List of genes to list of pathways (no enrichment)
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7.0 years ago
R.Blues ▴ 130

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.

genes pathways python reactome kegg • 2.7k views
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7.0 years ago
Newgene ▴ 360

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.

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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! :) )

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

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7.0 years ago

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
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Thank you VERY much. Ill take a look :)

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7.0 years ago
pixie@bioinfo ★ 1.4k

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

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7.0 years ago
EagleEye 7.0k

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)

 

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7.0 years ago

The wikipathways API will be useful. 

http://www.wikipathways.org/index.php/Help:WikiPathways_Webservice

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

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