Reactome Pathway View With Colored Genes

Question

[Michi]

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

[Michael]

Look here.

[Michi]

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

Answer 1

[Robin Haw]

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

Answer 2

[Pablacious]

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.