Can we predict/quantify transcription factor activation using gene expression data?

Question

[Diwan]

Hello,

I am interested in analyzing transcription factor (TF) activity. Activation/activity of TF will be reflected in the altered gene expression of target genes.

Can we predict/quantify transcription factor activation using gene expression data? Is there any well-known method/bioconductor/cytoscape pacakges to do that?

I am planning to collect the target gene list of TF and sum up whether they are differentially expressed as an indicator of TF activity. But the approach sounds too simple and there seems to volumes of papers on gene regulatory networks. Any suggestions or relevant papers/pointer will be helpful.

Thank you

Diwan

[Jean-Karim Heriche]

Maybe what you're looking for is similar to this paper. Otherwise, as you've already noted, this falls under gene regulatory network inference. The reason this is approached as a network is because there are multiple interactions between TFs leading to a particular expression pattern.

[James Ashmore]

Without topological information, your results will be patchy at best. If you can't get any topological information I'd recommend limiting your peaks to those right next to a TSS and just focusing on that subset.