List of genes to list of pathways (no enrichment)

Question

[R.Blues]

Hello everyone,

First of all, I have searched similar topics and I have not found what I am looking for. Maybe I didnt search well enough, but... at least I tried, I swear! ^^

I have a list of genes with their respective Entrez IDs that I can convert to any ID needed, and I would like to know if it is possible to query each of them to a database (I am thinking on Reactome and Kegg, mainly). I do not want to do an enrichment analysis, I just want to know in which pathway(s) is involved each one of them, and to retrieve that information.

I would like to automatize this through a Python script. Is it possible? Which are the established solutions?

Thank you very much for your help.

Answer 1

[Newgene]

Since you prefer Python, you can use mygene module, which is a wrapper for MyGene.info web services.

import mygene 
mg = mygene.MyGeneInfo() 
xli = [1017, 1018, 695] 
out = mg.getgenes(xli, fields="name,symbol,pathways")

This should give you what you need.

[R.Blues]

Finally I decided to use mygene, and it worked really well. Thank you very much!!

I'm thinking of using data from COSMIC database too. I would love to use myvariant.info too for this, but it seems it is still developing, so I guess I will have to use the Ensembl API.

(I guess you are one of the involved in the development of mygene and myvariant, as I found you in Github :P, so... congratulations and good luck! :) )

[gtsueng]

The python client for myvariant.info just became available, and COSMIC is one of the data sources accessible with the client.

Answer 2

[Pierre Lindenbaum]

under: ftp://ftp.ncbi.nih.gov/pub/biosystems/CURRENT

============================================ 
biosystems_gene.gz   
============================================ 

This file lists associations between biosystems and Entrez Gene records
that represent biosystem components.

and

===============================================================================
DETAILS for bsid2info.gz: 
===============================================================================

This file lists infomation about particular biosystems.  It is
formatted as: 

Column 1: bsid of biosystem  
Column 2: source database of biosystem
Column 3: source database accession
Column 4: name
Column 5: type of biosystem
Column 6: taxonomic scope of biosystem
Column 7: NCBI taxid
Column 8: description of biosystem

[R.Blues]

Thank you VERY much. Ill take a look :)

Answer 3

[pixie@bioinfo]

For information retrieval, this website is very cool http://www.genome.jp/linkdb/ , and you can also make use of the APIs.

Answer 4

[EagleEye]

If you have list from Human. This will cluster your genes based on biological functions (GO, KEGG, REACTOME and BIOCARTA). You can try this: Gene Set Clustering based on Functional annotation (GeneSCF)

Answer 5

[GouthamAtla]

The wikipathways API will be useful.

the examples mentioned are similar to your question. Get all the pathways in which the desired gene is involved.