Pathway Analysis In R

Question

[Avoks]

Hi all,

I was wondering if anyone could give some insight into the pathway analysis tools available in R. I would like to run an a pathway analysis to check for significantly enriched pathways using a genelist as the input. I did come across a gene2pathway package that is no longer supported and also a sigPathway tool but this is only available in the dev version of R.

I have read the post about tools to identify significantly altered pathways but it's been almost 10months and I would really appreciate any additional suggestions.

Thanks.

Avoks

Answer 1

[Gjain]

Hi,

KEGGgraph package

is one of R packages which will let you interface between KEGG pathways and graph modeling in R.

Here is the documentation: http://www.bioconductor.org/packages/2.6/bioc//vignettes/KEGGgraph/inst/doc/KEGGgraph.pdf

hope this helps.

[Martin Morgan]

The data in Bioconductor KEGG.db is a snapshot from before the subscription period, and is slowly becoming out-of-date; loading KEGG.db in a recent R / Bioconductor displays a prominent message about this. Other pathway tools work with GO.db, Reactome.db, or arbitrary gene sets. There are also facilities for interaction with Cytoscape.

[seidel]

Is this package affected by the recently required KEGG license subscription? The ftp site referenced int he docs is no longer accessible.

[Avoks]

Thanks a bunch, I'll check it out.

Answer 2

[Sean Davis]

You might check this list, available using the biocViews functionality from Bioconductor:

Pathway BiocViews

Also, sigPathway has been available since R-2.13 at least. Sounds like you might have to upgrade your R installation.

http://bioconductor.org/packages/2.9/bioc/html/sigPathway.html

[Avoks]

Thanks Sean, I now have.

Answer 3

[montoya.oscar]

Take a look at clusterProfiler, DOSE, and STRINGdb packages, all in Bioconductor.

Answer 4

[murphy.charlesj]

I've recently come across ReactomePA. Just supply Entrez gene IDs for pathway enrichment analysis using Reactome pathway database.

http://www.bioconductor.org/packages/devel/bioc/html/ReactomePA.html

Answer 5

[Qdjm]

Have you tried the GOstats package in Bioconductor?

[Avoks]

No, I haven't but will do. Thanks.

Answer 6

[Larry_Parnell]

I like g:Profiler and the g:GOSt tool, which performs statistical enrichment analysis to provide interpretation of gene lists, using gene ontology terms, biological pathways, regulatory motifs of transcription factors and microRNAs, human disease annotations and protein-protein interactions. I use it via web interface on an occasional basis. I have just noticed that there is an R package available.

[Avoks]

Thanks Larry. I will download the R package and try it out as well.

Answer 7

[theobroma22]

If you can get the Entrez IDs for your genelist I recommend the signaling pathway impact analysis aka SPIA bioconductor package.