KEGG pathway gene association data

superligang · 03-07-2011, 05:14 PM

I am trying to manually calculate the pathway enrichment for some genes. I have downloaded the panther and reactome data files which have the pathway annotations for genes. However, I couldn't find such files for KEGG pathway database. The one I downloaded from ftp://ftp.genome.jp/pub/kegg/pathway/pathway consists of only the descriptions of each pathway without the gene list. Could someone point me to the link of such files for KEGG?

I have also tried the KEGG python api, but I couldn't get a list returned with the following codes,

from SOAPpy import WSDL
wsdl = 'http://soap.genome.jp/KEGG.wsdl'
serv = WSDL.Proxy(wsdl)
serv.get_pathways_by_genes(['ENSG00000120328'])
serv.get_pathways_by_genes(['ENST00000361510'])
serv.get_pathways_by_genes(['OPA1'])

It did return a pathway list way by using gene names like,
serv.get_pathways_by_genes(['eco:b0077' , 'eco:b0078'])

But my gene names are either Ensembl gene id or official gene symbol. Is there a way do find the correspondence between this kind of eco gene and Ensembl gene?

Thanks

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
Pathway mining	scami	Bioinformatics	22	09-14-2012 06:07 AM
Pathway analysis recommendations?	Pesto	Bioinformatics	5	05-25-2012 11:55 AM
pathways API KEGG	svl	Bioinformatics	5	02-10-2011 02:37 PM
Pathway Analysis packages for microArray	BioSlayer	Bioinformatics	6	07-27-2010 06:29 AM

03-07-2011, 05:14 PM	#1
superligang Member Location: Los Angeles Join Date: Mar 2010 Posts: 12	KEGG pathway gene association data I am trying to manually calculate the pathway enrichment for some genes. I have downloaded the panther and reactome data files which have the pathway annotations for genes. However, I couldn't find such files for KEGG pathway database. The one I downloaded from ftp://ftp.genome.jp/pub/kegg/pathway/pathway consists of only the descriptions of each pathway without the gene list. Could someone point me to the link of such files for KEGG? I have also tried the KEGG python api, but I couldn't get a list returned with the following codes, from SOAPpy import WSDL wsdl = 'http://soap.genome.jp/KEGG.wsdl' serv = WSDL.Proxy(wsdl) serv.get_pathways_by_genes(['ENSG00000120328']) serv.get_pathways_by_genes(['ENST00000361510']) serv.get_pathways_by_genes(['OPA1']) It did return a pathway list way by using gene names like, serv.get_pathways_by_genes(['eco:b0077' , 'eco:b0078']) But my gene names are either Ensembl gene id or official gene symbol. Is there a way do find the correspondence between this kind of eco gene and Ensembl gene? Thanks