Question: Cant find database of Transcription factors' binding site
2
gravatar for parashar.dhapola
3.3 years ago by
United States
parashar.dhapola150 wrote:

Hi, 

Well, I was handed a BED file from a colleague, this contains genomic coordinates for putative binding sites of 602 TFs. 
The problem is, she has forgotten the database from which this file was downloaded. 

It would be great if I can get be directed onto databases/webportal that provide information on predicted genome wide binding sites fro TFs in Humans and makes the bulk data available to download.

I would be really grateful for any help.

ADD COMMENTlink modified 3.3 years ago by stevenlang123130 • written 3.3 years ago by parashar.dhapola150

The file should be named as matches.bed in the download page.

ADD REPLYlink written 3.3 years ago by parashar.dhapola150

If you post a handful of names, it is usually possible to tell the database they are from, given the naming scheme. For instance, genes that are named in the form "MA0123" are usually Jaspar. Genes named in the form "V_XYZ_0123" are Transfac, and so on.

ADD REPLYlink modified 3.3 years ago • written 3.3 years ago by Alex Reynolds26k

The names are exactly the names of transcription factors. They are not from JASPAR or TRANSFAC.

ADD REPLYlink written 3.3 years ago by parashar.dhapola150

Transcription factor names generally follow a naming scheme that can remind your colleague which database they came from, if she has forgotten. Hopefully this helps.

ADD REPLYlink written 3.3 years ago by Alex Reynolds26k
4
gravatar for Evgeniia Golovina
3.3 years ago by
New Zealand
Evgeniia Golovina940 wrote:

Hi!

Here is some of the databases:

1) JasPar

2) MotifMap

3) TRANSFAC Matrix models

4) UniPROBE

5) Human Protein-DNA Interactome (hPDI)

6) Factorbook

7) DBD - TF prediction db

8) HOCOMOCO

ADD COMMENTlink modified 3.3 years ago • written 3.3 years ago by Evgeniia Golovina940

In addition there is CIS-BP which includes the motifs from almost all of those database and more! You can then use all the motifs you're interested in and a program like FIMO to find all the motif occurrences and make a bed file

ADD REPLYlink written 3.3 years ago by UnivStudent380

Thanks for the reply. The data is not from any of the above database. 

ADD REPLYlink written 3.3 years ago by parashar.dhapola150
1
gravatar for roy.granit
3.3 years ago by
roy.granit740
Israel/LabWorm
roy.granit740 wrote:

Here is another list of DBs:

http://meme-suite.org/db/motifs

ADD COMMENTlink written 3.3 years ago by roy.granit740
0
gravatar for stevenlang123
3.3 years ago by
stevenlang123130
United States
stevenlang123130 wrote:

I've also found this use courtesy of The Broad: http://www.broadinstitute.org/mammals/haploreg/haploreg_v3.php

ADD COMMENTlink written 3.3 years ago by stevenlang123130
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