How To Do Pathway Analysis For Bacteria With David Or Other Tools

Question

[ana.l.wang]

I'm trying to do some pathway analysis of some of mass spec data of bacterial proteins. Is there some way to analyze a large list of them all at once? I have been playing with DAVID today, but it does not recognize what I am plugging in. I am plugging in locus IDs (ex: ZP_06090800.1), but DAVID does not recognize this format... I've tried almost all of the options in the drop-down menu, and none of them are working. I also can't figure out a way to go from the locus information to an actual gene name. Any ideas of other sites I can use to do this?

[Egon Willighagen]

Have you had a look at PathVisio? I am not sure if enough bacteria pathways are in WikiPathways, but you can check... If not mistaken, you can also load the KEGG pathways...

Answer 1

[ana.l.wang]

I'll give it a try. Where do I download the KEGG pathways?

[Egon Willighagen]

Check on this page: http://www.wikipathways.org/index.php/Download_Pathways I have not done this myself yet, so if it does not work, please ask on the mailing list: http://www.wikipathways.org/index.php/Contact_Us

Answer 2

[mail2smn07]

Please try ShinyGO.net