PlnTFDB: updated content and new features of the plant transcription factor database.

Paulino Pérez-Rodríguez, Diego Mauricio Riaño-Pachón, Luiz Gustavo Guedes Correa, Stefan A. Rensing, Birgit Kersten, Bernd Mueller-Roeber
January 2010
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Abstract

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.

Type
Journal article
Publication
Nucleic acids research
Computational Biology/*methods/trends Genetic Databases Protein Gene Expression Regulation Plant Gene Regulatory Networks Genes Genome Information Storage and Retrieval/methods Internet Plant Diseases/genetics Plant Proteins/metabolism Plants/*metabolism Protein Structure Tertiary *Software Transcription Factors/*metabolism
Diego Mauricio Riaño-Pachón
Diego Mauricio Riaño-Pachón
Assistant Professor (MS3.2) in Computational, Evolutionary and Sistems Biology

I am a computational biologist/bioinformatician at the University of São Paulo, Campus Luiz de Queiroz (Piracicaba/SP, Brazil).

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