How to color KEGG pathway maps?

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7.9 years ago

mike.thon ▴ 30

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 • 6.6k views

ADD COMMENT • link 7.9 years ago by mike.thon ▴ 30

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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 REPLY • link 7.9 years ago by Lars Juhl Jensen 11k

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

ADD REPLY • link 7.9 years ago by mike.thon ▴ 30

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