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Reactome Pathway View With Colored Genes

Hi community

I am looking for an option to view a pathway in Reactome with my genes of interest colored/marked. Does anybody know how this is done easily?

The only solution could find until now is, to downlaod the svg via webservice and do the coloring myself. But there has to be a more automatic way, no?

Thanks for any hints! Michi

pathway
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updated by Robin Haw Robin Haw • written by Michi Michi

Ok thanks. I can fake some expression, but still not very automatic ;-)

• 0 views • link
written by Michi Michi

2 answers

Hi Michi,

You can use the Analyse Expression Data feature to view a pathway in Reactome with your genes of interest colored/marked. If you would like to discuss this further, please email me at Reactome [help at reactome.org].

Robin

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written by Robin Haw Robin Haw

Although is not in Reactome, you can do this relatively easily using SRI's Pathway Tools software, either using the standalone version:

http://bioinformatics.ai.sri.com/ptools/

or through the web interface:

http://biocyc.org/ECOLI/new-image?type=OVERVIEW&force=t

(you should see a link with something like "Omics Viewer: Paint omics data onto this diagram"). Although the link I pasted here is for E.coli, you can change to the other biocyc databases for other organisms and achieve the same. The standalone version, for which you need an academic license, is much more flexible and I think it even accepts time series.

Pathway Tools is the engine in which all the BioCyc/MetaCyc/EcoCyc databases run.

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updated by Ram Ram • written by Pablacious Pablacious

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