Comparison of brain tissues from the Allen Brain Atlas Initiative


Project information:

Project name: 'AllenBrain'

EnsEMBL version: 57

UCSC build: hg19

ALEXA-Seq database: hs_57_37b

Species: Homo_sapiens (Human)

Lanes of data analysed: 18

Library count: 6

Comparisons defined: 3


Library statistics (link to library summary):

HS1810 (Frontal_mRNA)

HS1811 (Amygdala_mRNA)

HS1812 (Frontal_Ribo)

HS1813 (Amygdala_Ribo)

HS1814 (Frontal_Ampl)

HS1815 (Amygdala_Ampl)


Download package of all results files: AllenBrain_ResultFiles.tar.gz


View candidate gene lists for each comparison (DE+AE genes, AE genes only, Gains only, Losses only):

HS1811_vs_HS1810 (Amygdala_mRNA_vs_Frontal_mRNA)

HS1813_vs_HS1812 (Amygdala_Ribo_vs_Frontal_Ribo)

HS1815_vs_HS1814 (Amygdala_Ampl_vs_Frontal_Ampl)


View candidate peptide lists (peptides corresponding to: junction gains, junction losses, exon+junction gains, exon+junction losses):

HS1811_vs_HS1810 (Amygdala_mRNA_vs_Frontal_mRNA)

HS1813_vs_HS1812 (Amygdala_Ribo_vs_Frontal_Ribo)

HS1815_vs_HS1814 (Amygdala_Ampl_vs_Frontal_Ampl)


Summary of expressed, differentially expressed and alternatively expressed features:

The following table summarizes the expression, differential expression and alternative expression of each feature type (exons, junctions, introns, etc.) for all EnsEMBL loci. It does this by providing links to lists of: the most highly abundant expressed (EXP) features, all significant differentially expressed (DE) features and all significant alternatively expressed (AE) features. Click on an icon to view these lists for the desired feature type. The number of features is enumerated beneath each icon. Note that for EXP tables, only the top 1% of expressed features will be summarized. Example 1: to see the most highly expressed exons in each library, click the 'EXP' icon in the 'ExonRegion' row of the table. Example 2: to view a ranked list of significant differentially expressed transcripts, click the 'DE' icon in the 'Transcript row of the table. Example 3: to view a ranked list of alternatively expressed, novel exon-exon junctions click the 'AE' icon in the 'NovelJunction' row of the table. For a detailed description of the feature types and how the ALEXA-Seq data viewer works, refer to our manuscript. Note that AE and DE events are summarized individually for each feature type. Since alternative expression is determined relative to gene level expression, the AE analysis is not applicable (N/A) for the gene and intergenic feature rows of this table. To view data for a specific gene, use the 'SEARCH' link above.


Data TypeExpression
(All libraries)
Differential Expression
(All comparisons)
Alternative Expression
(Amygdala_mRNA_vs_Frontal_mRNA)
Alternative Expression
(Amygdala_Ribo_vs_Frontal_Ribo)
Alternative Expression
(Amygdala_Ampl_vs_Frontal_Ampl)
GeneExpression report for Gene
(16,622)
Differential Expression report for Gene
(6,932)
N/AN/AN/A
TranscriptExpression report for Transcript
(21,310)
Differential Expression report for Transcript
(5,952)
Alternative Expression report for Transcript
(645)
Alternative Expression report for Transcript
(290)
Alternative Expression report for Transcript
(626)
ExonRegionExpression report for ExonRegion
(224,987)
Differential Expression report for ExonRegion
(63,342)
Alternative Expression report for ExonRegion
(8,397)
Alternative Expression report for ExonRegion
(3,570)
Alternative Expression report for ExonRegion
(10,960)
JunctionExpression report for Junction
(155,700)
Differential Expression report for Junction
(31,489)
Alternative Expression report for Junction
(10,452)
Alternative Expression report for Junction
(5,178)
Alternative Expression report for Junction
(12,119)
KnownJunctionExpression report for KnownJunction
(150,400)
Differential Expression report for KnownJunction
(31,355)
Alternative Expression report for KnownJunction
(10,252)
Alternative Expression report for KnownJunction
(5,093)
Alternative Expression report for KnownJunction
(11,965)
NovelJunctionExpression report for NovelJunction
(5,300)
Differential Expression report for NovelJunction
(174)
Alternative Expression report for NovelJunction
(160)
Alternative Expression report for NovelJunction
(87)
Alternative Expression report for NovelJunction
(205)
BoundaryExpression report for Boundary
(144,079)
Differential Expression report for Boundary
(15,658)
Alternative Expression report for Boundary
(6,568)
Alternative Expression report for Boundary
(2,996)
Alternative Expression report for Boundary
(5,734)
KnownBoundaryExpression report for KnownBoundary
(54,810)
Differential Expression report for KnownBoundary
(11,159)
Alternative Expression report for KnownBoundary
(3,440)
Alternative Expression report for KnownBoundary
(1,501)
Alternative Expression report for KnownBoundary
(2,920)
NovelBoundaryExpression report for NovelBoundary
(89,269)
Differential Expression report for NovelBoundary
(4,875)
Alternative Expression report for NovelBoundary
(2,952)
Alternative Expression report for NovelBoundary
(1,418)
Alternative Expression report for NovelBoundary
(2,938)
IntronExpression report for Intron
(10,866)
Differential Expression report for Intron
(264)
Alternative Expression report for Intron
(111)
Alternative Expression report for Intron
(30)
Alternative Expression report for Intron
(169)
ActiveIntronRegionExpression report for ActiveIntronRegion
(39,849)
Differential Expression report for ActiveIntronRegion
(3,118)
Alternative Expression report for ActiveIntronRegion
(716)
Alternative Expression report for ActiveIntronRegion
(449)
Alternative Expression report for ActiveIntronRegion
(1,929)
SilentIntronRegionExpression report for SilentIntronRegion
(20,397)
Differential Expression report for SilentIntronRegion
(659)
Alternative Expression report for SilentIntronRegion
(285)
Alternative Expression report for SilentIntronRegion
(159)
Alternative Expression report for SilentIntronRegion
(492)
IntergenicExpression report for Intergenic
(1,162)
Differential Expression report for Intergenic
(193)
N/AN/AN/A
ActiveIntergenicRegionExpression report for ActiveIntergenicRegion
(10,823)
Differential Expression report for ActiveIntergenicRegion
(1,153)
N/AN/AN/A
SilentIntergenicRegionExpression report for SilentIntergenicRegion
(4,941)
Differential Expression report for SilentIntergenicRegion
(302)
N/AN/AN/A