfotransferas e GN6ST 2 2.00 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1630 9448 MAP4K4 mitogen-activated protein kinase kinase kinase kinase 4 affy_probe_2_Entrez 1 1 55 2.13 up 1 0 1/0 2.13 1 55 2.13 2.13 218181_s_at 218181_s_at mitogen-activated protein kinase kinase kinase kinase 4 MAP4K4 2.130 2.13 up 0.001822074 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 15 22 1035 9451 EIF2AK3 eukaryotic translation initiation factor 2-alpha kinase 3 Gene_symbol_2_NCBI_Entrez 1 1 7 -2 down 1 0 0/1 -2 1 7 -2.00 -2.00 Eukaryotic translation initiation factor 2 alpha kinase 3 EIF2AK3 0.5 -2.00 down FTC FA 3 4 publication 15475448 9 14 669 9452 ITM2A integral membrane protein 2A affy_probe_2_Entrez 1 1 24 3.72 up 1 0 1/0 3.72 1 24 3.72 3.72 202746_at 202746_at integral membrane protein 2A -3.72 3.72 up 0.000192 FA FTC 12 12 provided by authors 15713710 2 4 102 9510 ADAMTS1 a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -5.8 down 1 0 0/1 -5.8 1 2 -5.80 -5.80 NM_006988 NM_006988 A disintegrin-like and metalloprotease with thrombospondin type 1 motif ADAMTS1 5.8 -5.80 down PCL Norm 1 1 publication 15785240 24 33 1522 9515 STXBP5L syntaxin binding protein 5-like Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 32 -1.5 down 1 0 0/1 -1.5 1 32 -1.50 -1.50 Tomosyn-like KIAA1006 -0.585 -1.50 down PTC Norm 16 16 publication 15735049 12 19 842 9518 GDF15 growth differentiation factor 15 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 45 0.739999999999999 even 1 1 1/1 0.37 2 45 8.60 -7.86 AF019770 AF019770 MIC-1 8.6 8.60 up PTC Norm 18 3 publication 12538453 9 14 605 9518 GDF15 growth differentiation factor 15 affy_probe_2_Entrez 2 2 45 0.739999999999999 even 1 1 1/1 0.37 2 45 8.60 -7.86 221577_x_at 221577_x_at prostate differentiation factor 7.86 -7.86 down 0.003934 FA FTC 12 12 provided by authors 15713710 11 18 837 9564 BCAR1 breast cancer anti-estrogen resistance 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 W69766 W69766 IMAGE:343903 down ACL;ATC Norm 21 10 publication 15613457 10 17 748 9568 GPR51 G protein-coupled receptor 51 affy_probe_2_Entrez 3 3 107 17.01 up 3 0 3/0 5.67 3 107 8.26 3.30 33764_at 33764_at G protein-coupled receptor 51 GPR51 8.26 8.26 up no PTC Norm 8 8 publication 15515157 18 31 1318 9568 GPR51 G protein-coupled receptor 51 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 107 17.01 up 3 0 3/0 5.67 3 107 8.26 3.30 AF056085 AF056085 G protein-coupled receptor GABABR2 3.3 3.30 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1472 9568 GPR51 G protein-coupled receptor 51 Gene_symbol_2_NCBI_Entrez 3 3 107 17.01 up 3 0 3/0 5.67 3 107 8.26 3.30 G protein-coupled receptor 51 GPR51 2.445 5.45 up PTC Norm 16 16 publication 15735049 5 10 389 9586 CREB5 cAMP responsive element binding protein 5 tag_2_refseq_or_mgc_2_Entrez 1 1 3 0 up 1 0 1/0 0 0 0 0 0 TAAATACTTG TAAATACTTG PDK4 up no FTC FA;Norm 1 2 publication 15085203 25 34 1688 9592 IER2 immediate early response 2 affy_probe_2_Entrez 1 1 55 -2.89 down 1 0 0/1 -2.89 1 55 -2.89 -2.89 202081_at 202081_at immediate early response 2 IER2 -2.894 -2.89 down 0.038446886 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 17 26 1262 9607 CART cocaine- and amphetamine-regulated transcript tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 TGTGACGCCG TGTGACGCCG up FTC FA 1 1 publication 11076659 24 33 1517 9641 IKBKE inhibitor of kappa light polypeptide gene enhancer in B-cells, kinase epsilon Gene_symbol_2_NCBI_Entrez 1 1 32 1.24 up 1 0 1/0 1.24 1 32 1.24 1.24 Inhibitor of light polypeptide gene enhancer in B-cells, kinase epsilon IKBKE 0.315 1.24 up PTC Norm 16 16 publication 15735049 25 34 1631 9695 EDEM1 ER degradation enhancer, mannosidase alpha-like 1 affy_probe_2_Entrez 1 1 55 2.13 up 1 0 1/0 2.13 1 55 2.13 2.13 203279_at 203279_at ER degradation enhancer, mannosidase alpha-like 1 EDEM1 2.128 2.13 up 0.007204821 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 18 31 1389 9697 TRAM2 translocation associated membrane protein 2 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 114 -4.82 down 2 0 0/2 -2.41 2 114 -2.10 -2.72 D31762 D31762 LIM protein SLIMMER mRNA KIAA0057 2.1 -2.10 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1676 9697 TRAM2 translocation associated membrane protein 2 affy_probe_2_Entrez 2 2 114 -4.82 down 2 0 0/2 -2.41 2 114 -2.10 -2.72 202368_s_at 202368_s_at translocation associated membrane protein 2 TRAM2 -2.722 -2.72 down 0.000853362 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 892 9746 CLSTN3 calsyntenin 3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 AB018269 AB018269 KIAA0726 gene product KIAA0726 up FTC FA 9 10 publication 12738736 9 14 629 9749 PHACTR2 phosphatase and actin regulator 2 affy_probe_2_Entrez 1 1 24 3.16 up 1 0 1/0 3.16 1 24 3.16 3.16 204049_s_at 204049_s_at KIAA0680 gene product -2.89 2.89 up 0.000036 FA FTC 12 12 provided by authors 15713710 9 14 646 9749 PHACTR2 phosphatase and actin regulator 2 affy_probe_2_Entrez 1 1 24 3.16 up 1 0 1/0 3.16 1 24 3.16 3.16 204048_s_at 204048_s_at KIAA0680 gene product -3.16 3.16 up 0.000045 FA FTC 12 12 provided by authors 15713710 9 14 686 9774 BCLAF1 BCL2-associated transcription factor 1 affy_probe_2_Entrez 1 1 24 4.34 up 1 0 1/0 4.34 1 24 4.34 4.34 214499_s_at 214499_s_at Bcl-2-associated transcription factor -4.34 4.34 up 0.000008 FA FTC 12 12 provided by authors 15713710 13 20 929 9844 ELMO1 engulfment and cell motility 1 (ced-12 homolog, C. elegans) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 -2.3 down 2 0 0/2 -2.3 1 59 -2.30 -2.30 D87457 D87457 Engulfment and cell motility 1 ELMO1 down FTC FA 9 10 publication 12738736 18 31 1362 9844 ELMO1 engulfment and cell motility 1 (ced-12 homolog, C. elegans) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 -2.3 down 2 0 0/2 -2.3 1 59 -2.30 -2.30 D87457 D87457 KIAA0281 gene KIAA0281 2.3 -2.30 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1709 9882 TBC1D4 TBC1 domain family, member 4 affy_probe_2_Entrez 1 1 55 -3.69 down 1 0 0/1 -3.69 1 55 -3.69 -3.69 203387_s_at 203387_s_at TBC1 domain family, member 4 TBC1D4 -3.389 -3.39 down 0.001948548 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1721 9882 TBC1D4 TBC1 domain family, member 4 affy_probe_2_Entrez 1 1 55 -3.69 down 1 0 0/1 -3.69 1 55 -3.69 -3.69 203386_at 203386_at TBC1 domain family, member 4 TBC1D4 -3.694 -3.69 down 0.008659612 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 11 18 781 9894 KIAA0683 KIAA0683 gene product clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 NM_016111 NM_016111 KIAA0683 protein up ACL;ATC Norm 21 10 publication 15613457 2 2 60 9901 SRGAP3 SLIT-ROBO Rho GTPase activating protein 3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -12.5 down 1 0 0/1 -12.5 1 2 -12.50 -12.50 NM_014850 NM_014850 SLIT-ROBO Rho GTPase-activating protein 2 SRGAP2 12.5 -12.50 down FCL Norm 1 1 publication 15785240 24 33 1491 9902 MRC2 mannose receptor, C type 2 Gene_symbol_2_NCBI_Entrez 1 1 32 2.88 up 1 0 1/0 2.88 1 32 2.88 2.88 Mannose receptor, C type 2 MRC2 1.525 2.88 up PTC Norm 16 16 publication 15735049 25 34 1728 9914 KIAA0703 KIAA0703 gene product affy_probe_2_Entrez 1 1 55 -4.05 down 1 0 0/1 -4.05 1 55 -4.05 -4.05 206043_s_at 206043_s_at KIAA0703 gene product KIAA0703 -4.054 -4.05 down 1.31194E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1752 9935 MAFB v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (avian) affy_probe_2_Entrez 1 1 55 -5.87 down 1 0 0/1 -5.87 1 55 -5.87 -5.87 218559_s_at 218559_s_at v-maf musculoaponeurotic fibrosarcoma oncogene homolog B (avian) MAFB -5.871 -5.87 down 0.041986197 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1497 9961 MVP major vault protein Gene_symbol_2_NCBI_Entrez 2 2 87 5.82 up 2 0 2/0 2.91 2 87 3.24 2.58 Major vault protein MVP 1.37 2.58 up PTC Norm 16 16 publication 15735049 25 34 1598 9961 MVP major vault protein affy_probe_2_Entrez 2 2 87 5.82 up 2 0 2/0 2.91 2 87 3.24 2.58 202180_s_at 202180_s_at major vault protein MVP 3.239 3.24 up 0.011233219 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 2 2 64 9967 THRAP3 thyroid hormone receptor associated protein 3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -9.9 down 1 0 0/1 -9.9 1 2 -9.90 -9.90 NM_005119 NM_005119 Thyroid hormone receptor-associated protein TRAP150 9.9 -9.90 down FCL Norm 1 1 publication 15785240 13 20 914 9969 THRAP1 thyroid hormone receptor associated protein 1 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 74 2.46 up 2 0 2/0 2.46 1 55 2.46 2.46 AB011165 AB011165 Thyroid hormone receptor-associated protein 240kDa subunit TRAP240 up FTC FA 9 10 publication 12738736 25 34 1616 9969 THRAP1 thyroid hormone receptor associated protein 1 affy_probe_2_Entrez 2 2 74 2.46 up 2 0 2/0 2.46 1 55 2.46 2.46 201987_at 201987_at thyroid hormone receptor associated protein 1 THRAP1 2.463 2.46 up 0.043812497 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 11 18 823 10076 PTPRU protein tyrosine phosphatase, receptor type, U clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U73727 U73727 Receptor protein tyrosine phosphatase hPTP-J precursor down ACL;ATC Norm 21 10 publication 15613457 25 34 1718 10098 TSPAN5 tetraspanin 5 affy_probe_2_Entrez 1 1 55 -3.61 