DEG gene list and find common TF from public ChlP-Seq data

Question

[Joshua]

RNA-seq of treated sample gave me a list of DEG genes. am trying to find what transcriptional factor do these DEG have in common. have a bed file that contains all the publicly available TF ChiP-seq of a specific cell type. How do screen for potential common TF that regulates DEG? am currently trying to look at upstream and downstream of TSS, I have the location window of these genes. However, it seems tedious if were to enter the coordinate for each of these gene then take a screenshot, and then look for the binding sites across all of them. Is there a way to feed a list of coordinate and generate a track PNG using some kinda R or Python tool in batch? My initial thoughts were just generate PNG to screen visually, but there has to be an easier way to screen for this by calculating frequency of the BED annotation within the window. If you know any tools can help with this it would be very helpful thank you thank you

[Yogi]

Pull a reference gene BED file and subset that to the DEG genes. Next, use BedTools to intersect the regions with the subsetted reference BED file from above.

You can mess around with thresholds for how close the TF binding site needs to be to the gene with flags in the "intersect" command.

Answer 1

[Ian]

Hi. If this is human or mouse data you could try using EnrichR, which is free. Try comparing against 'Transcription_factor_PPIs' and 'TRANSFAC_JASPAR_PWMS'.

A paid option is Qiagen's IPA software.

Answer 2

[Trivas]

I've used the R package TFEA.ChIP but it feels a little limited and hard to explain to a general biology audience.