Re: Firegoose > KEGG, valid genes not found

[Christopher Bare]

Hi Mike,

Sorry 'bout that. An example that we could reproduce would help diagnose the issue.

Thanks,

- Chris

On Saturday, April 6, 2013 5:10:09 PM UTC-7, Mike Starr wrote:

Dear gaggle-discuss,

When I paste a list of genes into Boss's Clipboard, Broadcast it to Firegoose, and then broadcast that NameList to KEGG, many genes are not found. When directly queried individually, the majority of these genes are found in KEGG. I am concerned b/c this flaw will greatly skew the analysis I am performing, in terms of which pathways are enriched in my data sets.

Mike

[Mike Starr]

Christopher,

I sincerely apologize. Firegoose > KEGG returns only genes that are in KEGG pathways. The issue, which I didn't realize at the time, is that most of the genes I'm entering are not in KEGG pathways. I sincerely thank you for the quick reply--too many bioinformatic software packages these days aren't supported.

On a related note, have you considered Gaggle functionality for Metacyc or other pathway databases? I realize that would be a grand undertaking, but so as to make my mistaken post not not worthwhile...

Best,

Mike