Gene Set Enrichment Analysis

uqfgaiti

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Join Date: Nov 2012

Posts: 13
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#1

Gene Set Enrichment Analysis

07-12-2013, 09:20 PM

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
Tags: cuffdiff, gene annotation, gene expression pattern
pengchy

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Join Date: Feb 2009

Posts: 116
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#2

07-12-2014, 03:14 PM

Hi uqfgaiti,

have a look at this link:

Access Denied

http://www.broadinstitute.org/gsea/doc/GSEAUserGuideTEXT.htm#_Preparing_Data_Files

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