Transcription Factors in common

Question

[Mo]

Hello,

I have a list of genes that are effected by knockdown of a certain gene. I am looking at transcription factor binding sites for these genes promoters through GTRD. I need to compare which TF binding sites that they have in common. My main problem is that there are way to many TF binding sites per gene to compare on GTRD. I am not a bioinformatician so I do not know if there is an easy way to do this. Please let me know how to do this and if there is any tools I can use to make it easier. Thank You so much!

[ATpoint]

I am not a bioinformatician

In order to narrow down the possible approaches, do you know how to use R, Python or the Unix command line?

[Mo]

I do not know how to use those.

Answer 1

[liux.bio]

You can try iRegulon, which is a cytoscape app.

Answer 2

[Benn]

You can look for (DNA-binding) motifs before your genes with homer. This tool runs on unix/linux, so for this approach either you start learning unix command line or you find someone that is able to use unix.