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Extracting pathway participants from Reactome/Wikipathways

Hello everyone! I'm a bit new to bioinformatics and I have a question on pathway databases.

I'm trying to find pathways that are activated by particular ligands and lead to changes in gene expression. I have a list of transcriptional factors of my interest and I would like to know which signalling pathways could activate them. Primarily I am interested in starting (receptors) and final (TFs) nodes. I know that CellCall has constructed such a dataframe using KEGG data, and I have already downloaded it.

I would like to make/get a similar table " receptor - TF - pathway identifier " with Wikipathways and Reactome data. Is there a way to do it? Thank you in advance!

reactome r pathway wikipathways
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updated by Giuseppe • Giuseppe • written by sleepystudent • sleepystudent

1 answer

The OmnipathR vignette is a good start, although I'm not sure that it includes WP and Reactome.

However, since those are also available on msigdbr (as part of the C2 collection) you can easily find an overlap between databases.

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written by Giuseppe • Giuseppe

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