Cant find database of Transcription factors' binding site
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7.6 years ago

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.

BED transcription-factor • 3.6k views
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The file should be named as matches.bed in the download page.

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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.

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

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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.

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7.6 years ago

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
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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

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

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7.6 years ago
roy.granit ▴ 880

Here is another list of DBs: http://meme-suite.org/db/motifs

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7.6 years ago
stevenlang123 ▴ 200

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

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