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KEGG pathway maps

Hey guys,

I am tying to map the genes that are differentially expressed in RNA-Seq onto KEGG metabolic map. I have got the KO numbers of the differentially expressed genes, so can anyone give me an example of the particular formats of how you do multiple KO number pathway search and coloring in KEGG? Also, can anyone help me to show metabolic pathways that do not belong together on the same map (similar to a zoom-out view)? like Fig.3 in this paper:

http://mbio.asm.org/content/5/2/e01012-14.full

Thank you sooo much!

kegg rna-seq
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updated by liux.bio liux.bio • written by dazhudou1122 dazhudou1122

6 answers

Give a look to the Vanted program

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written by Antonio R. Franco Antonio R. Franco

The Bioconductor packages gage and pathview will produce kegg pathway maps, but as far as I know, only for one pathway at a time.

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written by mastal511 mastal511

kegga in limma, MAGENA ?

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written by ssv.bio ssv.bio

I think that pathview should do the job. There is also a R package http://www.bioconductor.org/packages/release/bioc/html/pathview.html

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written by dago dago

try clusterProfiler very easy to implement.

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written by Prasad Prasad

Try KeggExp. It highlights differentially-expressed genes on Kegg pathway map. enter image description here

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written by liux.bio liux.bio

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