Question: List Of Pathway Names For Each Gene/Protein
1
gravatar for I am
7.9 years ago by
I am80
United States
I am80 wrote:

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

pathway gene • 3.4k views
ADD COMMENTlink modified 20 months ago by Biostar ♦♦ 20 • written 7.9 years ago by I am80
1
gravatar for Justin
7.9 years ago by
Justin450
United States
Justin450 wrote:

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 :(

ADD COMMENTlink written 7.9 years ago by Justin450
1
gravatar for Alex Paciorkowski
7.9 years ago by
Rochester, NY USA
Alex Paciorkowski3.4k wrote:

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.

ADD COMMENTlink written 7.9 years ago by Alex Paciorkowski3.4k

There is also Pathway Commons

ADD REPLYlink written 7.9 years ago by Steve Lianoglou5.1k
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