How to map and visualize differentially expressed genes on KEGG pathways

Question

[seta]

Hi all experts,

I am looking for a tool for mapping and visualizing differentially expressed genes on KEGG pathways, so that up and down regulated genes highlight with different colors. I searched on net, but could not find a perfect tool. I tried Pathvisio software, but my issue with it was importing KEGG pathways into this tool. Could you please give me your comments and suggestions on this issue or introduce any tool?

Thanks

[nsmaan]

Liux, Others: My GE file (data.txt) has identification columns such as, ENTREZID, Genename, etc. and i also have logFC and pvalue and padj, for each gene. Could someone please give me headstart on how to use KeggExp, using this file? Thank you

[liux.bio]

You can follow the tutorial

Answer 1

[igor]

There are a few options, such as:

• clusterProfiler: https://www.bioconductor.org/packages/devel/bioc/vignettes/clusterProfiler/inst/doc/clusterProfiler.html

• Pathview: http://pathview.r-forge.r-project.org/

• Reactome: http://www.reactome.org/

• ReactomePA: https://www.bioconductor.org/packages/release/bioc/vignettes/ReactomePA/inst/doc/ReactomePA.html

[seta]

Thanks. Pathview sounds great, I'll try it.

Answer 2

[liux.bio]

Maybe you could try KeggExp. Here is a example for highlight differentially-expressed genes:

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For more information about KeggExp, see the post here

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PS: I am the author of KeggExp