Find which transcription factors are regulated in a set of genes

Question

[manashreed]

Hello Everyone,

I have 6 RNA-seq data-sets, 2 tissues and 3 strains. I have the differentially expressed genes across the strains in each tissue as well as across tissues in the same strain. I now want to find which transcription factors went up/down in each of these conditions. For example if factor X was down-regulated in a certain condition, all of it's target genes would most likely be in the list of the regulated genes. Does anyone know how I can find all the TFs that are changing in a certain condition?

Thanks,

Manashree

[zizigolu]

i think you can perform annotation for each sets of your genes deferentially expressed in tissues and strain then by considering the GO result (genes mapped to that GO ID) you may could define in each data-set which TF is up or down regulated,

for conforming if a TF is responsible for expression regulation of a gene set, you can perform reverse engineering by some tools that use TF as hub

Answer 1

[manashreed]

I ended up using this as a database for all the TFs in mouse.

[zizigolu]

Good job friend