PlnTFDB: updated content and new features of the plant transcription factor database
By P. Pérez-Rodríguez, Diego Mauricio Riaño-Pachón, L. Corrêa, S. Rensing, B. Kersten, B. Mueller‐Roeber. Nucleic Acids Res., 2009
680 citations recorded by the source corpus.
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.
Subfields: Molecular Biology, Plant Science
View Paper: https://www.semanticscholar.org/paper/9ef1416600fc5cc1a55634b6dea5b2f9e4359e22
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In Molecular Biology
- Björn Usadel
- G. Ponce-Soto
- B. Mueller‐Roeber
- G. Xue
- K. Krause
- Camila Caldana
- Miroslaw Kwasniewski
- Mark Stitt
In Plant Science
Citations in the corpus
- Transcriptome and Gene Expression Analysis of an Oleaginous Diatom Under Different Salinity Conditions (2013, positive): “Responses of Putative Transcription Factors To identify genes encoding putative transcription factors or transcriptional regulators, we used the Plant Transcription Factor Database [34] to search the Nitzschia sp. transcriptome dataset.”
- ORS1, an H2O2-Responsive NAC Transcription Factor, Controls Senescence in Arabidopsis thaliana (2011, positive): “, 2007) and the Plant Transcription Factor Database (http:// plntfdb.bio.uni-potsdam.de/v3.0/; Pérez-Rodrı́guez et al., 2010) were used.”
- MapMan4: A Refined Protein Classification and Annotation Framework Applicable to Multi-Omics Data Analysis. (2019, methodology): “, 2017) and PlnTFDB (Pérez-Rodrı́guez et al., 2010) as a guide, but in some cases sequence comparison suggested additional subdivision.”
- iTAK: A Program for Genome-wide Prediction and Classification of Plant Transcription Factors, Transcriptional Regulators, and Protein Kinases. (2016, neutral): “Databases presenting these regulatory pr teins, especially TFs, have been developed, such as PlnTFDB (Pérez-Rodríguez et al., 2010) and PlantTFDB (Jin et al., 2013).”
- AGRIS: the Arabidopsis Gene Regulatory Information Server, an update (2010, background): “Different from other community resources such as ATTED-II, which focuses primarily on co-expression analysis (4), Athena that focuses on promoter analysis (5) or PlnTFDB (6), which harbors computationally curated information on TF from many different plant species, AGRIS is Arabidopsis–centered, pri”
- PLAZA 3.0: an access point for plant comparative genomics (2014, background): “The functional annotation has been expanded and now comprises data from Gene Ontology, MapMan, UniProtKB/Swiss-Prot, PlnTFDB and PlantTFDB.”