Question: Transcription Factors in common
0
gravatar for Mo
23 months ago by
Mo0
Mo0 wrote:

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!

transcription factors gene • 537 views
ADD COMMENTlink modified 23 months ago by Benn8.0k • written 23 months ago by Mo0

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?

ADD REPLYlink written 23 months ago by ATpoint35k

I do not know how to use those.

ADD REPLYlink written 23 months ago by Mo0
0
gravatar for liux.bio
23 months ago by
liux.bio340
China
liux.bio340 wrote:

You can try iRegulon, which is a cytoscape app.

ADD COMMENTlink modified 23 months ago • written 23 months ago by liux.bio340
0
gravatar for Benn
23 months ago by
Benn8.0k
Netherlands
Benn8.0k wrote:

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.

ADD COMMENTlink written 23 months ago by Benn8.0k
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