Assigning Pathway Type to MSigDB gene sets

Question

[BioStarUser99]

I'm doing an analysis that requires the stratification of pathways from the C2/C5/C7 set of the molecular signatures database (http://www.broadinstitute.org/gsea/msigdb) to one of the following pathways: regulation, signaling, or metabolic. My current approach is to use the pathway names (they are from biocarta, KEGG, reactome, and PID,etc) to assign to signaling pathways as those that contain the strings "SIGNAL" "ERK","MAPK"; metabolic pathways as those that contain "METABOL", "CATABOL", "GLYCO","PENTOSE"; and regulatory pathways as those that contain "REGULAT", "UPREG", "ACTIV", or "INHIBI". Of course this is a "first-order" approximation!

Does anyone have an example of a method (pubmed id / with provided R code) that uses enrichment of GO terms to assign a gene set to one (the dominant one) of these types of pathways?

Thanks!

Answer 1

[Chris Evelo]

At WikiPathways we use the Pathway Ontology to classify pathway. Since WikiPathways pathways are included in the MSigDB sets (or are at least they were last time I checked) that might be useful to you. Some other resources like Reactome do the same thing, or they use a mixture of the pathway ontology and the gene ontology. You probably best look up these things at the source for the pathways you use, which is also a nice opportunity to check whether MSigDB has the latest pathways.

Answer 2

[hfang.shanghai]

Maybe irrelevant but you may look at 'http://supfam.org/dnet/dGSEA.html' in an R package 'dnet'.