KEGG pathway maps

Question

[dazhudou1122]

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!

Answer 1

[Antonio R. Franco]

Give a look to the Vanted program

Answer 2

[mastal511]

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

Answer 3

[ssv.bio]

kegga in limma, MAGENA ?

Answer 4

[dago]

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

Answer 5

[Prasad]

try clusterProfiler very easy to implement.

Answer 6

[liux.bio]

Try KeggExp. It highlights differentially-expressed genes on Kegg pathway map.