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Find all genes in pathways associated with a target gene

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)

gene pathway genome kegg systems-biology
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updated by Ram Ram • written by jolespin jolespin

2 answers

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
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written by EagleEye EagleEye

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

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updated by Ram Ram • written by jolespin jolespin

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
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updated by Ram Ram • written by Neilfws Neilfws

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