[BioC] Transcription factor genes

[Khan, Anar]

Hi Tae-Hoon,

The best method will depend on which organism you are working with. For
model organisms with comprehensive & accurate GO annotations, the GO
approach you have suggested would be suitable. Another approach might be
to search GenBank or SRS with the keyword "transcription factor,"
limiting it to your species of interest, this may provide a larger set.

There are also many species-specific transcription factor databases
available now, and typically these annotations are not entered in the
large public databases such as GenBank: 

TRANSFAC -
http://www.biobase-international.com/pages/index.php?id=transfac - good
coverage of mammalian TFs, some coverage of plant/fungal TFs
PlantTFDB - http://plntfdb.bio.uni-potsdam.de/v1.0/ - 5 plant species
DATF - http://datf.cbi.pku.edu.cn/ - Arabidopsis
DRTF - http://drtf.cbi.pku.edu.cn/ - Rice

You could BLAST your sequences of interest against one of these
databases, to identify homologs in your species of interest.

If you want a comprehensive list of TF candidates, you could use a
combination of BLAST, protein domain searches and nuclear localisation
signal identification, as described in Riechmann et al (2000)
(http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&T
ermToSearch=11118137) and Guo et al (2005)
(http://www.ncbi.nlm.nih.gov/sites/entrez?Db=pubmed&Cmd=ShowDetailView&T
ermToSearch=15731212). I found this method worked very well for my
obscure species of interest.

Regards,
Anar

____________________________
Anar Khan
Bioinformatician
T +64 3 489 9154
E anar.khan at agresearch.co.nz

AgResearch Limited
Invermay Agricultural Centre
Puddle Alley, Private Bag 50034, Mosgiel, New Zealand
T  +64 3 489 3809   F  +64 3 489 3739  www.agresearch.co.nz

Farming Food and Health. First
Te Ahuwhenua Te Kai me te Whai Ora. Tuatahi



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Message: 13
Date: Tue, 17 Jul 2007 09:26:06 -0700
From: Tae-Hoon Chung <thchung at tgen.org>
Subject: [BioC] Transcription factor genes
To: Bioconductor list list <bioconductor at stat.math.ethz.ch>
Message-ID: <5FFC0D77-6E10-44B5-AB6B-2E1BB0C8E3FC at tgen.org>
Content-Type: text/plain

Hi, All;

This may not be an appropriate question for Bioconductor mailing list  
but I need some help.
Is there anyone who can suggest what's the best way to gather  
transcription factor genes?
Collecting genes implicated in "transcription factor activity" in GO  
will do? Or any other
suggestions? Thanks in advance,

Tae-Hoon Chung

Post-Doctoral Researcher
Computational Biology Division, TGEN
445 N 5th St. Phoenix, AZ 85004 USA
O: 1-602-343-8724
F: 1-602-343-8840



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