Question: Gene expression differences- network or pathway analysis
0
gravatar for Mamta
4.3 years ago by
Mamta450
United States
Mamta450 wrote:

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

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by Mamta450
2
gravatar for Deepak Tanwar
4.3 years ago by
Deepak Tanwar4.0k
ETH Zürich, Switzerland
Deepak Tanwar4.0k wrote:

Mamta, You need WGCNA 

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

That's all you need.

ADD COMMENTlink written 4.3 years ago by Deepak Tanwar4.0k

Thanks for the quick reply.

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

ADD REPLYlink written 4.3 years ago by Mamta450
1

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

ADD REPLYlink written 4.3 years ago by Deepak Tanwar4.0k
1

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

ADD REPLYlink written 4.3 years ago by Mamta450
1

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

ADD REPLYlink written 4.3 years ago by Deepak Tanwar4.0k
1

Thanks Deepak! I will try WGCNA. 

ADD REPLYlink written 4.3 years ago by Mamta450
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