PlnTFDB:: an integrative plant transcription factor database

被引:316
作者
Riano-Pachon, Diego Mauricio
Ruzicic, Slobodan
Dreyer, Ingo
Mueller-Roeber, Bernd
机构
[1] Univ Potsdam, Dept Mol Biol, Inst Biochem & Biol, D-14476 Golm, Germany
[2] Max Planck Inst Mol Plant Physiol, Cooperat Res Grp, D-14476 Golm, Germany
关键词
D O I
10.1186/1471-2105-8-42
中图分类号
Q5 [生物化学];
学科分类号
071010 ; 081704 ;
摘要
Background: Transcription factors (TFs) are key regulatory proteins that enhance or repress the transcriptional rate of their target genes by binding to specific promoter regions (i.e. cis-acting elements) upon activation or de-activation of upstream signaling cascades. TFs thus constitute master control elements of dynamic transcriptional networks. TFs have fundamental roles in almost all biological processes ( development, growth and response to environmental factors) and it is assumed that they play immensely important functions in the evolution of species. In plants, TFs have been employed to manipulate various types of metabolic, developmental and stress response pathways. Cross-species comparison and identification of regulatory modules and hence TFs is thought to become increasingly important for the rational design of new plant biomass. Up to now, however, no computational repository is available that provides access to the largely complete sets of transcription factors of sequenced plant genomes. Description: PlnTFDB is an integrative plant transcription factor database that provides a web interface to access large ( close to complete) sets of transcription factors of several plant species, currently encompassing Arabidopsis thaliana (thale cress), Populus trichocarpa ( poplar), Oryza sativa ( rice), Chlamydomonas reinhardtii and Ostreococcus tauri. It also provides an access point to its daughter databases of a species-centered representation of transcription factors (OstreoTFDB, ChlamyTFDB, ArabTFDB, PoplarTFDB and RiceTFDB). Information including protein sequences, coding regions, genomic sequences, expressed sequence tags ( ESTs), domain architecture and scientific literature is provided for each family. Conclusion: We have created lists of putatively complete sets of transcription factors and other transcriptional regulators for five plant genomes. They are publicly available through http://plntfdb.bio.uni-potsdam.de. Further data will be included in the future when the sequences of other plant genomes become available.
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页数:10
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共 44 条
[1]   STATISTICS NOTES - DIAGNOSTIC-TESTS-1 - SENSITIVITY AND SPECIFICITY .3. [J].
ALTMAN, DG ;
BLAND, JM .
BRITISH MEDICAL JOURNAL, 1994, 308 (6943) :1552-1552
[2]   DIAGNOSTIC-TESTS-2 - PREDICTIVE VALUES .4. [J].
ALTMAN, DG ;
BLAND, JM .
BRITISH MEDICAL JOURNAL, 1994, 309 (6947) :102-102
[3]   SIMAP -: The similarity matrix of proteins [J].
Arnold, R ;
Rattei, T ;
Tischler, P ;
Truong, MD ;
Stümpflen, V ;
Mewes, W .
BIOINFORMATICS, 2005, 21 :42-46
[4]   Update on the basic helix-loop-helix transcription factor gene family in Arabidopsis thaliana [J].
Bailey, PC ;
Martin, C ;
Toledo-Ortiz, G ;
Quail, PH ;
Huq, E ;
Heim, MA ;
Jakoby, M ;
Werber, M ;
Weisshaar, B .
PLANT CELL, 2003, 15 (11) :2497-2501
[5]   The role of GRAS proteins in plant signal transduction and development [J].
Bolle, C .
PLANTA, 2004, 218 (05) :683-692
[6]   The MYB transcription factor superfamily of arabidopsis: Expression analysis and phylogenetic comparison with the rice MYB family [J].
Chen, YH ;
Yang, XY ;
He, K ;
Liu, MH ;
Li, JG ;
Gao, ZF ;
Lin, ZQ ;
Zhang, YF ;
Wang, XX ;
Qiu, XM ;
Shen, YP ;
Zhang, L ;
Deng, XH ;
Luo, JC ;
Deng, XW ;
Chen, ZL ;
Gu, HY ;
Qu, LJ .
PLANT MOLECULAR BIOLOGY, 2006, 60 (01) :107-124
[7]   AGRIS:: Arabidopsis Gene Regulatory Information Server, an information resource of Arabidopsis cis-regulatory elements and transcription factors -: art. no. 25 [J].
Davuluri, RV ;
Sun, H ;
Palaniswamy, SK ;
Matthews, N ;
Molina, C ;
Kurtz, M ;
Grotewold, E .
BMC BIOINFORMATICS, 2003, 4 (1)
[8]   Genome analysis of the smallest free-living eukaryote Ostreococcus tauri unveils many unique features [J].
Derelle, Evelyne ;
Ferraz, Conchita ;
Rombauts, Stephane ;
Rouze, Pierre ;
Worden, Alexandra Z. ;
Robbens, Steven ;
Partensky, Frederic ;
Degroeve, Sven ;
Echeynie, Sophie ;
Cooke, Richard ;
Saeys, Yvan ;
Wuyts, Jan ;
Jabbari, Kamel ;
Bowler, Chris ;
Panaud, Olivier ;
Piegu, Benoit ;
Ball, Steven G. ;
Ral, Jean-Philippe ;
Bouget, Francois-Yves ;
Piganeau, Gwenael ;
De Baets, Bernard ;
Picard, Andre ;
Delseny, Michel ;
Demaille, Jacques ;
Van de Peer, Yves ;
Moreau, Herve .
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2006, 103 (31) :11647-11652
[9]   Comparative plant genomics resources at PlantGDB [J].
Dong, QF ;
Lawrence, CJ ;
Schlueter, SD ;
Wilkerson, MD ;
Kurtz, S ;
Lushbough, C ;
Brendel, V .
PLANT PHYSIOLOGY, 2005, 139 (02) :610-618
[10]   An annotation update via cDNA sequence analysis and comprehensive profiling of developmental, hormonal or environmental responsiveness of the Arabidopsis AP2/EREBP transcription factor gene family [J].
Feng, JX ;
Liu, D ;
Pan, Y ;
Gong, W ;
Ma, LG ;
Luo, JC ;
Deng, XW ;
Zhu, YX .
PLANT MOLECULAR BIOLOGY, 2005, 59 (06) :853-868