C2:CGP pathways being labelled as C2:CP pathways

[rauldiul]

Hi!

thanks for the great software.

I'm using the latest version (v7.5.1), and when I load the gene sets as such: sets <- as.data.frame(msigdbr(species = "Homo sapiens")), I have seen that there are some pathways labelled with gs_subcat == CP but which are actually from gs_subcat == CGP. One example are pathways from the NABA study: NABA_BASEMENT_MEMBRANES, NABA_MATRISOME, etc. These are listed as CGP pathways in the MSigDB website (e.g.: https://www.gsea-msigdb.org/gsea/msigdb/cards/NABA_MATRISOME).

What do you think could have happened for these CGP pathways to end up labelled as CP within msigdbr and do you think you can provide a solution for this?

thanks a lot!

[igordot]

The gene sets can change categories between different versions of MSigDB. Although NABA_MATRISOME is in CGP now, it used to be in CP (see archived gene set page).