List Of Pathway Names For Each Gene/Protein

Question

[I am]

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

Answer 1

[Justin]

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 :(

Answer 2

[Alex Paciorkowski]

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.

[Steve Lianoglou]

There is also Pathway Commons