Question: Understanding KEGG-analysis; determination of activated pathways.
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gravatar for US-geek-012
2.2 years ago by
US-geek-0120 wrote:

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.

ADD COMMENTlink written 2.2 years ago by US-geek-0120

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?

ADD REPLYlink written 2.2 years ago by Benn6.6k

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

ADD REPLYlink written 2.2 years ago by US-geek-0120

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!

ADD REPLYlink written 2.2 years ago by Benn6.6k

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

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

ADD REPLYlink written 2.2 years ago by sridhar56100
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