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.
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.
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! :) )
The python client for myvariant.info just became available, and COSMIC is one of the data sources accessible with the client.
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
•
written
by
Pierre Lindenbaum
For information retrieval, this website is very cool http://www.genome.jp/linkdb/ , and you can also make use of the APIs.
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)
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.
•
written
by
GouthamAtla
Log in to answer this question.
