Any Tutorial For Co-Expression(Network) Analysis?
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7.6 years ago
kevolinchen ▴ 30

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 • 13k views
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7.6 years ago

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

Also, read their theory papers they are pretty good.

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+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

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

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+1 too, WGCNA usually give me very interesting modules

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

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

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Yeah, thx! I'm trying that!

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7.6 years ago
jobinv ★ 1.1k

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/

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

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Looks interesting, are there any publications for this?

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