[Genome] TFBS IMD:M000109

[Ann Zweig]

Hello Martijn,

	To create our TFBS annotation track, we use the Transfac Matrix 
Database (v7.0) created by Biobase: 
http://www.gene-regulation.com/pub/databases.html

	It appears that your model comes instead from the IMD database.
http://www-bimas.cit.nih.gov/molbio/matrixs/

Chen, Q.K., Hertz, J.Z. and Stormo, G.D. (1995) MATRIX SEARCH 1.0: a
computer program that scans DNA sequences for transcriptional elements
using a database of weight matrices. Comp. Appl. Biosciences
11:563-566.

	The model you refer to, M00109 (not M000109), is for the GATA-1 
transcription factor (consensus sequence of WGATAA).  Here is its IMD entry:

GATA-1 8.50  9.00 WGATAA   M00109
A |  42   0  76   0  66  49
C |   1   0   4   1   1   2
G |   0  80   0   0   4  27
T |  37   0   0  79   9   2


	Back in the UCSC Genome Browser, if you enter GATA1 into the search 
box, you will see the UCSC Known Gene, GATA1.  You can also turn on the 
TFBS track to see the corresponding TFBSs in that area. e.g.

V$GATA3_01
V$GATA1_04

	I hope this information is helpful to you.

Regards,

----------
Ann Zweig
UCSC Genome Bioinformatics Group
http://genome.ucsc.edu




> Subject:
> TFBS IMD:M000109
> From:
> Martijn Dolle <Martijn.Dolle at rivm.nl>
> Date:
> Fri, 2 May 2008 05:00:51 +0200
> To:
> genome at soe.ucsc.edu
> 
> To:
> genome at soe.ucsc.edu
> 
> 
> Dear Sir or Madam,
> 
> I am looking for any information regarding the definition of conserved 
> transcription factor binding site “IMD:M000109”.
> 
> I used a web tool for selecting SNPs for genetic association studies, 
> called SNP selector. According to its description this program uses a 
> database maintained at Pennsylvania State University to identify SNPs in 
> conserved transcription factor binding sites (TFBS). A frequently listed 
> TFBS in the result file is “IMD:M000109”. Unlike the other TFBS I have 
> been unsuccessful thus far retrieving information on the protein 
> recognizing this site and the nucleotide sequence defining the TFBS. A 
> request for more information at dbadmin at bio.cse.psu.edu, resulted in the 
> reference of the genome at soe.ucsc.edu mailing list and the suggestion 
> that Matt Weirauch might have created the respective TFBS track. Could 
> you please help me to retrieve more information on IMD:M000109?
> 
> Many thanks in advance. Sincerely,
> Martijn Dollé
> 
> 
> Martijn Dollé, Ph.D.
> National Institute of Public Health and the Environment
> Laboratory of Health Protection Research (pb12)
> Antonie van Leeuwenhoeklaan 9
> 3721 MA Bilthoven
> The Netherlands
> Postal address:
> P.O. Box 1
> 3720 BA Bilthoven
> The Netherlands
> Phone: +31-30-2742011
> Fax: +31-30-2744446
> Email: Martijn.Dolle at rivm.nl