a catalog of biological databases
|Full name:||Plant Transcription Factor Database|
|Description:||PlantTFDB provides genomic TF repertoires across Viridiplantae. Based on the family assignment rules, we identified 320,370 transcription factors from 165 species and classified them into 58 families. Species included in PlantTFDB 4.0 covers the main lineages of green plants, providing genomic TF repertoires across green plants.|
|Address:||1 State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Center for Bioinformatics, Peking University, Beijing 100871, People’s Republic of China. 2 Beijing Advanced Innovation Center for Genomics (ICG), Biomedical Pioneering Innovation Center (BIOPIC), Peking University, Beijing 100871, People’s Republic of China.|
|Contact name (PI/Team):||Ge Gao|
|Contact email (PI/Helpdesk):||email@example.com|
PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. [PMID: 24174544]
With the aim to provide a resource for functional and evolutionary study of plant transcription factors (TFs), we updated the plant TF database PlantTFDB to version 3.0 (http://planttfdb.cbi.pku.edu.cn). After refining the TF classification pipeline, we systematically identified 129 288 TFs from 83 species, of which 67 species have genome sequences, covering main lineages of green plants. Besides the abundant annotation provided in the previous version, we generated more annotations for identified TFs, including expression, regulation, interaction, conserved elements, phenotype information, expert-curated descriptions derived from UniProt, TAIR and NCBI GeneRIF, as well as references to provide clues for functional studies of TFs. To help identify evolutionary relationship among identified TFs, we assigned 69 450 TFs into 3924 orthologous groups, and constructed 9217 phylogenetic trees for TFs within the same families or same orthologous groups, respectively. In addition, we set up a TF prediction server in this version for users to identify TFs from their own sequences.
PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. [PMID: 21097470]
We updated the plant transcription factor (TF) database to version 2.0 (PlantTFDB 2.0, http://planttfdb.cbi.pku.edu.cn) which contains 53,319 putative TFs predicted from 49 species. We made detailed annotation including general information, domain feature, gene ontology, expression pattern and ortholog groups, as well as cross references to various databases and literature citations for these TFs classified into 58 newly defined families with computational approach and manual inspection. Multiple sequence alignments and phylogenetic trees for each family can be shown as Weblogo pictures or downloaded as text files. We have redesigned the user interface in the new version. Users can search TFs with much more flexibility through the improved advanced search page, and the search results can be exported into various formats for further analysis. In addition, we now provide web service for advanced users to access PlantTFDB 2.0 more efficiently.
PlantTFDB: a comprehensive plant transcription factor database. [PMID: 17933783]
Transcription factors (TFs) play key roles in controlling gene expression. Systematic identification and annotation of TFs, followed by construction of TF databases may serve as useful resources for studying the function and evolution of transcription factors. We developed a comprehensive plant transcription factor database PlantTFDB (http://planttfdb.cbi.pku.edu.cn), which contains 26,402 TFs predicted from 22 species, including five model organisms with available whole genome sequence and 17 plants with available EST sequences. To provide comprehensive information for those putative TFs, we made extensive annotation at both family and gene levels. A brief introduction and key references were presented for each family. Functional domain information and cross-references to various well-known public databases were available for each identified TF. In addition, we predicted putative orthologs of those TFs among the 22 species. PlantTFDB has a simple interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.