DISCOVERYspace Tutorial

Scenario 1:

I have installed the SAGE plugin, and I have a cancer library and a normal library loaded. I would like to see how genes involved in angiogenesis are regulated in the expression profile.

Remember, there are multiple ways of manipulating biological data and using the application to get the answer you're looking for. Below is one method of answering the question:

Step 1: Retrieve BIOCARTA Angiogenesis-Related Pathways

Click on the KDOM toolbar's "Pathway" button, click on "BIOCARTA". A "Create Dataset" dialog will appear. You can choose to search any of these fields ("identifier", "name", and "description"). Enter the word "angiogenesis" into the text field beside "Description". Click the "Search" button beside the text field.

Step 2: Get All of the Genes In The Pathways

Remember, you can drag a single Biocarta entry from the Discovery Viewer onto the work area, and you'll see a picture of the pathway and it's associated genes.

However, here we'll just get all of the genes for all angiogenesis-related pathways at once. Click on "Genes" on the KDOM toolbar, and right-drag "Human Unigene" onto the Discovery Viewer showing the pathways (there was two when I tried this). Another column, titled "Human Unigene" will appear and a number of combo boxes will be displayed showing all of the genes in each pathway.

Step 3: Isolate the Genes

Let's remove the genes and put them in their own Discovery Viewer. Right-drag the "Human Unigene" column header onto the work area. A new Discovery Viewer will appear listing all of the Human Unigene entries. At this point, you could choose to save this set of genes into "Knowledge XML", so that later you could load this set of genes into the application for a subsequent analysis.

Step 4: Tag Map the Genes

We need to know what SAGE tags correspond to each of these genes. Click on the KDOM toolbar button "SAGE Tags" and right-drag "Tags" onto the Human Unigene entries showing in the Discovery Viewer.

Step 5: Isolate the Tags

Lets compile a list of these putative tags by right-dragging the "Tags" column header onto the work area. You will now have a new Discovery Viewer showing our tags of interest.

At this point, you could drag the "Human Unigene" KDOM toolbar option back onto the tags to see which mappings are ambiguous. But we'll just pretend all of the mappings are great.

Step 6: See the Regulation of the Tags

We have two options here: we can drop the KDOM toolbar option ( SAGE Tags > Comparison ) onto the list of tags to see the raw data, but we'll do something a bit more visually appealing.

Open the 2D contour view for the expression profile. You'll see a plot of the expression profile for your libraries. Select all of the tags in the Discovery Viewer (you can manually click them all, or click the Discovery Viewer menu option Select > Select All Rows). Right drag the entries onto the contour plot.

Hurrah! We can see how those tags appear in the expression profile by viewing the highlighted dots.