Question: Pathway enrichment and analysis of mice gene sets in R platform
0
gravatar for slg.manti
12 months ago by
slg.manti0
slg.manti0 wrote:

I am working on RNA-Seq data of mice samples. Is there a R package for pathway(KEGG,Biocarta) enrichment and analysis for mice specific genesets?

ADD COMMENTlink modified 12 months ago by caggtaagtat930 • written 12 months ago by slg.manti0

Yes there are, what have you tried?

ADD REPLYlink written 12 months ago by Benn7.9k

I tried pathfindR . But it is not working due to default Human setup.

ADD REPLYlink written 12 months ago by slg.manti0
1

If you want to stick to pathfindR, you can use a custom dataset which you can get from biomaRt. I haven't tried it, but this describes how to do it.

Another option is to use GOseq, you can use KEGG and REACTOME datasets as well (I think there is a example in the manual with KEGG data).

ADD REPLYlink written 12 months ago by Benn7.9k

I got the custom genesets and custom pathways mice specific using KEGGREST package. I also need Protein-protein interaction network path mice specific. Is there any package for that?

ADD REPLYlink written 12 months ago by slg.manti0

Most popular ppi database is string, there is an R package called STRINGdb, but I am not sure if you can use that similar as the genesets/pathways.

ADD REPLYlink modified 12 months ago • written 12 months ago by Benn7.9k

I recommend you to use webgestalt, personally I think it works even better and easier than R packages.

ADD REPLYlink written 12 months ago by Buffo1.8k
1
gravatar for caggtaagtat
12 months ago by
caggtaagtat930
caggtaagtat930 wrote:

Hi, I like the EGESA package, which combines a set of already existing tools, into one output.

ADD COMMENTlink written 12 months ago by caggtaagtat930
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