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Database information

PlnTFDB (Plant Transcription Factor Database)

General information

Description: The Plant Transcription Factor Database is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species (sensu lato).
Year founded: 2009
Last update: 2010-01-01
Version: v3.0
Accessibility:
Manual:
Accessible
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Country/Region: Germany
Data type:
Data object:
Database category:
Major organism:
NA
Keywords:

Contact information

University/Institution: University of Potsdam
Address: Karl-Liebknecht-Str. 24-25, Haus 20, 14476 Potsdam-Golm, Germany
City: Potsdam-Golm
Province/State:
Country/Region: Germany
Contact name (PI/Team): Diego Mauricio Riaño-Pachón
Contact email (PI/Helpdesk): riano@mpimp-golm.mpg.de

Record metadata

Created on: 2015-07-17
Curated by:
huma shireen [2018-09-03]
Lina Ma [2018-06-11]
Shixiang Sun [2016-03-25]
Shixiang Sun [2015-11-21]

Ranking

All databases:
222/4549 (95.142%)
Gene genome and annotation:
85/1211 (93.064%)
222
Total Rank
423
Citations
32.539
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Publications

19858103
PlnTFDB: updated content and new features of the plant transcription factor database. [PMID: 19858103]
Pérez-Rodríguez P, Riaño-Pachón DM, Corrêa LG, Rensing SA, Kersten B, Mueller-Roeber B.

The Plant Transcription Factor Database (PlnTFDB; http://plntfdb.bio.uni-potsdam.de/v3.0/) is an integrative database that provides putatively complete sets of transcription factors (TFs) and other transcriptional regulators (TRs) in plant species (sensu lato) whose genomes have been completely sequenced and annotated. The complete sets of 84 families of TFs and TRs from 19 species ranging from unicellular red and green algae to angiosperms are included in PlnTFDB, representing >1.6 billion years of evolution of gene regulatory networks. For each gene family, a basic description is provided that is complemented by literature references, and multiple sequence alignments of protein domains. TF or TR gene entries include information of expressed sequence tags, 3D protein structures of homologous proteins, domain architecture and cross-links to other computational resources online. Moreover, the different species in PlnTFDB are linked to each other by means of orthologous genes facilitating cross-species comparisons.

Nucleic Acids Res. 2010:38(Database issue) | 261 Citations (from Europe PMC, 2020-02-15)
17286856
PlnTFDB: an integrative plant transcription factor database. [PMID: 17286856]
Riaño-Pachón DM, Ruzicic S, Dreyer I, Mueller-Roeber B.

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.

BMC Bioinformatics. 2007:8() | 162 Citations (from Europe PMC, 2020-02-08)