down 1 0 0/1 -3.61 1 55 -3.61 -3.61 209890_at 209890_at transmembrane 4 superfamily member 9 TM4SF9 -3.614 -3.61 down 0.003217913 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 2 3 94 10103 TSPAN1 tetraspanin 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 4 -2.5 down 1 0 0/1 -2.5 1 4 -2.50 -2.50 NM_005727 NM_005727 Tetraspan 1 TSPAN-1 2.5 -2.50 down FCL;PCL;UCL Norm 3 1 publication 15785240 9 14 614 10105 PPIF peptidylprolyl isomerase F (cyclophilin F) affy_probe_2_Entrez 1 1 24 -3.02 down 1 0 0/1 -3.02 1 24 -3.02 -3.02 201489_at 201489_at peptidylprolyl isomerase F (cyclophilin F) 3.02 -3.02 down 0.002756 FA FTC 12 12 provided by authors 15713710 13 20 906 10135 PBEF1 pre-B-cell colony enhancing factor 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 U02020 U02020 Pre-B-cell colony-enhancing factor PBEF up FTC FA 9 10 publication 12738736 16 24 1238 10144 FAM13A1 family with sequence similarity 13, member A1 Gene_symbol_2_NCBI_Entrez 1 1 63 -1.9 down 1 0 0/1 -1.9 1 63 -1.90 -1.90 FAM13A1 0.525925926 -1.90 down yes 0.02 PTC;FVPTC FA;HN 32 31 publication 15087409 18 31 1334 10154 PLXNC1 plexin C1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 2.7 up 1 0 1/0 2.7 1 59 2.70 2.70 AF030339 AF030339 Viral encoded semaphorin protein receptor PLXN-C1 2.7 2.70 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1456 10158 PDZK1IP1 PDZK1 interacting protein 1 Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 32 13.13 up 1 0 1/0 13.13 1 32 13.13 13.13 Membrane-associated protein 17 MAP17 3.715 13.13 up PTC Norm 16 16 publication 15735049 24 33 1540 10166 SLC25A15 solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15 Gene_symbol_2_NCBI_Entrez 1 1 32 -3.86 down 1 0 0/1 -3.86 1 32 -3.86 -3.86 Solute carrier family 25 (mitochondrial carrier; ornithine transporter) member 15 SLC25A15 -1.95 -3.86 down PTC Norm 16 16 publication 15735049 24 33 1477 10205 EVA1 epithelial V-like antigen 1 Gene_symbol_2_NCBI_Entrez 2 2 87 9.78 up 2 0 2/0 4.89 2 87 4.91 4.87 Epithelial V-like antigen 1 EVA1 2.285 4.87 up PTC Norm 16 16 publication 15735049 25 34 1552 10205 EVA1 epithelial V-like antigen 1 affy_probe_2_Entrez 2 2 87 9.78 up 2 0 2/0 4.89 2 87 4.91 4.87 203779_s_at 203779_s_at epithelial V-like antigen 1 EVA1 13.949 13.95 up 2.43333E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1578 10205 EVA1 epithelial V-like antigen 1 affy_probe_2_Entrez 2 2 87 9.78 up 2 0 2/0 4.89 2 87 4.91 4.87 203780_at 203780_at epithelial V-like antigen 1 EVA1 4.910 4.91 up 4.99938E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 11 18 811 10238 WDR68 WD repeat domain 68 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U94747 U94747 WD repeat protein HAN11 (AN11) down ACL;ATC Norm 21 10 publication 15613457 24 33 1523 10241 NDP52 nuclear domain 10 protein Gene_symbol_2_NCBI_Entrez 1 1 32 -1.53 down 1 0 0/1 -1.53 1 32 -1.53 -1.53 Nuclear domain 10 protein NDP52 -0.61 -1.53 down PTC Norm 16 16 publication 15735049 2 2 65 10252 SPRY1 sprouty homolog 1, antagonist of FGF signaling (Drosophila) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -9.8 down 1 0 0/1 -9.8 1 2 -9.80 -9.80 BC063856 BC063856 Sprouty homolog 1, antagonist of FGF signaling SPRY1 9.8 -9.80 down FCL Norm 1 1 publication 15785240 16 24 1225 10282 BET1 BET1 homolog (S. cerevisiae) Gene_symbol_2_NCBI_Entrez 1 1 63 -1.68 down 1 0 0/1 -1.68 1 63 -1.68 -1.68 BET1 0.594202899 -1.68 down 0.04 PTC;FVPTC FA;HN 32 31 publication 15087409 2 2 81 10322 SMYD5 SMYD family member 5 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 4.2 up 1 0 1/0 4.2 1 2 4.20 4.20 XM_039548 XM_039548 SMYD family member 5 SMYD5 4.2 4.20 up FCL Norm 1 1 publication 15785240 3 6 144 10370 CITED2 Cbp/p300-interacting transactivator, with Glu/Asp-rich carboxy-terminal domain, 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 -2.7 down 1 0 0/1 -2.7 1 16 -2.70 -2.70 U65093 U65093 Cbp/p300-interacting transactivator 2 CITED2 -2.7 -2.70 down no 0.0019 PTC Norm 8 8 suppl. materials 11752453 11 18 820 10385 BTN2A2 butyrophilin, subfamily 2, member A2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U90550 U90550 Butyrophilin (BTF2) down ACL;ATC Norm 21 10 publication 15613457 2 2 76 10397 NDRG1 N-myc downstream regulated gene 1 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 57 -8.67 down 2 0 0/2 -4.335 2 57 -2.07 -6.60 NM_006096 NM_006096 N-myc downstream regulated gene 1 NDRG1 6.6 -6.60 down FCL Norm 1 1 publication 15785240 25 34 1640 10397 NDRG1 N-myc downstream regulated gene 1 affy_probe_2_Entrez 2 2 57 -8.67 down 2 0 0/2 -4.335 2 57 -2.07 -6.60 200632_s_at 200632_s_at N-myc downstream regulated gene 1 NDRG1 -2.068 -2.07 down 0.041656945 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 18 31 1327 10404 PGCP plasma glutamate carboxypeptidase clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 83 0.63 even 1 1 1/1 0.315 2 83 3.53 -2.90 W28330 W28330 Plasma glutamate carboxypeptidase PGCP 2.9 -2.90 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 9 14 654 10404 PGCP plasma glutamate carboxypeptidase affy_probe_2_Entrez 2 2 83 0.63 even 1 1 1/1 0.315 2 83 3.53 -2.90 208454_s_at 208454_s_at plasma glutamate carboxypeptidase -3.29 3.29 up 0.000093 FA FTC 12 12 provided by authors 15713710 9 14 663 10404 PGCP plasma glutamate carboxypeptidase affy_probe_2_Entrez 2 2 83 0.63 even 1 1 1/1 0.315 2 83 3.53 -2.90 203501_at 203501_at plasma glutamate carboxypeptidase -3.53 3.53 up 0.000657 FA FTC 12 12 provided by authors 15713710 13 20 890 10437 IFI30 interferon, gamma-inducible protein 30 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 J03909 J03909 IFN, inducible protein 30 IFI30 up FTC FA 9 10 publication 12738736 13 20 891 10437 IFI30 interferon, gamma-inducible protein 30 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 J03909 J03909 Interferon, gamma-inducible protein 30 IFI30 up FTC FA 9 10 publication 12738736 18 31 1306 10439 OLFM1 olfactomedin 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 4.7 up 1 0 1/0 4.7 1 59 4.70 4.70 U79299 U79299 Neuronal olfactomedin-related ER localized protein NOE1 4.7 4.70 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 11 18 787 10445 MCRS1 microspherule protein 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 AF068007 AF068007 Cell cycle-regulated factor p78 down ACL;ATC Norm 21 10 publication 15613457 25 34 1593 10458 BAIAP2 BAI1-associated protein 2 affy_probe_2_Entrez 1 1 55 3.4 up 1 0 1/0 3.4 1 55 3.40 3.40 209502_s_at 209502_s_at BAI1-associated protein 2 BAIAP2 3.398 3.40 up 0.018405073 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 632 10492 SYNCRIP synaptotagmin binding, cytoplasmic RNA interacting protein affy_probe_2_Entrez 1 1 24 2.98 up 1 0 1/0 2.98 1 24 2.98 2.98 209025_s_at 209025_s_at NS1-associated protein 1 -2.98 2.98 up 0.000001 FA FTC 12 12 provided by authors 15713710 13 20 934 10516 FBLN5 fibulin 5 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 AF093118 AF093118 Fibulin 5 FBLN5 down FTC FA 9 10 publication 12738736 24 33 1455 10551 AGR2 anterior gradient 2 homolog (Xenopus laevis) Gene_symbol_2_NCBI_Entrez 1 1 32 13.93 up 1 0 1/0 13.93 1 32 13.93 13.93 Anterior gradient 2 homologue (Xenopus laevis) AGR2 3.8 13.93 up PTC Norm 16 16 publication 15735049 13 20 960 10558 SPTLC1 serine palmitoyltransferase, long chain base subunit 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 Y08685 Y08685 Serine palmitoyltransferase, long chain base subunit 1 SPTLC1 down FTC FA 9 10 publication 12738736 24 33 1451 10568 SLC34A2 solute carrier family 34 (sodium phosphate), member 2 Gene_symbol_2_NCBI_Entrez 1 1 32 18.57 up 1 0 1/0 18.57 1 32 18.57 18.57 Solute carrier family 34 (sodium phosphate), member 2 SLC34A2 4.215 18.57 up PTC Norm 16 16 publication 15735049 24 33 1496 10577 NPC2 Niemann-Pick disease, type C2 Gene_symbol_2_NCBI_Entrez 2 2 87 5.18 up 2 0 2/0 2.59 2 87 2.64 2.54 Niemann-Pick disease, type C2 NPC2 1.4 2.64 up PTC Norm 16 16 publication 15735049 25 34 1613 10577 NPC2 Niemann-Pick disease, type C2 affy_probe_2_Entrez 2 2 87 5.18 up 2 0 2/0 2.59 2 87 2.64 2.54 200701_at 200701_at Niemann-Pick disease, type C2 NPC2 2.536 2.54 up 5.9102E-08 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 871 10602 CDC42EP3 CDC42 effector protein (Rho GTPase binding) 3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 AF094521 AF094521 Cdc42 effector protein 3 CEP3 up FTC FA 9 10 publication 12738736 13 20 883 10616 C20orf18 chromosome 20 open reading frame 18 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 AA160708 AA160708 HBV-associated factor XAP4 up FTC FA 9 10 publication 12738736 14 21 996 10638 SPHAR S-phase response (cyclin-related) Gene_symbol_2_NCBI_Entrez 1 1 14 0 up 1 0 1/0 0 0 0 0 0 SPHAR gene for cyclin-related protein SPHAR up PTC Norm 7 7 publication The gene name for this entry was determined manually from the description 15041723 2 4 99 10658 CUGBP1 CUG triplet repeat, RNA binding protein 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -7.6 down 1 0 0/1 -7.6 1 2 -7.60 -7.60 NM_006560 NM_006560 CUG triplet repeat, RNA binding protein 1 CUGBP1 7.6 -7.60 down PCL Norm 1 1 publication 15785240 13 20 917 10695 TNRC5 trinucleotide repeat containing 5 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 