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 similar files for the KEGG pathway database.
The one I downloaded from ftp://ftp.genome.jp/pub/kegg/pathway/pathway consists of only the descriptions for each pathway without the gene list. Could someone point me to the link of a gene pathway association file 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 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?