Question: network analysis of DEGs
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gravatar for Shamim Sarhadi
2.8 years ago by
IRAN
Shamim Sarhadi210 wrote:

Hi I have 3 bunch of DEGs from 12-hour periods exposure to a drug, I've created network from each one, when I run a module finder plug-in in cytoscape, I found 2 module in networks of DEGs 12 and 24 hour after exposure to drug with p-value less than 0.05, but about 36 H , it did not find any significant module , how can I interpret that? Does it mean that the drug disturbed the network or...?

ADD COMMENTlink modified 2.8 years ago • written 2.8 years ago by Shamim Sarhadi210

I don't think we can interpret this without seeing the data or at least knowing more about it and knowing how you processed it and the algorithm(s) you used.

ADD REPLYlink written 2.8 years ago by Jean-Karim Heriche18k

Hi Jean-Karim Heriche,Thank you for your reply

I preprocessed my gene expression with FRMA method, then I did a class comparison test between control and each case group(time series drug exposed) with limma to finding DEG.I've selected toprank genes of limma output to creating network,but I created networks with two approach, first I just selected toprank gene-id of each bunch and I created network with networkanalyst(that mapped my gene names on PPI network of InnateDB) in this approach Walktrap Algorithm found signif modules for all of networks, but in the second approach I created networks with gene names and their log fold changes ,but this time Walktrap Algorithm found signif module for first two networks but it did not find for the third one(36 h drug exposed samples)

how can I explain that?

ADD REPLYlink modified 2.8 years ago • written 2.8 years ago by Shamim Sarhadi210
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