Any Tutorial For Co-Expression(Network) Analysis?

Question

[kevolinchen]

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!

Answer 1

[Ashutosh Pandey]

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

Also, read their theory papers they are pretty good.

[Sam]

+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

[kevolinchen]

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

[Hayssam]

+1 too, WGCNA usually give me very interesting modules

[Adamc]

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

[Hayssam]

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

[kevolinchen]

Yeah, thx! I'm trying that!

Answer 2

[jobinv]

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/

[kevolinchen]

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

[Adamc]

Looks interesting, are there any publications for this?