U80744 U80744 Trinucleotide repeat containing 5 TNRC5 up FTC FA 9 10 publication 12738736 24 33 1530 10732 TCFL5 transcription factor-like 5 (basic helix-loop-helix) Gene_symbol_2_NCBI_Entrez 1 1 32 -2.01 down 1 0 0/1 -2.01 1 32 -2.01 -2.01 Transcription factor-like 5 (basic helix-loop-helix) TCFL5 -1.01 -2.01 down PTC Norm 16 16 publication 15735049 15 22 1033 10769 PLK2 polo-like kinase 2 (Drosophila) Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 7 -2 down 1 0 0/1 -2 1 7 -2.00 -2.00 Serum-inducible SNK 0.5 -2.00 down FTC FA 3 4 publication 15475448 25 34 1641 10778 ZNF271 zinc finger protein 271 affy_probe_2_Entrez 1 1 55 -2.07 down 1 0 0/1 -2.07 1 55 -2.07 -2.07 211009_s_at 211009_s_at zinc finger protein 271 ZNF271 -2.068 -2.07 down 0.000422955 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 898 10797 MTHFD2 methylenetetrahydrofolate dehydrogenase (NADP+ dependent) 2, methenyltetrahydrofolate cyclohydrolase clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 X16396 X16396 Methylene tetrahydrofolate dehydrogenase (NADdependent), methenyltetrahydrofolate cyclohydrolase MTHFD2 up FTC FA 9 10 publication 12738736 2 2 62 10847 SRCAP Snf2-related CBP activator protein clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -10.6 down 1 0 0/1 -10.6 1 2 -10.60 -10.60 NM_006662 NM_006662 Snf2-related CBP activator protein SRCAP 10.6 -10.60 down FCL Norm 1 1 publication 15785240 3 6 140 10875 FGL2 fibrinogen-like 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 16 -2.3 down 1 0 0/1 -2.3 1 16 -2.30 -2.30 Z36531 Z36531 Fibrinogen-like protein (pT49 protein) FGL2 -2.3 -2.30 down no 0.0004 PTC Norm 8 8 suppl. materials 11752453 25 34 1739 10894 XLKD1 extracellular link domain containing 1 affy_probe_2_Entrez 1 1 55 -5.96 down 1 0 0/1 -5.96 1 55 -5.96 -5.96 220037_s_at 220037_s_at extracellular link domain containing 1 XLKD1 -4.832 -4.83 down 7.11835E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1753 10894 XLKD1 extracellular link domain containing 1 affy_probe_2_Entrez 1 1 55 -5.96 down 1 0 0/1 -5.96 1 55 -5.96 -5.96 219059_s_at 219059_s_at extracellular link domain containing 1 XLKD1 -5.956 -5.96 down 1.27637E-09 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1603 10963 STIP1 stress-induced-phosphoprotein 1 (Hsp70/Hsp90-organizing protein) affy_probe_2_Entrez 1 1 55 2.95 up 1 0 1/0 2.95 1 55 2.95 2.95 213330_s_at 213330_s_at stress-induced-phosphoprotein 1 (Hsp70/Hsp90-organizing protein) STIP1 2.954 2.95 up 0.028822821 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1624 10973 ASCC3 activating signal cointegrator 1 complex subunit 3 affy_probe_2_Entrez 1 1 55 2.27 up 1 0 1/0 2.27 1 55 2.27 2.27 212815_at 212815_at activating signal cointegrator 1 complex subunit 3 ASCC3 2.274 2.27 up 0.029602255 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 15 22 1056 10989 IMMT inner membrane protein, mitochondrial (mitofilin) Gene_symbol_2_NCBI_Entrez 1 1 7 -5 down 1 0 0/1 -5 1 7 -5.00 -5.00 Inner membrane protein, mitochondrial IMMT 0.2 -5.00 down FTC FA 3 4 publication 15475448 14 21 974 11004 KIF2C kinesin family member 2C clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 3.2 up 1 0 1/0 3.2 1 14 3.20 3.20 AA400476 AA400476 Mitotic centromere-associated kinesin 3.2 3.20 up PTC Norm 7 7 publication 15041723 11 18 758 11034 DSTN destrin (actin depolymerizing factor) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 NM_006870 NM_006870 DSTN-destrin (actin depolymerizing factor) up yes yes ACL;ATC Norm 21 10 publication 15613457 10 16 727 11039 SMA4 SMA4 affy_probe_2_Entrez 1 1 14 -2.74 down 1 0 0/1 -2.74 1 14 -2.74 -2.74 32921_at 32921_at SMA4 SMA4 -2.74 -2.74 down yes PTC GT 8 6 publication 15515157 13 20 954 11072 DUSP14 dual specificity phosphatase 14 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 AF038844 AF038844 MKP-1 like protein kinase phosphatase MKP-L down FTC FA 9 10 publication 12738736 24 33 1478 11098 PRSS23 protease, serine, 23 Gene_symbol_2_NCBI_Synonym_2_Entrez 2 2 48 11.42 up 2 0 2/0 5.71 2 48 6.70 4.72 Protease, serine, 23 SPUVE 2.24 4.72 up PTC Norm 16 16 publication 15735049 3 6 126 11098 PRSS23 protease, serine, 23 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 48 11.42 up 2 0 2/0 5.71 2 48 6.70 4.72 AF015287 AF015287 Serine protease SPUVE 6.7 6.70 up no 0.0002 PTC Norm 8 8 suppl. materials 11752453 2 3 89 11140 CDC37 CDC37 cell division cycle 37 homolog (S. cerevisiae) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 4 4.3 up 1 0 1/0 4.3 1 4 4.30 4.30 NM_007065 NM_007065 Cell division cycle 37 homologue CDC37 4.3 4.30 up FCL;PCL;UCL Norm 3 1 publication 15785240 13 20 918 11170 TU3A TU3A protein clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 AF035283 AF035283 TU3A protein TU3A up FTC FA 9 10 publication 12738736 25 34 1622 11177 BAZ1A bromodomain adjacent to zinc finger domain, 1A affy_probe_2_Entrez 1 1 55 2.31 up 1 0 1/0 2.31 1 55 2.31 2.31 217986_s_at 217986_s_at bromodomain adjacent to zinc finger domain, 1A BAZ1A 2.305 2.31 up 0.022075114 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 16 24 1221 11183 MAP4K5 mitogen-activated protein kinase kinase kinase kinase 5 Gene_symbol_2_NCBI_Entrez 1 1 63 -1.64 down 1 0 0/1 -1.64 1 63 -1.64 -1.64 MAP4K5 0.610062893 -1.64 down 0.04 PTC;FVPTC FA;HN 32 31 publication 15087409 24 33 1514 11237 RNF24 ring finger protein 24 Gene_symbol_2_NCBI_Entrez 1 1 32 1.55 up 1 0 1/0 1.55 1 32 1.55 1.55 Ring finger protein 24 RNF24 0.63 1.55 up PTC Norm 16 16 publication 15735049 25 34 1623 11275 KLHL2 kelch-like 2, Mayven (Drosophila) affy_probe_2_Entrez 1 1 55 2.3 up 1 0 1/0 2.3 1 55 2.30 2.30 219157_at 219157_at kelch-like 2, Mayven (Drosophila) KLHL2 2.305 2.30 up 0.005690622 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1561 11322 EVER1 epidermodysplasia verruciformis 1 affy_probe_2_Entrez 1 1 55 8.08 up 1 0 1/0 8.08 1 55 8.08 8.08 204328_at 204328_at epidermodysplasia verruciformis 1 EVER1 8.079 8.08 up 3.21272E-07 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 11 18 809 11332 BACH brain acyl-CoA hydrolase clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U91316 U91316 Acyl-CoA thioester hydrolase down ACL;ATC Norm 21 10 publication 15613457 13 20 955 22795 NID2 nidogen 2 (osteonidogen) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 D86425 D86425 Nidogen 2 NID2 down FTC FA 9 10 publication 12738736 13 20 863 22809 ATF5 activating transcription factor 5 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 AB021663 AB021663 Activating transcription factor 5 ATF5 up FTC FA 9 10 publication 12738736 25 34 1672 22848 AAK1 AP2 associated kinase 1 affy_probe_2_Entrez 1 1 55 -2.62 down 1 0 0/1 -2.62 1 55 -2.62 -2.62 205434_s_at 205434_s_at AP2 associated kinase 1 AAK1 -2.622 -2.62 down 0.014039369 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 637 22882 ZHX2 zinc fingers and homeoboxes 2 affy_probe_2_Entrez 1 1 24 3.09 up 1 0 1/0 3.09 1 24 3.09 3.09 203556_at 203556_at KIAA0854 protein -3.09 3.09 up 0.000038 FA FTC 12 12 provided by authors 15713710 13 20 894 22885 ABLIM3 actin binding LIM protein family, member 3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 AB020650 AB020650 KIAA0843 protein KIAA0843 up FTC FA 9 10 publication 12738736 9 14 623 22902 RIPX rap2 interacting protein x affy_probe_2_Entrez 1 1 24 2.8 up 1 0 1/0 2.8 1 24 2.8 2.8 213939_s_at 213939_s_at KIAA0871 protein -2.8 2.8 up 0.000288 FA FTC 12 12 provided by authors 15713710 25 34 1703 22915 MMRN1 multimerin 1 affy_probe_2_Entrez 1 1 55 -3.22 down 1 0 0/1 -3.22 1 55 -3.22 -3.22 205612_at 205612_at multimerin 1 MMRN1 -3.219 -3.22 down 9.8325E-07 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1653 22921 MSRB2 methionine sulfoxide reductase B2 affy_probe_2_Entrez 1 1 55 -2.24 down 1 0 0/1 -2.24 1 55 -2.24 -2.24 218773_s_at 218773_s_at methionine sulfoxide reductase B MSRB -2.237 -2.24 down 0.001408171 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1719 22925 PLA2R1 phospholipase A2 receptor 1, 180kDa affy_probe_2_Entrez 1 1 55 -4.6 down 1 0 0/1 -4.6 1 55 -4.60 -4.60 210194_at 210194_at phospholipase A2 receptor 1, 180kDa PLA2R1 -3.657 -3.66 down 0.000561768 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1731 22925 PLA2R1 phospholipase A2 receptor 1, 180kDa affy_probe_2_Entrez 1 1 55 -4.6 down 1 0 0/1 -4.6 1 55 -4.60 -4.60 207415_at 207415_at phospholipase A2 receptor 1, 180kDa PLA2R1 -4.600 -4.60 down 1.04937E-09 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1680 22941 SHANK2 SH3 and multiple ankyrin repeat domains 2 affy_probe_2_Entrez 1 1 55 -5.01 down 1 0 0/1 -5.01 1 55 -5.01 -5.01 213307_at 213307_at SH3 and multiple ankyrin repeat domains 2 SHANK2 -2.774 -2.77 down 0.000303351 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1742 22941 SHANK2 SH3 and multiple ankyrin repeat domains 2 affy_probe_2_Entrez 1 1 55 -5.01 down 1 0 0/1 -5.01 1 55 -5.01 -5.01 213308_at 213308_at SH3 and multiple ankyrin repeat domains 2 SHANK2 -5.010 -5.01 down 3.32102E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1518 22976 PAXIP1 PAX interacting (with transcription-activation domain) protein 1 Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 32 -1.38 down 1 0 0/1 -1.38 1 32 -1.38 -1.38 PAX