PlantTFDB
Plant Transcription Factor Database
v3.0
Center for Bioinformatics, Peking University, China Previous versions:v1.0 v2.0
Introduction
Based on the family assignment rules, we identified
129, 288
 transcription factors from
83
 species and classified them into
58
 families. Species included in PlantTFDB 3.0 covers the main lineages of green plants. Therefore, PlantTFDB provides genomic TF repertoires across Viridiplantae.
To provide comprehensive information for the TF family, a brief introduction and key references are presented for each family. Comprehensive annotations are made for each identified TF, including functional domains, 3D structures, gene ontology (GO), plant ontology (PO), expression information, expert-curated functional description, regulation information, interaction, conserved elements, references, and annotations in various databases such as UniProt, RefSeq, TransFac, STRING, and VISTA.
By inferring orthologous groups and constructing phylogenetic trees, evolutionary relationships among identified TFs were inferred. In addition, PlantTFDB has a simple and user-friendly interface to allow users to query based on combined conditions or make sequence similarity search using BLAST.
In this version, A TF prediction server has been set up for users to identify TFs in multiple sequences.
Updates in v3.0
  1. PlantTFDB 3.0 covers 83 species , of which 67 species with genome sequences, leading to a 139% growth compared with the previous release for species with genome sequences (28 species). Species collected in PlantTFDB covered green algae (ten species), moss (one species), ferns (one species), gymnosperms (four species), and angiosperms (67 species), covering main lineages of Viridiplantae.
  2. In this version, we just constructed protein sets for 16 species without genome sequences. For species with genome sequences, proteins from genome annotation were used to identify TFs.
  3. Acording to recent literature, we refined the TF assignment rules. HMM models used to predicted TFs have been updated to Pfam 27.0 and model thresholds were refined using established pipeline.
  4. Besides previous annotation types, useful information such as expert-curated functinal descriptions, plant ontology, regulation information (including binding site, binding matrix, ChIP-chip/ChIP-seq, miRNA regulation .etc), interaction, conserved elements, mutation and phenotype information, have been added.
  5. Phylogenetic trees have been re-constructed for families intra- and inter-species. Orthologous groups are inferred for 67 species with genome sequences and phylogenetic trees within orthologous groups are inferred. These will provide convenience for further analysis on TF evolution.
  6. A TF prediction server has been set up in this version. Users can use it to identify TFs in multiple sequences.
How To Cite
Jin JP, Zhang H, Kong L, Gao G and Luo JC. (2014). PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Research, 42(D1):D1182-D1187.[full text]

People
Developers
Jin Jinpu (jinjp at mail.cbi.pku.edu.cn)
Zhang He (zhangh at mail.cbi.pku.edu.cn)
Kong Lei (kongl at mail.cbi.pku.edu.cn)
Gao Ge (gaog at mail.cbi.pku.edu.cn)
Luo Jingchu (luojc at mail.cbi.pku.edu.cn)
Previous Developers and Maintainers
Guo Anyuan (guoay at mail.cbi.pku.edu.cn)
He Kun (hek at mail.cbi.pku.edu.cn)
Chen Xin (chenx at mail.cbi.pku.edu.cn)
Zhu Qihui (zhuqh at mail.cbi.pku.edu.cn)
Gu Xiaocheng
Publications
  1. Jin JP, He K, Tang X, Li Z, Lv L, Zhao Y, Luo JC, Gao G. (2015). An Arabidopsis transcriptional regulatory map reveals distinct functional and evolutionary features of novel transcription factors. Molecular Biology and Evolution, 32(7):1767-1773. [full text]
  2. Jin JP, Guo AY, He K, Zhang H, Zhu QH, Chen X, Gao G, Luo JC. (2015). Classification, prediction and database construction of plant transcription factors. Biotechnology Bulletin, 31(11):68-77. [In Chinese, PDF]
  3. Jin JP, Zhang H, Kong L, Gao G, Luo JC. (2014). PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors. Nucleic Acids Research, 42(D1):D1182-D1187.[full text]
  4. Jin JP. (2014). Systematic identification and annotation of plant transcription factors and analyses of Arabidopsis transcriptional regulatory networks. Peking University (PhD Thesis). [In Chinese, PDF]
  5. Zhang H, Jin JP, Tang L, Zhao Y, Gu XC, Gao G, Luo JC. (2011). PlantTFDB 2.0: update and improvement of the comprehensive plant transcription factor database. Nucleic Acids Research,39: D1114-D1117. [full text]
  6. He K, Guo AY, Gao G, Zhu QH, Liu XC, Zhang H, Chen X, Gu X, Luo J. (2010). Computational identification of plant transcription factors and the construction of the PlantTFDB database. Methods Mol Biol., 674:351-68. [Pubmed]
  7. Guo AY, Chen X, Gao G, Zhang H, Zhu QH, Liu XC, Zhong YF, Gu XC, He K, Luo JC. (2008). PlantTFDB: a comprehensive plant transcription factor database. Nucleic Acids Research, 36: D966-D969. [Pubmed]
  8. Zhu QH, Guo AY, Gao G, Zhong YF, Xu M, Huang MR, Luo JC. (2007). DPTF: a database of poplar transcription factors. Bioinformatics, 23: 1307-1308. [Pubmed]
  9. Gao G, Zhong Y, Guo A, Zhu Q, Tang W, Zheng W, Gu X, Wei L, Luo J. (2006). DRTF: a database of rice transcription factors. Bioinformatics, 22(10): 1286-7 [Pubmed]
  10. Guo A, He K, Liu D, Bai S, Gu X, Wei L, Luo J. (2005). DATF: a database of Arabidopsis transcription factors. Bioinformatics, 21:2568-9. [Pubmed]
Acknowledgement
We would like to extend our grateful acknowledgments and thanks to JGI for providing genome annotations for four genomes unpublished, thank AGD for providing genome annotations for Amborella trichopoda, ICGC for Citrus clementina, and AGI for three rice species. Anyone who uses the TF annotation of these unpublished genomes, please follow the usage policy of data providers.
This work was supported by China NSFC (31071160, 31171242), High-Tech Program (2006AA02Z334, 2012AA020409), National Key Basic Research Program (2011CBA01102), National Outstanding Youth Talents Program, as well as National Science and Technology Infrastructure Program (2009FY120100).