Question: Tf-Target Enrichment Analysis
0
gravatar for Jimbo
7.3 years ago by
Jimbo120
Jimbo120 wrote:

Given a list of DE genes, eg from a microarray experiment, of which 2 are known TFs, how can I see if any of the other genes are known or predicted to be regulated by the known TFs?

Many thanks,

Jim

microarray transcription • 2.7k views
ADD COMMENTlink written 7.3 years ago by Jimbo120

Have you checked a discussions at BioStar: http://biostar.stackexchange.com/questions/2149/how-to-identify-targets-of-a-transcription-factor ?

ADD REPLYlink written 7.2 years ago by Khader Shameer17k

If the answer is useful, please vote them up, Jimbo, and try to select the best for your purposes. This is an essential element of what makes BioStar so beneficial.

ADD REPLYlink written 7.2 years ago by Larry_Parnell16k

Ahh yes, apologies! I have selected the best answer for other people, although i would like to give credit to Anima mundi too, because he corresponded with me on further queries, so I "voted him up". I hope this is the correct procedure. Cheers

ADD REPLYlink written 7.2 years ago by Jimbo120
2
gravatar for Stephane Plaisance
7.2 years ago by
Leuven area (Belgium)
Stephane Plaisance380 wrote:

I used to run these querries at:

I am sure there are other sites all based on some adapatation of the UCSC conserved TFBS track

to go deeper and across species for a given region, use * http://bioit.dmbr.ugent.be/ConTra/index.php *... google it

these web-tools ar eeasy and give you results you of course will need to validate.

Good luck

ADD COMMENTlink modified 4.6 years ago • written 7.2 years ago by Stephane Plaisance380
1
gravatar for Anima Mundi
7.3 years ago by
Anima Mundi2.4k
Italy
Anima Mundi2.4k wrote:

Hello, I would suggest you the PSWM usage. You could download the matrices of the TFs, and use them to predict TFBS among the genes of the list. For known targets I would suggest iHOP, a tool capable of retrieving literature-based information about several genes.

ADD COMMENTlink written 7.3 years ago by Anima Mundi2.4k

This is what I was expecting. Is there any software you know of that can do this, i.e. you input a list, it automatically detects TFs, finds their "PSWM" matrices (or other), then automatically scans the remaining genes to look for TFBS (and perhaps ranks them, respectively for each TF)

ADD REPLYlink written 7.3 years ago by Jimbo120

Oh, and thanks a lot for the answer, of course :)

ADD REPLYlink written 7.3 years ago by Jimbo120

For what you desire I would suggest Motifviz's Possum. You can input your list using the JASPAR Core database (a database of PSWMs); the output is a series of stressed TFBSs for some TF in your sequences. This is a "quick and dirty" method, you could need something more complex and reliable, depending on your scopes.

ADD REPLYlink written 7.3 years ago by Anima Mundi2.4k

For what concerns the detection of the TFs you should somehow use the annotation of your sequences, then make a script to retrieve only the desired TFs from the JASPAR database, generate a file containing the resulting list of PSWMs and input it. But it is not useful, I would simply input the whole database.

ADD REPLYlink written 7.3 years ago by Anima Mundi2.4k

OK I see, so put in everything, then filter the output for the TFs that were in the original list?

ADD REPLYlink written 7.3 years ago by Jimbo120

Exactly, I would do so.

ADD REPLYlink written 7.3 years ago by Anima Mundi2.4k

I wanted to do the same thing and some of the replies can be found here: http://biostar.stackexchange.com/questions/2256/dump-upstream-sequence Unfortunately, I haven't gotten around to doing it yet (waiting for data on more TFs)

ADD REPLYlink written 7.2 years ago by Ying W3.9k
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1287 users visited in the last hour