transcription activation domain interacting protein 1-like PAXIP1L -0.465 -1.38 down PTC Norm 16 16 publication 15735049 25 34 1657 23005 MAPKBP1 mitogen activated protein kinase binding protein 1 affy_probe_2_Entrez 1 1 55 -2.27 down 1 0 0/1 -2.27 1 55 -2.27 -2.27 213394_at 213394_at likely ortholog of mouse mitogen activated protein kinase binding proten 1 MAPKBP1 -2.274 -2.27 down 0.015438141 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 18 31 1369 23007 PLCL3 phospholipase C-like 3 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 114 -5.5 down 2 0 0/2 -2.75 2 114 -2.20 -3.30 AB028992 AB028992 KIAA1069 protein KIAA1069 2.2 -2.20 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1705 23007 PLCL3 phospholipase C-like 3 affy_probe_2_Entrez 2 2 114 -5.5 down 2 0 0/2 -2.75 2 114 -2.20 -3.30 214745_at 214745_at phospholipase C-like 3 PLCL3 -3.296 -3.30 down 0.009969013 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1583 23043 TNIK TRAF2 and NCK interacting kinase affy_probe_2_Entrez 1 1 55 3.16 up 1 0 1/0 3.16 1 55 3.16 3.16 211828_s_at 211828_s_at TRAF2 and NCK interacting kinase TNIK 4.317 4.32 up 7.49126E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1600 23043 TNIK TRAF2 and NCK interacting kinase affy_probe_2_Entrez 1 1 55 3.16 up 1 0 1/0 3.16 1 55 3.16 3.16 213107_at 213107_at TRAF2 and NCK interacting kinase TNIK 3.158 3.16 up 0.001257775 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1508 23052 KIAA0830 KIAA0830 protein Gene_symbol_2_NCBI_Entrez 1 1 32 2.01 up 1 0 1/0 2.01 1 32 2.01 2.01 KIAA0830 protein KIAA0830 1.01 2.01 up PTC Norm 16 16 publication 15735049 13 20 901 23089 PEG10 paternally expressed 10 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 2.4 up 2 0 2/0 2.4 1 59 2.40 2.40 AB028974 AB028974 Paternally expressed 10 PEG10 up FTC FA 9 10 publication 12738736 18 31 1350 23089 PEG10 paternally expressed 10 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 78 2.4 up 2 0 2/0 2.4 1 59 2.40 2.40 AB028974 AB028974 KIAA1051 protein KIAA1051 2.4 2.40 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 9 14 690 23150 FRMD4B FERM domain containing 4B affy_probe_2_Entrez 1 1 24 4.66 up 1 0 1/0 4.66 1 24 4.66 4.66 213056_at 213056_at KIAA1013 protein -4.66 4.66 up 0.002559 FA FTC 12 12 provided by authors 15713710 16 24 1235 23171 GPD1L glycerol-3-phosphate dehydrogenase 1-like Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 63 -1.88 down 1 0 0/1 -1.88 1 63 -1.88 -1.88 KIAA0089 0.531468531 -1.88 down 0.03 PTC;FVPTC FA;HN 32 31 publication 15087409 25 34 1650 23177 KIAA0582 KIAA0582 affy_probe_2_Entrez 1 1 55 -2.21 down 1 0 0/1 -2.21 1 55 -2.21 -2.21 212677_s_at 212677_s_at KIAA0582 KIAA0582 -2.211 -2.21 down 0.019167189 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 949 23180 RAFTLIN raft-linking protein clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 43 3.27 even 1 1 1/1 3.27 1 24 3.27 3.27 D42043 D42043 KIAA0084 protein KIAA0084 down FTC FA 9 10 publication 12738736 9 14 650 23180 RAFTLIN raft-linking protein affy_probe_2_Entrez 2 2 43 3.27 even 1 1 1/1 3.27 1 24 3.27 3.27 212646_at 212646_at KIAA0084 protein -3.27 3.27 up 0.000001 FA FTC 12 12 provided by authors 15713710 24 33 1470 23220 DTX4 deltex 4 homolog (Drosophila) Gene_symbol_2_NCBI_Synonym_2_Entrez 2 2 48 9.62 up 2 0 2/0 4.81 2 48 5.62 4.00 KIAA0937 protein KIAA0937 2.49 5.62 up PTC Norm 16 16 publication 15735049 3 6 134 23220 DTX4 deltex 4 homolog (Drosophila) clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 48 9.62 up 2 0 2/0 4.81 2 48 5.62 4.00 AB023154 AB023154 KIAA0937 KIAA0937 4 4.00 up no 0.0001 PTC Norm 8 8 suppl. materials 11752453 18 31 1380 23231 KIAA0746 KIAA0746 protein clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 59 2.1 up 1 0 1/0 2.1 1 59 2.10 2.10 AB018289 AB018289 KIAA0746 protein KIAA0746 2.1 2.10 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1596 23250 ATP11A ATPase, Class VI, type 11A affy_probe_2_Entrez 2 2 79 6.42 up 2 0 2/0 3.21 2 79 3.30 3.12 216488_s_at 216488_s_at ATPase, Class VI, type 11A ATP11A 3.296 3.30 up 0.037241031 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 641 23250 ATP11A ATPase, Class VI, type 11A affy_probe_2_Entrez 2 2 79 6.42 up 2 0 2/0 3.21 2 79 3.30 3.12 213582_at 213582_at ATPase, Class VI, type 11A -3.12 3.12 up 0.004345 FA FTC 12 12 provided by authors 15713710 16 24 1217 23272 RAP140 retinoblastoma-associated protein 140 Gene_symbol_2_NCBI_Entrez 1 1 63 -1.6 down 1 0 0/1 -1.6 1 63 -1.60 -1.60 RAP140 0.625 -1.60 down 0.01 PTC;FVPTC FA;HN 32 31 publication 15087409 25 34 1734 23345 SYNE1 spectrin repeat containing, nuclear envelope 1 affy_probe_2_Entrez 1 1 55 -4.63 down 1 0 0/1 -4.63 1 55 -4.63 -4.63 215350_at 215350_at spectrin repeat containing, nuclear envelope 1 SYNE1 -4.629 -4.63 down 2.471E-09 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 18 31 1368 23348 DOCK9 dedicator of cytokinesis 9 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 114 4.94 up 2 0 2/0 2.47 2 114 2.74 2.20 AB028981 AB028981 KIAA1058 protein KIAA1058 2.2 2.20 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 25 34 1608 23348 DOCK9 dedicator of cytokinesis 9 affy_probe_2_Entrez 2 2 114 4.94 up 2 0 2/0 2.47 2 114 2.74 2.20 212538_at 212538_at dedicator of cytokinesis 9 DOCK9 2.740 2.74 up 0.00395343 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 18 31 1335 23362 PSD3 pleckstrin and Sec7 domain containing 3 clone_accession_2_NCBI_rna_accession_2_Entrez 3 3 146 11.97 up 3 0 3/0 3.99 3 146 5.50 2.70 AB023159 AB023159 KIAA0942 protein KIAA0942 2.7 2.70 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1485 23362 PSD3 pleckstrin and Sec7 domain containing 3 Gene_symbol_2_NCBI_Synonym_2_Entrez 3 3 146 11.97 up 3 0 3/0 3.99 3 146 5.50 2.70 Hypothetical protein DKFZp761K1423 DKFZp761K1423 1.915 3.77 up PTC Norm 16 16 publication 15735049 25 34 1560 23362 PSD3 pleckstrin and Sec7 domain containing 3 affy_probe_2_Entrez 3 3 146 11.97 up 3 0 3/0 3.99 3 146 5.50 2.70 203354_s_at 203354_s_at pleckstrin and Sec7 domain containing 3 PSD3 8.253 8.25 up 0.007461741 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1572 23362 PSD3 pleckstrin and Sec7 domain containing 3 affy_probe_2_Entrez 3 3 146 11.97 up 3 0 3/0 3.99 3 146 5.50 2.70 218613_at 218613_at pleckstrin and Sec7 domain containing 3 PSD3 5.726 5.73 up 1.1507E-08 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1575 23362 PSD3 pleckstrin and Sec7 domain containing 3 affy_probe_2_Entrez 3 3 146 11.97 up 3 0 3/0 3.99 3 146 5.50 2.70 203355_s_at 203355_s_at pleckstrin and Sec7 domain containing 3 PSD3 5.503 5.50 up 2.71768E-07 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 893 23367 LARP1 La ribonucleoprotein domain family, member 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 AB018274 AB018274 KIAA0731 protein KIAA0731 up FTC FA 9 10 publication 12738736 25 34 1599 23381 EST1B Est1p-like protein B affy_probe_2_Entrez 1 1 55 3.17 up 1 0 1/0 3.17 1 55 3.17 3.17 212147_at 212147_at Est1p-like protein B EST1B 3.172 3.17 up 0.007667858 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1745 23414 ZFPM2 zinc finger protein, multitype 2 affy_probe_2_Entrez 1 1 55 -5.16 down 1 0 0/1 -5.16 1 55 -5.16 -5.16 219778_at 219778_at zinc finger protein, multitype 2 ZFPM2 -5.161 -5.16 down 0.00053732 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 12 19 853 23468 CBX5 chromobox homolog 5 (HP1 alpha homolog, Drosophila) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 21 -2.04 down 1 0 0/1 -2.04 1 21 -2.04 -2.04 L07515 L07515 HP1-alpha 0.49 -2.04 down PTC Norm 18 3 publication 12538453 9 14 617 23469 PHF3 PHD finger protein 3 affy_probe_2_Entrez 1 1 24 2.68 up 1 0 1/0 2.68 1 24 2.68 2.68 215718_s_at 215718_s_at PHD finger protein 3 -2.68 2.68 up 0.000017 FA FTC 12 12 provided by authors 15713710 11 18 833 23471 TRAM1 translocation associated membrane protein 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 X63679 X63679 TRAMP protein down ACL;ATC Norm 21 10 publication 15613457 16 24 1243 23516 SLC39A14 solute carrier family 39 (zinc transporter), member 14 Gene_symbol_2_NCBI_Synonym_2_Entrez 2 2 122 -4.24 down 2 0 0/2 -2.12 2 122 -2.00 -2.24 KIAA0062 0.446601942 -2.24 down 0.001 PTC;FVPTC FA;HN 32 31 publication 15087409 18 31 1398 23516 SLC39A14 solute carrier family 39 (zinc transporter), member 14 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 122 -4.24 down 2 0 0/2 -2.12 2 122 -2.00 -2.24 D31887 D31887 KIAA0062 gene KIAA0062 2 -2.00 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 15 22 1030 23544 SEZ6L seizure related 6 homolog (mouse)-like Gene_symbol_2_NCBI_Entrez 1 1 7 2 up 1 0 1/0 2 1 7 2.00 2.00 Seizure related gene 6 (mouse)-like SEZ6L 2 2.00 up FTC FA 3 4 publication 15475448 24 33 1520 23609 MKRN2 makorin, ring finger protein, 2 Gene_symbol_2_NCBI_Entrez 1 1 32 -1.44 down 1 0 0/1 -1.44 1 32 -1.44 -1.44 Makorin, ring finger protein, 2 MKRN2 -0.525 -1.44 down PTC Norm 16 16 publication 15735049 9 14 664 23635 SSBP2 single-stranded DNA binding protein 2 affy_probe_2_Entrez 1 1 24 3.61 up 1 0 1/0 3.61 1 24 3.61 3.61 210829_s_at 210829_s_at single-stranded DNA binding protein 2 -3.61 3.61 up 0.009525 FA FTC 12 12 provided by authors 15713710 25 34 1716 23645 