There is also Pathway Commons
Hi all,
I need a flat file, which has list of pathway names for all human and yeast proteins.
I searched in "KEGG MEDICUS on GenomeNet FTP" in the KEGG FTP site (http://www.kegg.jp/kegg/download/). But I could not find related information.
Can someone provide me related info/web resource?
Thanks in advance
2 answers
You can use the tool at http://www.genome.jp/kegg/tool/map_pathway1.html
Under "Search against", choose "Homo sapiens"
Under "Enter objects", enter the gene names in this format, example:
hsa:GABRG1
hsa:GABRA2
hsa:GABRA4
hsa:GABRB1
You could probably parse the result and write a script to turn it to a flat file with format "geneName, pathways"
This is the only way I can think of because you need to pay to access the KEGG ftp servers :(
I'm not sure what you plan to do with this file when you have it -- but remember when it comes to pathways in biology the bottom line is curation, curation, curation. There really isn't a good standardized naming convention for pathways and which genes that belong to them and when -- many are canonical "biochemical" pathways, or signal-transduction pathways -- and I would hazard that the membership of a gene in many/most pathways is very cell-type and context-specific (so membership is different from cell-type to cell-type during development vs adult life). I would also be cautious about assuming pathway membership in yeast would be equivalent to pathway membership in humans.
For some examples, you can get a limited set from NetPath. HPRD has a file of protein-protein interactions -- but without pathways "named" it seems, and the last release was 2010. BioGRID has their data available for download (and as a nice cytoscape plugin), but again -- the grouping genes into named pathways is up to curation.
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