I am kind of confused and lost with network building in cytoscape and the whole methodology.
What I have got.
I have a set of transcription factors for which a ChIP-Seq experiment was performed and annotating the peaks of these TFs with nearby genes I have a target geneset for each of the transcription factor. Ofcourse of the target genes are shared between the TF's.
What I did
I made the TF-gene network for this set of data using cytoscape.
The table looks like this
TF1 gene1 TF1 gene2 TF1 gene3 TF2 gene2 TF2 gene4 TF2 gene5 TF3 gene1 TF3 gene2 TF3 gene3 TF3 gene4 TF3 gene6
What I want to integrate this network with expression values in normal and in diseased state and to compare the two networks in terms of their hubs and subnetworks and to identify network drivers for the two.
hence the complete set will look like this
TF1 gene1 1.3 2 TF1 gene2 0.9 2.3 TF1 gene3 2 0.3 TF2 gene2 0.9 2.3 TF2 gene4 4 2 TF2 gene5 6 3 TF3 gene1 1.3 2 TF3 gene2 0.9 2.3 TF3 gene3 2 0.3 TF3 gene4 4 2 TF3 gene6 0.8 3
column3 is for normal state and column 4 is for diseased state.