PPP1R15A protein phosphatase 1, regulatory (inhibitor) subunit 15A affy_probe_2_Entrez 1 1 55 -3.57 down 1 0 0/1 -3.57 1 55 -3.57 -3.57 37028_at 37028_at protein phosphatase 1, regulatory (inhibitor) subunit 15A PPP1R15A -3.571 -3.57 down 0.002055442 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 913 23646 PLD3 phospholipase D family, member 3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 U60644 U60644 Similar to vaccinia virus HindIII K4L ORF HU_K4 up FTC FA 9 10 publication 12738736 14 21 968 23649 POLA2 polymerase (DNA directed), alpha 2 (70kD subunit) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 37 up 1 0 1/0 37 1 14 37.00 37.00 AA486289 AA486289 DNA polymerase 37 37.00 up PTC Norm 7 7 publication 15041723 13 20 941 23673 STX12 syntaxin 12 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 AL035306 AL035306 Hypothetical protein MGC14797 MCG14797 down FTC FA 9 10 publication 12738736 9 14 625 23741 CRI1 CREBBP/EP300 inhibitor 1 affy_probe_2_Entrez 1 1 24 2.84 up 1 0 1/0 2.84 1 24 2.84 2.84 208670_s_at 208670_s_at CREBBP/EP300 inhibitory protein 1 -2.84 2.84 up 0.000004 FA FTC 12 12 provided by authors 15713710 24 33 1492 23767 FLRT3 fibronectin leucine rich transmembrane protein 3 Gene_symbol_2_NCBI_Entrez 1 1 32 2.85 up 1 0 1/0 2.85 1 32 2.85 2.85 Fibronectin leucine-rich transmembrane protein 3 FLRT3 1.51 2.85 up PTC Norm 16 16 publication 15735049 11 18 840 25770 HS747E2A hypothetical protein HS747E2A clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 AL035364 AL035364 HS747E2A hypothetical protein HS747E2A down ACL;ATC Norm 21 10 publication 15613457 15 22 1021 25797 QPCT glutaminyl-peptide cyclotransferase (glutaminyl cyclase) Gene_symbol_2_NCBI_Entrez 4 4 153 29.25 up 4 0 4/0 7.3125 4 153 11.67 3.40 Glutaminyl-peptide cyclotransferase QPCT 4 4.00 up FTC FA 3 4 publication 15475448 18 31 1316 25797 QPCT glutaminyl-peptide cyclotransferase (glutaminyl cyclase) clone_accession_2_NCBI_rna_accession_2_Entrez 4 4 153 29.25 up 4 0 4/0 7.3125 4 153 11.67 3.40 X71125 X71125 Glutamine cyclotransferase GCT 3.4 3.40 up FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1458 25797 QPCT glutaminyl-peptide cyclotransferase (glutaminyl cyclase) Gene_symbol_2_NCBI_Entrez 4 4 153 29.25 up 4 0 4/0 7.3125 4 153 11.67 3.40 Glutaminyl-peptide cyclotransferase (glutaminyl cyclase) QPCT 3.545 11.67 up PTC Norm 16 16 publication 15735049 25 34 1556 25797 QPCT glutaminyl-peptide cyclotransferase (glutaminyl cyclase) affy_probe_2_Entrez 4 4 153 29.25 up 4 0 4/0 7.3125 4 153 11.67 3.40 205174_s_at 205174_s_at glutaminyl-peptide cyclotransferase (glutaminyl cyclase) QPCT 10.178 10.18 up 1.64137E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1714 25802 LMOD1 leiomodin 1 (smooth muscle) affy_probe_2_Entrez 1 1 55 -8.46 down 1 0 0/1 -8.46 1 55 -8.46 -8.46 211562_s_at 211562_s_at leiomodin 1 (smooth muscle) LMOD1 -3.518 -3.52 down 0.015264131 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1770 25802 LMOD1 leiomodin 1 (smooth muscle) affy_probe_2_Entrez 1 1 55 -8.46 down 1 0 0/1 -8.46 1 55 -8.46 -8.46 203766_s_at 203766_s_at leiomodin 1 (smooth muscle) LMOD1 -8.458 -8.46 down 7.9874E-07 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 957 25807 C22orf3 chromosome 22 open reading frame 3 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 AL031186 AL031186 Putative emu1 LOC129080 down FTC FA 9 10 publication 12738736 25 34 1682 25890 ABI3BP ABI gene family, member 3 (NESH) binding protein affy_probe_2_Entrez 1 1 55 -2.8 down 1 0 0/1 -2.8 1 55 -2.80 -2.80 220518_at 220518_at target of Nesh-SH3 TARSH -2.800 -2.80 down 0.006377425 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1544 25928 SOSTDC1 sclerostin domain containing 1 Gene_symbol_2_NCBI_Entrez 1 1 32 -10.3 down 1 0 0/1 -10.3 1 32 -10.30 -10.30 Sclerostin domain containing 1 SOSTDC1 -3.365 -10.30 down PTC Norm 16 16 publication 15735049 25 34 1698 26018 LRIG1 leucine-rich repeats and immunoglobulin-like domains 1 affy_probe_2_Entrez 1 1 55 -3.12 down 1 0 0/1 -3.12 1 55 -3.12 -3.12 211596_s_at 211596_s_at leucine-rich repeats and immunoglobulin-like domains 1 /// leucine-rich repeats and immunoglobulin-like domains 1 LRIG1 -3.116 -3.12 down 0.005129109 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1771 26034 PIP3-E phosphoinositide-binding protein PIP3-E affy_probe_2_Entrez 1 1 55 -8.53 down 1 0 0/1 -8.53 1 55 -8.53 -8.53 214735_at 214735_at phosphoinositide-binding protein PIP3-E PIP3-E -8.534 -8.53 down 3.72471E-13 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1693 26040 SETBP1 SET binding protein 1 affy_probe_2_Entrez 1 1 55 -2.97 down 1 0 0/1 -2.97 1 55 -2.97 -2.97 205933_at 205933_at SET binding protein 1 SETBP1 -2.973 -2.97 down 0.007628938 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 927 26130 GAPVD1 GTPase activating protein and VPS9 domains 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 AL080196 AL080196 DKFZP434C212 protein DKFZP434C212 down FTC FA 9 10 publication 12738736 2 2 70 26191 PTPN22 protein tyrosine phosphatase, non-receptor type 22 (lymphoid) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -7.8 down 1 0 0/1 -7.8 1 2 -7.80 -7.80 NM_012411 NM_012411 Protein tyrosine phosphatase, nonreceptor type 22 PTPN22 7.8 -7.80 down FCL Norm 1 1 publication 15785240 9 14 607 26471 P8 p8 protein (candidate of metastasis 1) affy_probe_2_Entrez 1 1 24 -4.44 down 1 0 0/1 -4.44 1 24 -4.44 -4.44 209230_s_at 209230_s_at p8 protein (candidate of metastasis 1) 4.44 -4.44 down 0.001643 FA FTC 12 12 provided by authors 15713710 25 34 1611 26503 SLC17A5 solute carrier family 17 (anion/sugar transporter), member 5 affy_probe_2_Entrez 1 1 55 2.58 up 1 0 1/0 2.58 1 55 2.58 2.58 221041_s_at 221041_s_at solute carrier family 17 (anion/sugar transporter), member 5 SLC17A5 2.582 2.58 up 0.028162674 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 14 21 977 26578 OSTF1 osteoclast stimulating factor 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 2.9 up 1 0 1/0 2.9 1 14 2.90 2.90 AA283693 AA283693 Osteoclast-stimulating factor 2.9 2.90 up PTC Norm 7 7 publication 15041723 25 34 1576 27161 EIF2C2 eukaryotic translation initiation factor 2C, 2 affy_probe_2_Entrez 2 2 79 9.58 up 2 0 2/0 4.79 2 79 5.24 4.34 222294_s_at 222294_s_at --- --- 5.237 5.24 up 7.86214E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 687 27161 EIF2C2 eukaryotic translation initiation factor 2C, 2 affy_probe_2_Entrez 2 2 79 9.58 up 2 0 2/0 4.79 2 79 5.24 4.34 222294_s_at 222294_s_at ESTs -4.34 4.34 up 0.002698 FA FTC 12 12 provided by authors 15713710 13 20 952 27258 LSM3 LSM3 homolog, U6 small nuclear RNA associated (S. cerevisiae) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 N98670 N98670 LSM 3 protein LSM3 down FTC FA 9 10 publication 12738736 9 14 611 27333 GOLPH4 golgi phosphoprotein 4 affy_probe_2_Entrez 1 1 24 -3.53 down 1 0 0/1 -3.53 1 24 -3.53 -3.53 204324_s_at 204324_s_at golgi phosphoprotein 4 3.53 -3.53 down 0.000843 FA FTC 12 12 provided by authors 15713710 13 20 920 27338 UBE2S ubiquitin-conjugating enzyme E2S clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 M91670 M91670 Ubiquitin carrier protein E2-EPF up FTC FA 9 10 publication 12738736 24 33 1460 28965 SLC27A6 solute carrier family 27 (fatty acid transporter), member 6 Gene_symbol_2_NCBI_Entrez 1 1 32 10.97 up 1 0 1/0 10.97 1 32 10.97 10.97 Solute carrier family 27 ( fatty acid transporter), member 6 SLC27A6 3.455 10.97 up PTC Norm 16 16 publication 15735049 25 34 1685 29118 DDX25 DEAD (Asp-Glu-Ala-Asp) box polypeptide 25 affy_probe_2_Entrez 1 1 55 -2.87 down 1 0 0/1 -2.87 1 55 -2.87 -2.87 219945_at 219945_at DEAD (Asp-Glu-Ala-Asp) box polypeptide 25 DDX25 -2.868 -2.87 down 0.005312359 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1648 29842 TFCP2L1 transcription factor CP2-like 1 affy_probe_2_Entrez 1 1 55 -2.17 down 1 0 0/1 -2.17 1 55 -2.17 -2.17 219735_s_at 219735_s_at transcription factor CP2-like 1 TFCP2L1 -2.172 -2.17 down 4.2665E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 626 30008 EFEMP2 EGF-containing fibulin-like extracellular matrix protein 2 affy_probe_2_Entrez 1 1 24 2.86 up 1 0 1/0 2.86 1 24 2.86 2.86 209356_x_at 209356_x_at EGF-containing fibulin-like extracellular matrix protein 2 -2.86 2.86 up 0.000001 FA FTC 12 12 provided by authors 15713710 2 4 103 50488 MINK1 misshapen-like kinase 1 (zebrafish) clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -5.6 down 1 0 0/1 -5.6 1 2 -5.60 -5.60 NM_015716 NM_015716 Misshapen/NIK-related kinase MINK 5.6 -5.60 down PCL Norm 1 1 publication 15785240 9 14 674 50506 DUOX2 dual oxidase 2 affy_probe_2_Entrez 1 1 24 3.82 up 1 0 1/0 3.82 1 24 3.82 3.82 219727_at 219727_at dual oxidase 2 -3.82 3.82 up 0.003596 FA FTC 12 12 provided by authors 15713710 25 34 1660 51011 FAHD2A fumarylacetoacetate hydrolase domain containing 2A affy_probe_2_Entrez 1 1 55 -2.49 down 1 0 0/1 -2.49 1 55 -2.49 -2.49 222056_s_at 222056_s_at fumarylacetoacetate hydrolase domain containing 2A FAHD2A -2.421 -2.42 down 0.000948018 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1664 51011 FAHD2A fumarylacetoacetate hydrolase domain containing 2A affy_probe_2_Entrez 1 1 55 -2.49 down 1 0 0/1 -2.49 1 55 -2.49 -2.49 218504_at 218504_at