Understanding KEGG-analysis; determination of activated pathways.

Question

[US-geek-012]

Hi guys,

I have performed KEGG analysis on a set significant peptides obtained from LPS-infected cells. I obtained several different pathways. My main question is how do I determine which pathways have been activated by LPS ?

Thanks.

[Benn]

Maybe you should explain more on how you did your analysis. I mean KEGG analysis can mean different things, what tool did you use?, what settings?

[US-geek-012]

Using WebGestalt 2013 version Analysis parameters: Id Type: uniprot_swissprot_accession, Ref Set: genome, i.e. entire entrez gene list, Statistic: Hypergeometric, Signficance Level: Top10, MTC: BH, Minimum: 2

[Benn]

Thanks for more details, I have never used these web tools so wouldn't know how to help. But hopefully some others have used it and can help you instead.

Good luck!

[sridhar56]

I guess you could try Lefse which will show you the differentially abundant features

Here is the link, https://huttenhower.sph.harvard.edu/galaxy/