Question: How to map and visualize differentially expressed genes on KEGG pathways
2
gravatar for seta
4.1 years ago by
seta1.3k
Sweden
seta1.3k wrote:

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

ADD COMMENTlink modified 18 months ago by nsmaan10 • written 4.1 years ago by seta1.3k

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

ADD REPLYlink written 18 months ago by nsmaan10

You can follow the tutorial

ADD REPLYlink written 17 months ago by liux.bio340
3
gravatar for igor
4.1 years ago by
igor11k
United States
igor11k wrote:

There are a few options, such as:

ADD COMMENTlink written 4.1 years ago by igor11k

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

ADD REPLYlink written 4.1 years ago by seta1.3k
0
gravatar for liux.bio
2.2 years ago by
liux.bio340
China
liux.bio340 wrote:

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


For more information about KeggExp, see the post here


PS: I am the author of KeggExp

ADD COMMENTlink modified 18 months ago • written 2.2 years ago by liux.bio340
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