The following steps are designed for users to try out GoSurfer software in about 15 minutes.

1. Download files:
    (1) the main GoSurfer program (GS2-beta.exe)
    (2) a GO structure file, which describes the GO term relationships (GoPath.txt)
    (3) a Gene Information File, which describes the association between genes and GO terms (MOE430A_GoSufer-2006.xls)
    (4) a gene ID file. It includes Affymetrix probe set ids, which are supposed to represent genes that are highly expressed in prostate cancer (inputgeneIDs.txt)

2. Input files:
    (1) Open GS.exe
    (2) Use menu "File->Input". In the popup dialog, assign the inputgeneIDs.txt file as the first input file. Leave the radio button unchanged.
    (3) Click "Step 2", in the dialog. Assign MOE430A_GoSufer-2006.xls to the Gene information file, and GoPath.txt as the GO structure file. Leave the radio button unchanged.
    (4) Click OK.

3. View GO structure:
    (1) Use menu "View->Biological Process" to view the structure of all the GO terms that are associated with at least one gene in either of inputted gene lists.
    (2) Use arrow keys in the keyboard to adjust the GO structure

4. Highlight significant GO terms
    (1) Use menu "Analysis->Highlight". Choose the radio button of "Test for significance: highlight the nodes that are enriched by one input gene list". Leave the p-value unchanged. Click OK.
    (2) Use menu "View->Color and Width" to manipulate the graphical output.

5. More adventures
    (1) Double-click on a GO term. In the popup dialog, double-click on a LocusLink id, and then the internet explorer should be automatically opened and the webpage for this particular gene should be shown.
    (2) Use menu "File->Export->GO info" to export the information for every GO term, including the number of genes that are associated with it, the p-value for the whether it is enriched in a gene list, and so on.

This site was last updated 12/11/06