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You *could* use GO to just get some of the well known answers quickly. A colleague of mine pointed me to this very nice resource that they have compiled: http://www.pazar.info/cgi-bin/links.pl good luck, Marc Tae-Hoon Chung wrote: > 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 > > > > [[alternative HTML version deleted]] > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor > >

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 ------------------------------ Message: 13 Date: Tue, 17 Jul 2007 09:26:06 -0700 From: Tae-Hoon Chung <thchung@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 [[alternative HTML version deleted]] ------------------------------ ====================================================================== = Attention: The information contained in this message and/or ...{{dropped}}