Using Jactivemodules Cytoscape Plugin For Proteomics Data

Question

[Woa]

Does anyone use the 'jActivemodules' cytoscape plugin for finding out subgraphs in a protein-protein interaction network? In that case how do you provide the 'p-value' for expression which is required as input? Will 'log fold change' value converted to a p-value assuming normal distribution work?

Are there some good alternative software available?

Thanks

Answer 1

[Sudeep]

Have you figured this out ? if not, you have to give p value along with log fold change in the expression matrix. like,

ID\tExp1\tExp2\tExp1\tExp2
id1\tlog.Exp1\tlog.Exp2\tpval.Exp1\tpval.Exp2

download & look into the sample data provided here. hope this helps.