Hello,

I am interested in analyzing transcription factor (TF) activity using altered gene expression of target genes.

Can we predict/quantify transcription factor activation using microarray gene expression data? Is there any bioconductor 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 I am trying to find out whether there are other methods or tools available. Any suggestions or relevant papers/pointer will be very helpful.

Thank you for your time

Diwan

One strategy might be to treat each target gene list as a gene set, and then do gene set enrichment analysis. There are many algorithms available; see the packages under the "GeneSetEnrichment" biocViews term.