Find all genes in pathways associated with a target gene

Question

[jolespin]

Let's say you had gene_X and you wanted to find all the pathways (path_1, path_2, path_3) that gene_X plays a role in. Is there a way to find ALL GENES associated with (path_1, path_2, path_3)?

I am fluent in Python, so it would be cool if there was a package that could be used for that to do this. I am going to experiment with some modules that I found but I don't think they are able to do this.

Basically, I'd like to input gene_X and get back (gene_a, gene_b, gene_c, gene_d..gene_z) from (path_1, path_2, path_3)

Answer 1

[EagleEye]

Try geneSCF Gene Set Clustering based on Functional annotation (GeneSCF) For using your own reference annotations, follow these steps A: GO enrichment analysis using a Text file with all the genes and GO ids associat

[jolespin]

thanks, do you know of any tools that do this for you?

Answer 2

[Neilfws]

Is there a way to find ALL GENES associated with (path_1, path_2, path_3)?

There is, if you have a KEGG pathway ID, you can use the TogoWS REST service. For example, to retrieve genes in the human MAPK pathway:

curl http://togows.dbcls.jp/entry/pathway/hsa04010/genes.json