r - Gene Set Enrichment Analysis -

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i have used cummerbund function findsimilar() find 10 similar genes differentially expressed genes identified using cuffdiff. used jensen-shannon distance , produced ranked ordered gene list want test go enrichment. file looks 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 go terms each of similar genes i'd more robust analysis. trying run gsea, java application broad institute.

i made ranked list file format (*.rnk) , have choose gene set database.

i working on sponge species can't use database provided.

how can create own gene sets database? should like?

my strategy different after assisted assembly. extract sequences of newly discovered genes using cufflinks, find cds, blast, , go terms. option use genes have known ids , use gprofiler enrichment analysis. example, can free trial of blast2go analyses. can install databases locally , blast faster. can enrichment analyses blast2go. can use install instance of galaxy , blast2go tool shed repository.


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