Hi, I have some gene expression data from induced cells by some small molecule in vitro (different kind of small molecules in different data sets) that convert to a kind of tissue and of course the real tissue expression from part of body (for instance DEGs of converted cell to brain and DEGs of a real brain) to show how similar are this conversion to real tissue and how successful is in the aspect of gene expression and their Gene Regulatory Networks? .Then to construct a gene-TF interaction network for this data, deferentially expressed genes with a typical filters were used and TFs with highest probability interactions were found, finally these interaction were given to the Cytoscape. my final goal is to find modules for both induced cells gene-TF interactions and that of tissue and compare these to kind of networks to show similarities and differences.
So my questions are, 1- Is finding modules a good way? 2-what is the best plugin to find module base on DEGs and TFs interaction for my gene regulatory network? 3-Is it possible to use JActivemadule plugin to find modules?since I have read in some papers that JActivemodule is used for finding modules of genes with their p.value and fold change not for gene-TF interactions.
any suggestion would be helpful