fumarylacetoacetate hydrolase domain containing 2A FAHD2A -2.486 -2.49 down 0.006361772 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 662 51196 PLCE1 phospholipase C, epsilon 1 affy_probe_2_Entrez 1 1 24 3.5 up 1 0 1/0 3.5 1 24 3.5 3.5 205111_s_at 205111_s_at phospholipase C, epsilon 1 -3.5 3.5 up 0.004579 FA FTC 12 12 provided by authors 15713710 16 24 1226 51340 CRNKL1 Crn, crooked neck-like 1 (Drosophila) Gene_symbol_2_NCBI_Entrez 1 1 63 -1.68 down 1 0 0/1 -1.68 1 63 -1.68 -1.68 CRNKL1 0.593984962 -1.68 down 0.01 PTC;FVPTC FA;HN 32 31 publication 15087409 16 24 1231 51382 ATP6V1D ATPase, H+ transporting, lysosomal 34kDa, V1 subunit D Gene_symbol_2_NCBI_Entrez 1 1 63 -1.82 down 1 0 0/1 -1.82 1 63 -1.82 -1.82 ATP6V1D 0.549707602 -1.82 down 0.01 PTC;FVPTC FA;HN 32 31 publication 15087409 15 22 1028 51440 HPCAL4 hippocalcin like 4 Gene_symbol_2_NCBI_Entrez 1 1 7 3 up 1 0 1/0 3 1 7 3.00 3.00 Hippocalcin-like protein 4 HPCAL4 3 3.00 up FTC FA 3 4 publication 15475448 13 20 872 51454 GULP1 GULP, engulfment adaptor PTB domain containing 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 AL080142 AL080142 CED-6 protein CED-6 up FTC FA 9 10 publication 12738736 16 24 1233 51690 LSM7 LSM7 homolog, U6 small nuclear RNA associated (S. cerevisiae) Gene_symbol_2_NCBI_Entrez 1 1 63 -1.86 down 1 0 0/1 -1.86 1 63 -1.86 -1.86 LSM7 0.5390625 -1.86 down yes 0.001 PTC;FVPTC FA;HN 32 31 publication 15087409 24 33 1537 51741 WWOX WW domain containing oxidoreductase Gene_symbol_2_NCBI_Entrez 2 2 87 -6.34 down 2 0 0/2 -3.17 2 87 -2.85 -3.49 WW domain containing oxidoreductase WWOX -1.51 -2.85 down PTC Norm 16 16 publication 15735049 25 34 1713 51741 WWOX WW domain containing oxidoreductase affy_probe_2_Entrez 2 2 87 -6.34 down 2 0 0/2 -3.17 2 87 -2.85 -3.49 219077_s_at 219077_s_at WW domain containing oxidoreductase WWOX -3.486 -3.49 down 0.045866957 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1571 51809 GALNT7 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7) affy_probe_2_Entrez 1 1 55 5.76 up 1 0 1/0 5.76 1 55 5.76 5.76 218313_s_at 218313_s_at UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 7 (GalNAc-T7) GALNT7 5.760 5.76 up 4.17933E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1720 53353 LRP1B low density lipoprotein-related protein 1B (deleted in tumors) affy_probe_2_Entrez 1 1 55 -3.69 down 1 0 0/1 -3.69 1 55 -3.69 -3.69 219643_at 219643_at low density lipoprotein-related protein 1B (deleted in tumors) LRP1B -3.690 -3.69 down 3.55901E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 11 18 790 53588 ZWINTAS ZW10 interactor antisense clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 X98261 X98261 M-phase phosphoprotein, mpp5 down ACL;ATC Norm 21 10 publication 15613457 16 24 1219 54065 C21orf51 chromosome 21 open reading frame 51 Gene_symbol_2_NCBI_Entrez 1 1 63 -1.6 down 1 0 0/1 -1.6 1 63 -1.60 -1.60 C21orf51 0.623762376 -1.60 down 0.02 PTC;FVPTC FA;HN 32 31 publication 15087409 24 33 1481 54210 TREM1 triggering receptor expressed on myeloid cells 1 Gene_symbol_2_NCBI_Entrez 1 1 32 4.63 up 1 0 1/0 4.63 1 32 4.63 4.63 Triggering receptor expressed on myeloid cells 1 TREM1 2.21 4.63 up PTC Norm 16 16 publication 15735049 16 24 1240 54462 KIAA1128 KIAA1128 Gene_symbol_2_NCBI_Entrez 1 1 63 -1.96 down 1 0 0/1 -1.96 1 63 -1.96 -1.96 KIAA1128 0.511363636 -1.96 down yes 0.03 PTC;FVPTC FA;HN 32 31 publication 15087409 25 34 1654 54556 ING3 inhibitor of growth family, member 3 affy_probe_2_Entrez 1 1 55 -2.24 down 1 0 0/1 -2.24 1 55 -2.24 -2.24 205070_at 205070_at inhibitor of growth family, member 3 ING3 -2.239 -2.24 down 0.000425855 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 2 2 86 54888 NSUN2 NOL1/NOP2/Sun domain family, member 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 3.04 up 1 0 1/0 3.04 1 2 3.04 3.04 BE154215 BE154215 Unknown EST 3.04 3.04 up FCL Norm 1 1 publication 15785240 25 34 1667 54959 APIN APin protein affy_probe_2_Entrez 1 1 55 -2.54 down 1 0 0/1 -2.54 1 55 -2.54 -2.54 220133_at 220133_at APin protein APIN -2.541 -2.54 down 2.50295E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 16 24 1230 54969 FLJ20534 hypothetical protein FLJ20534 Gene_symbol_2_NCBI_Entrez 1 1 63 -1.8 down 1 0 0/1 -1.8 1 63 -1.80 -1.80 FLJ20534 0.556701031 -1.80 down 0.02 PTC;FVPTC FA;HN 32 31 publication 15087409 25 34 1699 54996 MOSC2 MOCO sulphurase C-terminal domain containing 2 affy_probe_2_Entrez 1 1 55 -3.14 down 1 0 0/1 -3.14 1 55 -3.14 -3.14 221636_s_at 221636_s_at hypothetical protein FLJ20605 FLJ20605 -3.143 -3.14 down 6.37944E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1707 55022 FLJ20701 hypothetical protein FLJ20701 affy_probe_2_Entrez 1 1 55 -3.31 down 1 0 0/1 -3.31 1 55 -3.31 -3.31 219093_at 219093_at hypothetical protein FLJ20701 FLJ20701 -3.314 -3.31 down 5.24947E-09 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 647 55084 FLJ10159 hypothetical protein FLJ10159 affy_probe_2_Entrez 1 1 24 3.17 up 1 0 1/0 3.17 1 24 3.17 3.17 218974_at 218974_at hypothetical protein FLJ10159 -3.17 3.17 up 0.000017 FA FTC 12 12 provided by authors 15713710 24 33 1543 55086 FLJ10178 hypothetical protein FLJ10178 Gene_symbol_2_NCBI_Entrez 1 1 32 -8.17 down 1 0 0/1 -8.17 1 32 -8.17 -8.17 Hypothetical protein FLJ10178 FLJ10178 -3.03 -8.17 down PTC Norm 16 16 publication 15735049 15 22 1046 55160 ARHGEF10L Rho guanine nucleotide exchange factor (GEF) 10-like Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 7 -2.5 down 1 0 0/1 -2.5 1 7 -2.50 -2.50 Highly similar to rho guanyl nucleotide exchange factor FLJ10521 0.4 -2.50 down FTC FA 3 4 publication 15475448 24 33 1480 55220 FLJ10748 hypothetical protein FLJ10748 Gene_symbol_2_NCBI_Entrez 1 1 32 4.68 up 1 0 1/0 4.68 1 32 4.68 4.68 Hypothetical protein FLJ10748 FLJ10748 2.225 4.68 up PTC Norm 16 16 publication 15735049 24 33 1525 55274 PHF10 PHD finger protein 10 Gene_symbol_2_NCBI_Entrez 1 1 32 -1.59 down 1 0 0/1 -1.59 1 32 -1.59 -1.59 PHD finger protein 10 PHF10 -0.665 -1.59 down PTC Norm 16 16 publication 15735049 16 24 1213 55364 IMPACT hypothetical protein IMPACT Gene_symbol_2_NCBI_Entrez 1 1 63 -1.53 down 1 0 0/1 -1.53 1 63 -1.53 -1.53 IMPACT 0.651515152 -1.53 down yes 0.03 PTC;FVPTC FA;HN 32 31 publication 15087409 2 2 61 55573 H41 hypothetical protein H41 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -12.2 down 1 0 0/1 -12.2 1 2 -12.20 -12.20 NM_017548 NM_017548 Unknown EST 12.2 -12.20 down FCL Norm 1 1 publication 15785240 13 20 868 55643 BTBD2 BTB (POZ) domain containing 2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 W68046 W68046 BTB domain containing 2 BTBD2 up FTC FA 9 10 publication 12738736 16 24 1212 55650 PIGV phosphatidylinositol glycan, class V Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 63 -1.53 down 1 0 0/1 -1.53 1 63 -1.53 -1.53 FLJ20477 0.655172414 -1.53 down 0.0001 PTC;FVPTC FA;HN 32 31 publication 15087409 25 34 1761 55753 OGDHL oxoglutarate dehydrogenase-like affy_probe_2_Entrez 1 1 55 -6.78 down 1 0 0/1 -6.78 1 55 -6.78 -6.78 219277_s_at 219277_s_at oxoglutarate dehydrogenase-like OGDHL -6.778 -6.78 down 0.026741097 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1609 55784 MCTP2 multiple C2-domains with two transmembrane regions 2 affy_probe_2_Entrez 1 1 55 2.69 up 1 0 1/0 2.69 1 55 2.69 2.69 220603_s_at 220603_s_at multiple C2-domains with two transmembrane regions 2 MCTP2 2.691 2.69 up 3.06294E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1750 55790 ChGn chondroitin beta1,4 N-acetylgalactosaminyltransferase affy_probe_2_Entrez 1 1 55 -5.62 down 1 0 0/1 -5.62 1 55 -5.62 -5.62 219049_at 219049_at chondroitin beta1,4 N-acetylgalactosaminyltransferase ChGn -5.620 -5.62 down 0.002724696 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 938 55830 GLT8D1 glycosyltransferase 8 domain containing 1 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 82 -1.87 down 2 0 0/2 -1.87 1 63 -1.87 -1.87 L13435 L13435 Glucosyltransferase AD-017 AD017 down FTC FA 9 10 publication 12738736 16 24 1234 55830 GLT8D1 glycosyltransferase 8 domain containing 1 Gene_symbol_2_NCBI_Synonym_2_Entrez 2 2 82 -1.87 down 2 0 0/2 -1.87 1 63 -1.87 -1.87 AD-017 0.535031847 -1.87 down 0.01 PTC;FVPTC FA;HN 32 31 publication 15087409 9 14 681 55885 LMO3 LIM domain only 3 (rhombotin-like 2) affy_probe_2_Entrez 1 1 24 4 up 1 0 1/0 4 1 24 4 4 204424_s_at 204424_s_at neuronal specific transcription factor DAT1 -4 4 up 0.003594 FA FTC 12 12 provided by authors 15713710 13 20 886 56255 DJ971N18.2 hypothetical protein DJ971N18.2 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 AL021396 AL021396 Hypothetical protein DJ971N18.2 up FTC FA 9 10 publication 12738736 25 34 1671 56603 CYP26B1 cytochrome P450, family 26, subfamily B, polypeptide 1 affy_probe_2_Entrez 1 1 55 -2.61 down 1 0 0/1 -2.61 1 55 -2.61 -2.61 219825_at 219825_at cytochrome P450, family 26, subfamily B, polypeptide 1 CYP26B1 -2.609 -2.61 down 0.020528648 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1448 56649 TMPRSS4 transmembrane protease, serine 4 Gene_symbol_2_NCBI_Entrez 1 1 32 19.77 up 1 0 1/0 19.77 1 32 19.77 19.77 Transmembrane protease, serine 4 TMPRSS4 4.305 19.77 up PTC Norm 16 16 publication 15735049 16 24 1209 56943 ENY2 enhancer of yellow 2 