Transfac
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12.1 years ago

(for a friend) is there any free database that could replace TRANSFAC ?

TRANSFAC® provides data on eukaryotic transcription factors, their experimentally-proven binding sites, consensus binding sequences (positional weight matrices) and regulated genes. 
(...)
The data provided here is only a snapshot from 2005. For a modest academic/non-profit price, subscription to TRANSFAC® Professional provides full access to regularly updated content that goes well beyond the breadth and depth of content offered by others, as well as more advanced tools and an easy-to-use interface.

Thank you,

Pierre

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12.1 years ago
ff.cc.cc ★ 1.3k

Hi, I'm citing from the homepage (http://jaspar.genereg.net/):

The JASPAR CORE database contains a curated, non-redundant set of profiles, derived from published collections of experimentally defined transcription factor binding sites for eukaryotes. The prime difference to similar resources (TRANSFAC, etc) consist of the open data acess, non-redundancy and quality. When should it be used? When seeking models for specific factors or structural classes, or if experimental evidence is paramount

maybe also a few tracks from ucsc can help, e.g. encode chipseq results and tfbs conserved, but you can't get weight matrices for these (or you have to compute them).

hope could help

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12.1 years ago

If you are interested in yeast, then you can have a look at Yeastract, it's a:

curated repository of more than 48333 regulatory associations between transcription factors (TF) and target genes in Saccharomyces cerevisiae, based on more than 1200 bibliographic references.

It's a very complete database, but sadly, for yeast researchers only.

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12.1 years ago
Ying W ★ 4.3k

There was a recent thread on the bioconductor listserv on this topic starting with Paul Shannon's post

They mentioned two other resources:

http://www.athamap.de (arabidopsis)

http://pgfe.umassmed.edu/TFDBS/ (Drosophila)

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12.0 years ago
Assa Yeroslaviz ★ 1.9k

Do you know of any for C. elegans?

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have you tried the one on wombase? http://www.wormbase.org/resources/motif#0-1-5

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