Up To Date Kegg Pathways And Genes List For Gsea

Question

[dradamfreeman]

HI ALl,

I'm wondering if anyone has an up to date KEGG datafile with lists of Genes, SNPs and Pathways I can use for GSEA?

I'm using SRT and a few other pathway analysis programs and I can only find old ones in dbSNP32 and HG18.

I'm unfortunately a nube, so I can throw data around but I have no idea how to use the KEGG / GO / Entrez dBs to find this data myself.

An e.g. of the files I have for SNP Ratio Test (SRT) from their download...

hsa00010    rs61487361
hsa00010    rs2286168
hsa00010    rs41275697

The others: GO, Kegg and Entrez at 1kb: http://bioinfo.utu.fi/biforcetoolbox/download-and-running-guide

Thanks to any and all for your help!

Adam

Answer 1

[Guangchuang Yu]

You may want to try clusterProfiler:

KEGG enrichment analysis with latest online data using clusterProfiler

Answer 2

[Sudeep]

To retrieve KEGG pathway mappings to genes you can use REST-style KEGG API.

This example will give you KEGG human pathway to Kegg gene ids. If you remove "hsa:" tag from kegg gene ids (2nd column) you will get the corresponding Entrez gene ids. I guess mapping pathways to SNPs in exonic and intronic region should be straight froward from this point, but mapping SNPs in intergenic region to genes and pathways might require some reading and experimentation

Answer 3

[andrew]

FYI... KEGG is no longer a "free" resource even for academics (except through the KEGG website, and even that, I believe. has restrictions on it's use). We offer a pathway analysis application called iPathwayGuide, that uses KEGG and allows you to map SNPs, Drugs, and miRNA targets directly on the pathway of interest. Currently this is offered as a gene-expression analysis tool, but we will be offering it as a browser in the next month or so.

iPathwayGuide is completely free to try. Each dataset you run comes with a 72-hour preview period. There is no obligation to buy anything. You can run as much data as you want. Oh... and we are an authorized KEGG service provider. I hope this helps.

Here is an image where the user is mapping SNPs directly on the pathway (red circle).