homolog (Drosophila) Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 63 -1.47 down 1 0 0/1 -1.47 1 63 -1.47 -1.47 DC6 0.680672269 -1.47 down 0.04 PTC;FVPTC FA;HN 32 31 publication 15087409 25 34 1715 57088 PLSCR4 phospholipid scramblase 4 affy_probe_2_Entrez 1 1 55 -3.55 down 1 0 0/1 -3.55 1 55 -3.55 -3.55 218901_at 218901_at --- --- -3.555 -3.55 down 0.001250845 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 11 18 814 57292 KIR2DL5A killer cell immunoglobulin-like receptor, two domains, long cytoplasmic tail, 5A clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 L76672 L76672 nkat9 down ACL;ATC Norm 21 10 publication 15613457 24 33 1501 57402 S100A14 S100 calcium binding protein A14 Gene_symbol_2_NCBI_Entrez 1 1 32 2.32 up 1 0 1/0 2.32 1 32 2.32 2.32 S100 calcium-binding protein A14 (calgizzarin) S100A14 1.215 2.32 up PTC Norm 16 16 publication 15735049 9 14 616 57460 PPM1H protein phosphatase 1H (PP2C domain containing) affy_probe_2_Entrez 1 1 24 -2.71 down 1 0 0/1 -2.71 1 24 -2.71 -2.71 212686_at 212686_at KIAA1157 protein 2.71 -2.71 down 0.000065 FA FTC 12 12 provided by authors 15713710 9 14 618 57509 MTUS1 mitochondrial tumor suppressor 1 affy_probe_2_Entrez 1 1 24 2.71 up 1 0 1/0 2.71 1 24 2.71 2.71 212096_s_at 212096_s_at AT2 receptor-interacting protein 1 -2.71 2.71 up 0.000493 FA FTC 12 12 provided by authors 15713710 19 32 1417 57561 ARRDC3 arrestin domain containing 3 tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 AAGCAAGAAT AAGCAAGAAT KIAA1376 protein up 0.0245 FVPTC Norm 1 1 publication 14715705 9 14 619 57599 WDR48 WD repeat domain 48 affy_probe_2_Entrez 1 1 24 2.72 up 1 0 1/0 2.72 1 24 2.72 2.72 221735_at 221735_at WD repeat endosomal protein -2.72 2.72 up 0.000016 FA FTC 12 12 provided by authors 15713710 25 34 1647 57613 KIAA1467 KIAA1467 protein affy_probe_2_Entrez 1 1 55 -2.16 down 1 0 0/1 -2.16 1 55 -2.16 -2.16 213234_at 213234_at KIAA1467 protein KIAA1467 -2.158 -2.16 down 0.038062468 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 11 18 810 57862 ZNF410 zinc finger protein 410 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 U90919 U90919 Clones 23667 and 23775 zinc finger protein down ACL;ATC Norm 21 10 publication 15613457 16 24 1214 58497 PRUNE prune homolog (Drosophila) Gene_symbol_2_NCBI_Synonym_2_Entrez 2 2 95 -3.4 down 2 0 0/2 -1.7 2 95 -1.56 -1.84 HTCD37 0.639344262 -1.56 down 0.01 PTC;FVPTC FA;HN 32 31 publication 15087409 24 33 1528 58497 PRUNE prune homolog (Drosophila) Gene_symbol_2_NCBI_Synonym_2_Entrez 2 2 95 -3.4 down 2 0 0/2 -1.7 2 95 -1.56 -1.84 TcD37 homologue HTCD37 -0.88 -1.84 down PTC Norm 16 16 publication 15735049 9 14 672 58517 RBM25 RNA binding motif protein 25 affy_probe_2_Entrez 1 1 24 3.75 up 1 0 1/0 3.75 1 24 3.75 3.75 212030_at 212030_at S164 protein -3.75 3.75 up 0.000038 FA FTC 12 12 provided by authors 15713710 11 18 838 60685 TEX27 testis expressed sequence 27 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 AL137302 AL137302 TEX27 testis expressed sequence 27 down ACL;ATC Norm 21 10 publication 15613457 15 22 1051 63826 SRR serine racemase Gene_symbol_2_NCBI_Entrez 1 1 7 -3.33 down 1 0 0/1 -3.33 1 7 -3.33 -3.33 Serine racemase SRR 0.3 -3.33 down FTC FA 3 4 publication 15475448 24 33 1502 64220 STRA6 stimulated by retinoic acid gene 6 homolog (mouse) Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 32 2.31 up 1 0 1/0 2.31 1 32 2.31 2.31 Stimulated by retinoic acid gene 6 FLJ12541 1.21 2.31 up PTC Norm 16 16 publication 15735049 25 34 1674 64283 RGNEF Rho-guanine nucleotide exchange factor affy_probe_2_Entrez 1 1 55 -2.63 down 1 0 0/1 -2.63 1 55 -2.63 -2.63 219610_at 219610_at Rho-guanine nucleotide exchange factor RGNEF -2.634 -2.63 down 0.000282681 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1595 64393 WIG1 p53 target zinc finger protein affy_probe_2_Entrez 1 1 55 3.33 up 1 0 1/0 3.33 1 55 3.33 3.33 219628_at 219628_at p53 target zinc finger protein WIG1 3.326 3.33 up 0.034418855 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 5 10 387 64418 FLJ13576 hypothetical protein FLJ13576 tag_2_refseq_or_mgc_2_Entrez 1 1 3 0 up 1 0 1/0 0 0 0 0 0 TAATGTATTC TAATGTATTC FLJ13576 up no FTC FA;Norm 1 2 publication 15085203 25 34 1711 64759 TNS3 tensin 3 affy_probe_2_Entrez 1 1 55 -3.46 down 1 0 0/1 -3.46 1 55 -3.46 -3.46 217853_at 217853_at tensin-like SH2 domain containing 1 TENS1 -3.458 -3.46 down 0.029759472 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 622 64778 FNDC3B fibronectin type III domain containing 3B affy_probe_2_Entrez 1 1 24 2.77 up 1 0 1/0 2.77 1 24 2.77 2.77 218618_s_at 218618_s_at hypothetical protein FLJ23399 -2.77 2.77 up 0.000021 FA FTC 12 12 provided by authors 15713710 24 33 1463 64838 FNDC4 fibronectin type III domain containing 4 Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 32 8.43 up 1 0 1/0 8.43 1 32 8.43 8.43 Likely orthologue of mouse fibronectin type III repeat containing protein 1 FRCP1 3.075 8.43 up PTC Norm 16 16 publication 15735049 13 20 887 79017 C7orf24 chromosome 7 open reading frame 24 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 AI620381 AI620381 Hypothetical protein MCG3077 McG3077 up FTC FA 9 10 publication 12738736 9 14 683 79695 GALNT12 UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 12 (GalNAc-T12) affy_probe_2_Entrez 1 1 24 4.14 up 1 0 1/0 4.14 1 24 4.14 4.14 218885_s_at 218885_s_at hypothetical protein FLJ21212 -4.14 4.14 up 0.000078 FA FTC 12 12 provided by authors 15713710 25 34 1755 79698 ZMAT4 zinc finger, matrin type 4 affy_probe_2_Entrez 1 1 55 -6.19 down 1 0 0/1 -6.19 1 55 -6.19 -6.19 219877_at 219877_at hypothetical protein FLJ13842 FLJ13842 -6.189 -6.19 down 0.000543866 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1614 79745 RSNL2 restin-like 2 affy_probe_2_Entrez 1 1 55 2.51 up 1 0 1/0 2.51 1 55 2.51 2.51 219944_at 219944_at hypothetical protein FLJ21069 FLJ21069 2.511 2.51 up 0.015516611 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 11 18 768 79921 TCEAL4 transcription elongation factor A (SII)-like 4 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 AF271783 AF271783 NPD017 up ACL;ATC Norm 21 10 publication 15613457 25 34 1706 79953 C20orf39 chromosome 20 open reading frame 39 affy_probe_2_Entrez 1 1 55 -3.3 down 1 0 0/1 -3.3 1 55 -3.30 -3.30 219310_at 219310_at chromosome 20 open reading frame 39 C20orf39 -3.304 -3.30 down 1.67171E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1541 80157 FLJ21511 hypothetical protein FLJ21511 Gene_symbol_2_NCBI_Entrez 2 2 87 -11.76 down 2 0 0/2 -5.88 2 87 -4.64 -7.12 Hypothetical protein FLJ21511 FLJ21511 -2.215 -4.64 down PTC Norm 16 16 publication 15735049 25 34 1759 80157 FLJ21511 hypothetical protein FLJ21511 affy_probe_2_Entrez 2 2 87 -11.76 down 2 0 0/2 -5.88 2 87 -4.64 -7.12 220723_s_at 220723_s_at hypothetical protein FLJ21511 FLJ21511 -6.593 -6.59 down 0.000104549 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1766 80157 FLJ21511 hypothetical protein FLJ21511 affy_probe_2_Entrez 2 2 87 -11.76 down 2 0 0/2 -5.88 2 87 -4.64 -7.12 220724_at 220724_at hypothetical protein FLJ21511 FLJ21511 -7.115 -7.12 down 0.000193981 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 692 80204 FBXO11 F-box protein 11 affy_probe_2_Entrez 1 1 24 5 up 1 0 1/0 5 1 24 5 5 222119_s_at 222119_s_at vitiligo-associated protein VIT-1 -5 5 up 0.000029 FA FTC 12 12 provided by authors 15713710 9 14 682 80778 ZNF34 zinc finger protein 34 (KOX 32) affy_probe_2_Entrez 1 1 24 4.04 up 1 0 1/0 4.04 1 24 4.04 4.04 219801_at 219801_at hypothetical protein MGC10520 -4.04 4.04 up 0.000003 FA FTC 12 12 provided by authors 15713710 25 34 1604 81569 ACTL8 actin-like 8 affy_probe_2_Entrez 1 1 55 2.87 up 1 0 1/0 2.87 1 55 2.87 2.87 214957_at 214957_at actin like protein LOC81569 2.867 2.87 up 0.017874849 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 16 24 1236 81689 HBLD2 HESB like domain containing 2 Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 63 -1.89 down 1 0 0/1 -1.89 1 63 -1.89 -1.89 MGC4276 0.529411765 -1.89 down 0.0001 PTC;FVPTC FA;HN 32 31 publication 15087409 15 22 1058 81706 PPP1R14C protein phosphatase 1, regulatory (inhibitor) subunit 14C Gene_symbol_2_NCBI_Entrez 1 1 7 -5 down 1 0 0/1 -5 1 7 -5.00 -5.00 Protein phosphatase 1 regulatory (inhibitor) subunit 14C PPP1R14C 0.2 -5.00 down FTC FA 3 4 publication 15475448 25 34 1646 81839 VANGL1 vang-like 1 (van gogh, Drosophila) affy_probe_2_Entrez 1 1 55 -2.13 down 1 0 0/1 -2.13 1 55 -2.13 -2.13 219330_at 219330_at vang-like 1 (van gogh, Drosophila) VANGL1 -2.130 -2.13 down 0.000634148 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1689 83439 TCF7L1 transcription factor 7-like 1 (T-cell specific, HMG-box) affy_probe_2_Entrez 1 1 55 -2.93 down 1 0 0/1 -2.93 1 55 -2.93 -2.93 221016_s_at 221016_s_at transcription factor 7-like 1 (T-cell specific, HMG-box) /// transcription factor 7-like 1 (T-cell specific, HMG-box) TCF7L1 -2.931 -2.93 down 0.002847923 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1756 83468 GLT8D2 glycosyltransferase 8 domain containing 2 affy_probe_2_Entrez 1 1 55 -6.23 down 1 0 0/1 -6.23 1 55 -6.23 -6.23 221447_s_at 221447_s_at gycosyltransferase /// gycosyltransferase LOC83468 -6.227 -6.23 down 2.16432E-07 