Gene expression differences- network or pathway analysis

Question

[datanerd]

HI all,

I have a set of gene expression dataset from 3 different disorders. I know i can find similarities using co expression analysis. But is there a way to find differences (function / network/pathway) between datasets? And how do I accomplish this. Maybe most variable genes? Please help with ideas or any papers.

Thanks so much!

Mamta

Answer 1

[Deepak Tanwar]

Mamta, You need WGCNA

Meta-analyses of data from two (or more) microarray data sets

That's all you need.

[datanerd]

Thanks for the quick reply.

I looked at this. Iam not sure so just confirming , can WGCNA be used for highlight differences too?

[Deepak Tanwar]

Did you mean differences between pathways enriched in 3 different datasets?

[datanerd]

yes sort of. Like what are the key differences between the three dataset. Guess I have to do a pairwise differential expression here?

[Deepak Tanwar]

I believe that WGCNA would be able to do so, but not sure. I haven't used this package for such analysis.

You could also do pathway analysis using QuSAGE package and compare the pathways expressed in different datasets. WGCNA is basically for Gene co-expression analysis

[datanerd]

Thanks Deepak! I will try WGCNA.