Question: How to color KEGG pathway maps?
gravatar for mike.thon
3.2 years ago by
mike.thon30 wrote:

I'm trying to use the KEGG Mapper to create a colored pathway map based on gene expression. The tool seems to work on the provided test data but not on my data/pathway combination. I select my desired pathway in the first box (zma00940) and then select my data file, which has the following genes and colors:

#zma    test
zma:100381820   #ff0000
zma:100273579   #ff0000
zma:103627433   #ff0000
zma:542166  #ff0000
zma:542258  #ff0000

That data set should color a few genes red. When I click the exec button I am shown the standard pathway map with none of my coloring. Can anyone see what I'm doing wrong?

kegg • 3.3k views
ADD COMMENTlink written 3.2 years ago by mike.thon30

It works fine for me with your data. Please check that your file is tab delimited. I simply copied your data into a file, edited it to make it tab delimited, and submitted it to the service. The resulting map had some proteins highlighted in red.

ADD REPLYlink written 3.2 years ago by Lars Juhl Jensen11k

Thanks! I just discovered my text editor was set to auto-expand tabs, converting them to spaces. Now its working.

ADD REPLYlink written 3.2 years ago by mike.thon30
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