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 25 34 1696 83478 ARHGAP24 Rho GTPase activating protein 24 affy_probe_2_Entrez 1 1 55 -3.08 down 1 0 0/1 -3.08 1 55 -3.08 -3.08 221030_s_at 221030_s_at Rho GTPase activating protein 24 /// Rho GTPase activating protein 24 ARHGAP24 -3.085 -3.08 down 0.000138869 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 9 14 638 83483 PLVAP plasmalemma vesicle associated protein affy_probe_2_Entrez 1 1 24 3.09 up 1 0 1/0 3.09 1 24 3.09 3.09 221529_s_at 221529_s_at plasmalemma vesicle associated protein -3.09 3.09 up 0.000263 FA FTC 12 12 provided by authors 15713710 25 34 1644 84187 RP13-360B22.2 hypothetical protein FLJ22679 affy_probe_2_Entrez 1 1 55 -2.11 down 1 0 0/1 -2.11 1 55 -2.11 -2.11 220486_x_at 220486_x_at hypothetical protein FLJ22679 FLJ22679 -2.114 -2.11 down 0.025028009 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 19 32 1408 84525 HOP homeodomain-only protein tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 ATGACAGATG ATGACAGATG SMAP31/homeodomain only protein (HOP) up 0.0001 FVPTC Norm 1 1 publication 14715705 18 31 1358 84864 MINA MYC induced nuclear antigen clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 91 -4.63 down 2 0 0/2 -2.315 2 91 -2.23 -2.40 W27666 W27666 Mina53, a novel Myc target gene MINA53 2.4 -2.40 down FTC;PTC;FVPTC FA;HN 33 26 publication NOTE: This study seems very similar to Study #7 and may contain overlap in the tissue samples used. Waiting for author response on this matter. 15319714 24 33 1532 84864 MINA MYC induced nuclear antigen Gene_symbol_2_NCBI_Synonym_2_Entrez 2 2 91 -4.63 down 2 0 0/2 -2.315 2 91 -2.23 -2.40 Myc-induced nuclear antigen, 53 kDa MINA53 -1.16 -2.23 down PTC Norm 16 16 publication 15735049 25 34 1712 90627 STARD13 START domain containing 13 affy_probe_2_Entrez 1 1 55 -3.46 down 1 0 0/1 -3.46 1 55 -3.46 -3.46 213103_at 213103_at START domain containing 13 STARD13 -3.463 -3.46 down 3.5504E-06 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 19 32 1437 91746 YT521 splicing factor YT521-B tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 TAGTTGCACA TAGTTGCACA NoMatch B59 up 0.0245 FVPTC Norm 1 1 publication 14715705 25 34 1758 91851 CHRDL1 chordin-like 1 affy_probe_2_Entrez 1 1 55 -6.52 down 1 0 0/1 -6.52 1 55 -6.52 -6.52 209763_at 209763_at chordin-like 1 CHRDL1 -6.519 -6.52 down 0.001912108 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1534 92104 FLJ13946 hypothetical protein FLJ13946 Gene_symbol_2_NCBI_Entrez 1 1 32 -2.45 down 1 0 0/1 -2.45 1 32 -2.45 -2.45 Hypothetical protein FLJ13946 FLJ13946 -1.295 -2.45 down PTC Norm 16 16 publication 15735049 11 18 841 93659 CGB5 chorionic gonadotropin, beta polypeptide 5 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 AI160936 AI160936 IMAGE:1715637 30 similar to gb:J00117 choriogonadotropin b chain precursor down ACL;ATC Norm 21 10 publication 15613457 19 32 1440 94239 H2AFV H2A histone family, member V tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 down 1 0 0/1 0 0 0 0 0 TGGTGAAAAA TGGTGAAAAA NoMatch B44 down 0.0006 FVPTC Norm 1 1 publication 14715705 25 34 1677 114876 OSBPL1A oxysterol binding protein-like 1A affy_probe_2_Entrez 1 1 55 -2.73 down 1 0 0/1 -2.73 1 55 -2.73 -2.73 209485_s_at 209485_s_at oxysterol binding protein-like 1A OSBPL1A -2.726 -2.73 down 0.000496751 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 19 32 1418 114926 C8orf40 chromosome 8 open reading frame 40 tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 AACAGCTTTA AACAGCTTTA hypothetical protein BC013035 up 0.0245 FVPTC Norm 1 1 publication 14715705 11 18 755 114971 PTPMT1 protein tyrosine phosphatase, mitochondrial 1 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 up 1 0 1/0 0 0 0 0 0 AK096680 AK096680 FLJ39361 fis, clone PEBLM 2004733 up ACL;ATC Norm 21 10 publication 15613457 5 10 382 116496 C1orf24 chromosome 1 open reading frame 24 tag_2_refseq_or_mgc_2_Entrez 1 1 3 0 up 1 0 1/0 0 0 0 0 0 TATTTACTCT TATTTACTCT C1orf24 up yes FTC FA;Norm 1 2 publication 15085203 19 32 1429 121053 MGC40397 hypothetical protein MGC40397 tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 down 1 0 0/1 0 0 0 0 0 GCAAGCCCCA GCAAGCCCCA hypothetical protein MGC40397 down 0.0186 FVPTC Norm 1 1 publication 14715705 11 18 812 126208 LOC126208 hypothetical protein LOC126208 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 31 0 down 1 0 0/1 0 0 0 0 0 AF000560 AF000560 TTF-I interacting peptide 20 down ACL;ATC Norm 21 10 publication 15613457 9 14 685 140597 TCEAL2 transcription elongation factor A (SII)-like 2 affy_probe_2_Entrez 1 1 24 4.29 up 1 0 1/0 4.29 1 24 4.29 4.29 211276_at 211276_at my048 protein -4.29 4.29 up 0.003021 FA FTC 12 12 provided by authors 15713710 19 32 1428 146556 MGC45438 hypothetical protein MGC45438 tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 down 1 0 0/1 0 0 0 0 0 CCAGCTGCCT CCAGCTGCCT hypothetical protein MGC45438 down 0.0186 FVPTC Norm 1 1 publication 14715705 2 2 68 159013 CXorf38 chromosome X open reading frame 38 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 -8 down 1 0 0/1 -8 1 2 -8.00 -8.00 NM_144970 NM_144970 Hypothetical protein MGC39350 MGC39350 8 -8.00 down FCL Norm 1 1 publication 15785240 25 34 1726 166647 GPR125 G protein-coupled receptor 125 affy_probe_2_Entrez 1 1 55 -3.91 down 1 0 0/1 -3.91 1 55 -3.91 -3.91 210473_s_at 210473_s_at G protein-coupled receptor 125 GPR125 -3.908 -3.91 down 1.21446E-05 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 942 169611 OLFML2A olfactomedin-like 2A clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 down 1 0 0/1 0 0 0 0 0 AL050002 AL050002 IMAGE clone 3140802 down FTC FA 9 10 publication 12738736 2 2 83 197320 FLJ31875 hypothetical protein FLJ31875 clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 2 3.44 up 1 0 1/0 3.44 1 2 3.44 3.44 NM_182531 NM_182531 Hypothetical protein FLJ31875 FLJ31875 3.44 3.44 up FCL Norm 1 1 publication 15785240 19 32 1411 197370 NSMCE1 non-SMC element 1 homolog (S. cerevisiae) tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 ACCGCAGTGC ACCGCAGTGC insulin-like growth factor binding protein 4 up 0.0245 FVPTC Norm 1 1 publication 14715705 9 14 624 220988 HNRPA3 heterogeneous nuclear ribonucleoprotein A3 affy_probe_2_Entrez 1 1 24 2.82 up 1 0 1/0 2.82 1 24 2.82 2.82 211930_at 211930_at Homo sapiens mRNA; cDNA DKFZp686N1377 (from clone DKFZp686N1377) -2.82 2.82 up 0.00002 FA FTC 12 12 provided by authors 15713710 13 20 950 221395 GPR116 G protein-coupled receptor 116 clone_accession_2_NCBI_rna_accession_2_Entrez 2 2 43 3.08 even 1 1 1/1 3.08 1 24 3.08 3.08 AB018301 AB018301 KIAA0758 protein KIAA0758 down FTC FA 9 10 publication 12738736 9 14 636 221395 GPR116 G protein-coupled receptor 116 affy_probe_2_Entrez 2 2 43 3.08 even 1 1 1/1 3.08 1 24 3.08 3.08 212950_at 212950_at KIAA0758 protein -3.08 3.08 up 0.000297 FA FTC 12 12 provided by authors 15713710 25 34 1695 223117 SEMA3D sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D affy_probe_2_Entrez 1 1 55 -3.06 down 1 0 0/1 -3.06 1 55 -3.06 -3.06 215643_at 215643_at sema domain, immunoglobulin domain (Ig), short basic domain, secreted, (semaphorin) 3D SEMA3D -3.057 -3.06 down 2.98547E-07 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 13 20 885 283131 TncRNA trophoblast-derived noncoding RNA clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 19 0 up 1 0 1/0 0 0 0 0 0 AW006742 AW006742 Human clone 137308 mRNA partial cds up FTC FA 9 10 publication 12738736 25 34 1662 284244 LOC284244 hypothetical protein LOC284244 affy_probe_2_Entrez 1 1 55 -2.47 down 1 0 0/1 -2.47 1 55 -2.47 -2.47 214162_at 214162_at hypothetical protein LOC284244 LOC284244 -2.469 -2.47 down 0.013913616 PTC Norm 51 4 suppl. Materials Performed calculation of differential expression between PTC and Normal myself in excel. Included all 2fold changes with bonferonni corrected pvalue > 0.5 16007166 24 33 1526 375056 UNQ6077 AAAP6077 Gene_symbol_2_NCBI_Synonym_2_Entrez 1 1 32 -1.68 down 1 0 0/1 -1.68 1 32 -1.68 -1.68 C219-reactive peptide FLJ39207 -0.75 -1.68 down PTC Norm 16 16 publication 15735049 10 16 725 399563 FLJ43806 hypothetical protein FLJ43806 affy_probe_2_Entrez 1 1 14 -2.56 down 1 0 0/1 -2.56 1 14 -2.56 -2.56 37151_at 37151_at Clone 23836 mRNA sequence 20 -2.56 -2.56 down no PTC GT 8 6 publication 15515157 9 14 645 439921 MXRA7 matrix-remodelling associated 7 affy_probe_2_Entrez 1 1 24 3.15 up 1 0 1/0 3.15 1 24 3.15 3.15 212509_s_at 212509_s_at ESTs, Weakly similar to hypothetical protein FLJ22184 [Homo sapiens] [H.sapiens] -3.15 3.15 up 0.000001 FA FTC 12 12 provided by authors 15713710 10 16 720 439957 LOC439957 similar to Ig kappa chain V region (Z4) - human affy_probe_2_Entrez 1 1 14 -2.23 down 1 0 0/1 -2.23 1 14 -2.23 -2.23 31386_at 31386_at Human kappa immunoglobulin IGK -2.23 -2.23 down yes PTC GT 8 6 publication 15515157 19 32 1405 440270 LOC440270 golgin-67 tag_2_refseq_or_mgc_2_Entrez 1 1 2 0 up 1 0 1/0 0 0 0 0 0 ATCCTTTTAT ATCCTTTTAT golgin-67 up 0.0001 FVPTC Norm 1 1 publication 14715705 14 21 980 442472 LOC442472 similar to H2A-Bbd clone_accession_2_NCBI_rna_accession_2_Entrez 1 1 14 2.8 up 1 0 1/0 2.8 1 14 2.80 2.80 AA703660 AA703660 H2A histone family 2.8 2.80 up PTC Norm 7 7 publication 15041723