Msigdb GO:BP
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4 weeks ago
AriBo • 0

Hi all, a couple of months ago I created a "matrix" to subselect "gene set name" and "gene symbol" from msigdbr. I used this command:

genes <- msigdbr(species = "Mus musculus", category = "C5", subcategory ="GO:BP" )  %>% dplyr::select(gs_name, gene_symbol)

Today I'm trying to replicate the same matrix using the same script but it doesn't work. In particular it creates a matrix as expected but I can't find some gene set that I used two months ago (e.g. the gene set named "GOBP_CHROMATIN_SILENCING"). Is there someone who is having the same problem? Is it a problem related to different versions?

Thanks, AriBo

msigdb • 121 views
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Entering edit mode
4 weeks ago
igor 12k

This looks like a version-related issue. GOBP_CHROMATIN_SILENCING is not in the latest version of MSigDB.

You can check the gene sets that are present in the current version here: http://www.gsea-msigdb.org/gsea/msigdb/genesets.jsp

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