Question: Any Tutorial For Co-Expression(Network) Analysis?
3
gravatar for kevolinchen
5.5 years ago by
kevolinchen30
China
kevolinchen30 wrote:

I'm now learning co-expression analysis & co-expression network construction... I'm looking for tutorials about that. Any recommended tutorial for co-expression(network) analysis from microarray data by R or other tools? Tutorials for Cytoscape could be helpful,too! Thank you!

R cytoscape microarray • 11k views
ADD COMMENTlink modified 5.1 years ago by Biostar ♦♦ 20 • written 5.5 years ago by kevolinchen30
5
gravatar for Ashutosh Pandey
5.5 years ago by
Philadelphia
Ashutosh Pandey11k wrote:

Have u tried WGCNA. http://labs.genetics.ucla.edu/horvath/CoexpressionNetwork/Rpackages/WGCNA/

Also, read their theory papers they are pretty good.

ADD COMMENTlink written 5.5 years ago by Ashutosh Pandey11k
2

+1 their tutorials are very clear and comprehensive, they also teach you how to plugin the data output from WGCNA to cytoscape, so you might want to give it a try. Another possible option will be GSEA or you can also try SPIA, so far I really like the data produced from SPIA so you might want to give it a try. These tools are all easy to use so you might want to play around with them

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Sam2.3k

Thank you, I'm now trying WGCNA. I may try GSEA & SPIA later

ADD REPLYlink written 5.5 years ago by kevolinchen30

+1 too, WGCNA usually give me very interesting modules

ADD REPLYlink modified 5.5 years ago • written 5.5 years ago by Hayssam270

Out of curiosity, how many samples do you usually use it with?

ADD REPLYlink written 5.4 years ago by Adamc590
1

Last time was with 400 samples (time course RNA-Seq).

ADD REPLYlink written 5.4 years ago by Hayssam270

Yeah, thx! I'm trying that!

ADD REPLYlink written 5.5 years ago by kevolinchen30
3
gravatar for jobinv
5.5 years ago by
jobinv1.1k
Bergen, Norway
jobinv1.1k wrote:

Might this tool be helpful for you? It includes a manual, which I guess is what you were specifically asking for.

CoExpress: http://bioinformatics.lu/CoExpress/

ADD COMMENTlink written 5.5 years ago by jobinv1.1k

Thank you! I noticed that this tool have a GUI , I'll work on that later!

ADD REPLYlink written 5.5 years ago by kevolinchen30

Looks interesting, are there any publications for this?

ADD REPLYlink written 5.4 years ago by Adamc590
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