How to use Jactivemodule plugin from Cytoscape?

Question

[Calangoa]

Hi there, I want to construct a lot of networks to show, what are the effects of different culture medium to convert a specific cells to another. actually my desired goal is construct a huge gene regulatory network for DNA-Protein interactions (at least for 20000 interactions) by Cytoscape and then extraction of significant transcription factors or genes with their interactions (modules) as output. after whole searching I found Jactivemadule plugin from Cyto which can identify important modules. as I read in their paper [1] If I understand good, we need gene names, interaction and p.value as an input for Cytoscape but my questions are: 1. Is it not better to give gene expression, p.value and interaction of gene-protein instead of p.value and interactions only? 2. if the answer of question 1 is yes, how should I give the input to Cyto? I mean, how to construct an input with two kinds of numbers, p.value and gene expression (base on log fold change)? 3.After constructing networks, Is the first module of each networks, contain the most important module among others? and should I take it for comparing with first module of other networks?

Answer 1

[xanderpico]

I haven't used jactivemodules in years, but it seems like the tutorial linked to from the Cytoscape App Store page answers your questions... http://apps.cytoscape.org/apps/jactivemodules --> http://opentutorials.cgl.ucsf.edu/index.php/Tutorial:JActiveModules_3

1. Yes, it works with a combination of expression and p.value columns: gal80Rexp is fold change values and gal80Rsig are p.values.
2. The screenshot of module results shows a overview of all 5 modules and then separate networks for each module. I don't see or read any suggestions about "most important" module or comparisons.

Answer 2

[Calangoa]

Thanks Xanderpico. it was really helpful.