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  • Gene Set Enrichment Analysis

    Hi all,

    I have used the cummeRbund function findSimilar() to find the 10 most similar genes to the differentially expressed genes I identified using Cuffdiff. This used the Jensen-Shannon distance and produced a ranked ordered gene list which I now want to test for GO enrichment. The file looks like this:

    "XLOC_007917" 0
    "XLOC_008881" 0.00417099861122699
    "XLOC_017692" 0.0178758082512721
    "XLOC_008901" 0.0180682577435933
    "XLOC_014267" 0.0333227735282459
    "XLOC_013408" 0.0400392521794019
    "XLOC_013497" 0.0412541820119971
    "XLOC_010554" 0.0453928603025379
    "XLOC_000570" 0.0461264880687295
    "XLOC_010786" 0.0469577467848723

    I first searched manually for GO terms for each of the most similar genes but I'd like to do a more robust analysis. I am trying to run GSEA, the Java application from Broad Institute.

    I made my Ranked list file format (*.rnk) and now I have to choose a gene set database.

    I am working on a sponge species so I can't use the database already provided.

    How can I create my own gene sets database? What should it look like?

    Any tips or advice will be appreciated!

    Thanks

    Federico

  • #2
    Hi uqfgaiti,

    have a look at this link:

    For customized species, you can create your own gene set files for enrichment.

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