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PMID: 19721806 Published · ppublish English Journal Article

Comparative analyses of plant transcription factor databases.

Current genomics ·Vol. 10 ·No. 1 ·2009-03-00 ·Pages 10-7

Ramirez SR, Basu C

Abstract

Transcription factors (TFs) are proteinaceous complex, which bind to the promoter regions in the DNA and affect transcription initiation. Plant TFs control gene expressions and genes control many physiological processes, which in turn trigger cascades of biochemical reactions in plant cells. The databases available for plant TFs are somewhat abundant but all convey different information and in different formats. Some of the publicly available plant TF databases may be narrow, while others are broad in scopes. For example, some of the best TF databases are ones that are very specific with just one plant species, but there are also other databases that contain a total of up to 20 different plant species. In this review plant TF databases ranging from a single species to many will be assessed and described. The comparative analyses of all the databases and their advantages and disadvantages are also discussed.

Keywords
Plant transcription factor databases bioinformatics.
Authors & Affiliations
2 authors, click to expand affiliations / ORCID
Ramirez Silvia R
School of Biological Sciences, University of Northern Colorado, Greeley, Colorado, USA.
Basu Chhandak
References (33)
33 references, click to expand
  1. PlnTFDB: an integrative plant transcription factor database.
    BMC Bioinformatics. 2007 Feb 07;8:42 PMID: 17286856
  2. DATF: a database of Arabidopsis transcription factors.
    Bioinformatics. 2005 May 15;21(10):2568-9 PMID: 15731212
  3. NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D61-5 PMID: 17130148
  4. A draft sequence of the rice genome (Oryza sativa L. ssp. japonica).
    Science. 2002 Apr 5;296(5565):92-100 PMID: 11935018
  5. GenBank: update.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6 PMID: 14681350
  6. Microarrays: biotechnology's discovery platform for functional genomics.
    Trends Biotechnol. 1998 Jul;16(7):301-6 PMID: 9675914
  7. Database resources of the National Center for Biotechnology Information.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D13-21 PMID: 18045790
  8. RARGE: a large-scale database of RIKEN Arabidopsis resources ranging from transcriptome to phenome.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D647-50 PMID: 15608280
  9. MIPS: analysis and annotation of genome information in 2007.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D196-201 PMID: 18158298
  10. RARTF: database and tools for complete sets of Arabidopsis transcription factors.
    DNA Res. 2005;12(4):247-56 PMID: 16769687
  11. PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences.
    Nucleic Acids Res. 2002 Jan 1;30(1):325-7 PMID: 11752327
  12. Hidden Markov Models, grammars, and biology: a tutorial.
    J Bioinform Comput Biol. 2005 Apr;3(2):491-526 PMID: 15852517
  13. Basic local alignment search tool.
    J Mol Biol. 1990 Oct 5;215(3):403-10 PMID: 2231712
  14. Overexpression analysis of plant transcription factors.
    Curr Opin Plant Biol. 2003 Oct;6(5):430-40 PMID: 12972043
  15. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana.
    Nature. 2000 Dec 14;408(6814):796-815 PMID: 11130711
  16. UniProt: the Universal Protein knowledgebase.
    Nucleic Acids Res. 2004 Jan 1;32(Database issue):D115-9 PMID: 14681372
  17. TRANSFAC: transcriptional regulation, from patterns to profiles.
    Nucleic Acids Res. 2003 Jan 1;31(1):374-8 PMID: 12520026
  18. AGRIS and AtRegNet. a platform to link cis-regulatory elements and transcription factors into regulatory networks.
    Plant Physiol. 2006 Mar;140(3):818-29 PMID: 16524982
  19. The Pfam protein families database.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D281-8 PMID: 18039703
  20. RIKEN Arabidopsis full-length (RAFL) cDNA and its applications for expression profiling under abiotic stress conditions.
    J Exp Bot. 2004 Jan;55(395):213-23 PMID: 14673034
  21. The EMBL Nucleotide Sequence Database.
    Nucleic Acids Res. 2005 Jan 1;33(Database issue):D29-33 PMID: 15608199
  22. DRTF: a database of rice transcription factors.
    Bioinformatics. 2006 May 15;22(10):1286-7 PMID: 16551659
  23. dbEST--database for "expressed sequence tags".
    Nat Genet. 1993 Aug;4(4):332-3 PMID: 8401577
  24. PlantTFDB: a comprehensive plant transcription factor database.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D966-9 PMID: 17933783
  25. The Arabidopsis Information Resource (TAIR): a model organism database providing a centralized, curated gateway to Arabidopsis biology, research materials and community.
    Nucleic Acids Res. 2003 Jan 1;31(1):224-8 PMID: 12519987
  26. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray).
    Science. 2006 Sep 15;313(5793):1596-604 PMID: 16973872
  27. DBD--taxonomically broad transcription factor predictions: new content and functionality.
    Nucleic Acids Res. 2008 Jan;36(Database issue):D88-92 PMID: 18073188
  28. The SUPERFAMILY database in 2007: families and functions.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D308-13 PMID: 17098927
  29. AthaMap web tools for the analysis and identification of co-regulated genes.
    Nucleic Acids Res. 2007 Jan;35(Database issue):D857-62 PMID: 17148485
  30. TOBFAC: the database of tobacco transcription factors.
    BMC Bioinformatics. 2008 Jan 25;9:53 PMID: 18221524
  31. Plant cis-acting regulatory DNA elements (PLACE) database: 1999.
    Nucleic Acids Res. 1999 Jan 1;27(1):297-300 PMID: 9847208
  32. DPTF: a database of poplar transcription factors.
    Bioinformatics. 2007 May 15;23(10):1307-8 PMID: 17392330
  33. Expressed sequence tags: alternative or complement to whole genome sequences?
    Trends Plant Sci. 2003 Jul;8(7):321-9 PMID: 12878016
Article Info
Journal
Current genomics
Abbr.
Curr Genomics
ISSN
1389-2029
DOI
10.2174/138920209787581253
Published
2009-03-00
Pages
10-7
Language
English
Region
United Arab Emirates
NLM ID
100960527
PMCID
PMC2699837
External Links
PubMed source DOI: 10.2174/138920209787581253 PMC Full Text View journal details
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