Question: Map genes to Reactome pathways
0
gravatar for joshf
3.1 years ago by
joshf20
Netherlands
joshf20 wrote:

I want to map a large list of genes (basically all of UCSC's known genes) to Reactome pathways. I tried using the UCSC Table Browser and it mapped a lot of the genes to pathways, but there's still a lot missing.
For example, I know the gene SETD2 plays a role in R-HSA-3214841, but according to the Table Browser it doesn't

On the Reactome download page there's a list of mapping files but oddly they don't include all the pathways that are in the 'complete list of pathways.txt' file.
Again, the example being that R-HSA-3214841 is only in the complete pathways file, NOT in any of the mapping files.

Anyone know how can map the remaining genes to pathways? Am I completely missing something?

 

reactome genes pathway • 1.0k views
ADD COMMENTlink modified 3.1 years ago by Jean-Karim Heriche18k • written 3.1 years ago by joshf20
1
gravatar for Jean-Karim Heriche
3.1 years ago by
EMBL Heidelberg, Germany
Jean-Karim Heriche18k wrote:

Use the UniProt to Reactome mapping file, R-HSA-3214841 is in there as well as its association with SETD2.

ADD COMMENTlink written 3.1 years ago by Jean-Karim Heriche18k

Ah, I see what I did wrong originally haha. I WAS completely missing something. thanks!

ADD REPLYlink written 3.1 years ago by joshf20
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