Question: Assigning Pathway Type to MSigDB gene sets
1
gravatar for BioStarUser99
4.0 years ago by
United States
BioStarUser9930 wrote:

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 (pub med 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!

 

 

 

ADD COMMENTlink modified 4.0 years ago by hfang.shanghai140 • written 4.0 years ago by BioStarUser9930
0
gravatar for Chris Evelo
4.0 years ago by
Chris Evelo9.9k
Maastricht, The Netherlands
Chris Evelo9.9k wrote:

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.

ADD COMMENTlink written 4.0 years ago by Chris Evelo9.9k
0
gravatar for hfang.shanghai
4.0 years ago by
United Kingdom
hfang.shanghai140 wrote:

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

ADD COMMENTlink written 4.0 years ago by hfang.shanghai140
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