PlnTFDB: an integrative plant transcription factor database

By Diego Mauricio Riaño-Pachón, Slobodan Ruzicic, Ingo Dreyer, B. Mueller‐Roeber. BMC Bioinformatics, 2007

393 citations recorded by the source corpus.

BackgroundTranscription 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.DescriptionPlnTFDB 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.ConclusionWe 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.

Subfields: Molecular Biology, Plant Science

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Citations in the corpus

A High Quality Draft Consensus Sequence of the Genome of a Heterozygous Grapevine Variety (2007, methodology): “The reference information was from PlnTFDB, an integrate plant transcription factor database [63] including genes from A. thaliana (ArabTFDB), P. trichocarpa (PoplarTFDB) and O. sativa (Rice TFDB) (available at http://plntfdb.bio.uni-potsdam.de).”
Genome-wide analysis of NAC transcription factor family in rice. (2010, background): “edu/), Rice Transcription Factor Database (Rice-TFDB, http://ricetfdb.bio.unipotsdam.de/v2.1/; Riano-Pachon et al., 2007), National Centre for Biotechnology Information (NCBI; http://www.”
WRKY transcription factors (2014, background): “Functions of WRKY TFs Plants devote a large portion of their genome capacity to transcription, with the Arabidopsis and rice genomes coding for more than 2100 and 2300 TFs, respectively.(52) The WRKY gene family has been suggested to play important roles in the regulation of transcriptional reprogra”
ATTED-II provides coexpressed gene networks for Arabidopsis (2008, neutral): “We are also investigating annotations from other transcription factor databases (25,26), which may be incorporated to ATTED-II in the future.”
PlnTFDB: updated content and new features of the plant transcription factor database (2009, methodology): “Here we present the current status of the Plant Transcription Factor Database, PlnTFDB (4), which in its updated version (v3.”
Poplar and Pathogen Interactions: Insights from Populus Genome-Wide Analyses of Resistance and Defense Gene Families and Gene Expression Profiling (2009, background): “There are 22 ZIM encoding genes in the poplar genome (Riano-Pachon et al., 2007), 14 of which encode JAZ proteins.”
A Bioinformatic Analysis of NAC Genes for Plant Cell Wall Development in Relation to Lignocellulosic Bioenergy Production (2009, background): “However, genome-wide transcription factor search in photosynthetic species found that no NAC transcription factors exist in the algae [54].”
Transcriptional regulation of fatty acid production in higher plants: Molecular bases and biotechnological outcomes (2014, neutral): “A genome‐wide search identified 147 TF belonging to this family [59, 60].”
The role of WRKY transcription factors in plant abiotic stresses. (2012, background): “Plants devote a large portion of their genome capacity to transcription, with the Arabidopsis (Arabidopsis thaliana) and rice (Oryza sativa) genome coding for more than 2100 and 2300 transcription factors respectively [5].”
A Snapshot of the Emerging Tomato Genome Sequence (2009, methodology): “For Arabidopsis, 5.9 to 7% (Riechmann et al., 2000; Riano-Pachon et al., 2007) and rice, 4% (Goff et al., 2002; Riano-Pachon et al., 2007) of the total genes are TFs.”