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Old 07-12-2013, 10:20 PM   #1
Location: Australia, Brisbane

Join Date: Nov 2012
Posts: 13
Default 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!


uqfgaiti is offline   Reply With Quote
Old 07-12-2014, 04:14 PM   #2
Senior Member
Location: China

Join Date: Feb 2009
Posts: 116

Hi uqfgaiti,

have a look at this link:
For customized species, you can create your own gene set files for enrichment.
pengchy is offline   Reply With Quote

cuffdiff, gene annotation, gene expression pattern

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