Why is number of geneset present in MSigDB C2:CP:KEGG geneset different from the original KEGG pathway? · Biostar

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Why is number of geneset present in MSigDB C2:CP:KEGG geneset different from the original KEGG pathway?

Hello all, I was trying to do GSEA and then realized that MSigDB is showing only 186 genesets from C2:CP KEGG (http://software.broadinstitute.org/gsea/msigdb/collection_details.jsp#C2) while ~260actually genesets exist in the original KEGG pathway. Why are many genesets missing? And from where can we download the complete KEGG geneset (human)? Thanks in advance!

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written 8.1 years ago by mariet1051 •

There may be many reasons, but best not to speculate. I recommend that you contact the GSEA team: http://software.broadinstitute.org/gsea/contact.jsp

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written 8.1 years ago by Kevin Blighe

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