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Gene expression differences- network or pathway analysis

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

microarray gene expression network analysis
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updated by Ram Ram • written by datanerd datanerd

1 answer

Mamta, You need WGCNA

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

That's all you need.

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updated by Ram Ram • written by Deepak Tanwar Deepak Tanwar

Thanks for the quick reply.

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

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written by datanerd datanerd

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

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written by Deepak Tanwar Deepak Tanwar

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

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written by datanerd datanerd

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

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updated by Ram Ram • written by Deepak Tanwar Deepak Tanwar

Thanks Deepak! I will try WGCNA.

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updated by Ram Ram • written by datanerd datanerd

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