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Old 03-07-2011, 04:14 PM   #1
superligang
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Location: Los Angeles

Join Date: Mar 2010
Posts: 12
Default 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
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