Hello everyone,

I have a set of differentially expressed genes in an "A" tissue when compared with other tissues, most of these genes being typical protein coding genes, and the rest of them being transcription factors. I have obtained this set from RNA-seq data from several samples of this "A" tissue and the rest of the tissues. This far, I can assume these typical protein coding genes are regulated by the transcription factors.

However, my problem is, is there any way or tool to know which genes are regulated by each transcription factor without using any database or experiment, but only my data?

Thank you very much for your help and kind regards.
<p>If we rule out using any database (I don&#39;t know why we&#39;d do that, using a database of TF binding sites would be convenient), then one possibility would be to look at covariation between the various DE genes (e.g., with WGCNA). The assumption would be that a TF driving a bunch of genes to be DE should be near the center of a module containing them and possibly be its eigengene.</p>
