PlantRegMap/PlantTFDB v5.0
Plant Transcription
Factor Database
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Introduction
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 covers the main lineages of green plants, providing genomic TF repertoires across green plants (Summary of TF repertoires in different taxonomic lineages of green plants and the origination stage of TF families).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, binding motifs, regulation information, interaction, references, and cross-linsk to various databases such as UniProt, RefSeq, STRING and Entrez Gene.
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 using TF IDs and common names in Quick Search, or sequences in BLAST.
A TF prediction server, which supports both protein and nucleic acid sequences, has been set up for users to identify TFs from multiple sequences (file up to 100M).
Users can access the conservation and regulation data, prediction and analysis tools as well as the architecture and evolutionary features of plant transcriptional regulatory networks at the main website PlantRegMap (Brief Guidance in English and Chinese).
Updates in v5.0
- Updated annotation for the collected TFs.
- A module TFext (extended TF repertoires) to release the TF repertoires of newly sequenced species in time.
How To Cite
- Jin JP, Tian F, Yang DC, Meng YQ, Kong L, Luo JC and Gao G. (2017). PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research, 45(D1):D1040-D1045. [full text]
- 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]
- 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]
People
Developers
Jin Jinpu (jinjp at mail.cbi.pku.edu.cn)
Tian Feng (tianf at mail.cbi.pku.edu.cn)
Yang Dechang (yangdc at mail.cbi.pku.edu.cn)
Meng Yuqi (mengyq at mail.cbi.pku.edu.cn)
Kong Lei (kongl at mail.cbi.pku.edu.cn)
Luo Jingchu (luojc at mail.cbi.pku.edu.cn)
Gao Ge (gaog at mail.cbi.pku.edu.cn)
Previous Developers and Maintainers
Zhang He (zhangh at mail.cbi.pku.edu.cn)
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
- Jin JP, Tian F, Yang DC, Meng YQ, Kong L, Luo JC and Gao G. (2017). PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research, 45(D1):D1040-D1045. [full text]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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]
- 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 to Joint Genome Institute for the genome annotation of 13 unpublished species, AGI for six rice species and Leersia perrieri, THGP for Castanea mollissima, BTI for Nicotiana benthamiana and JHU for Juglans regia. Anyone who uses the TF annotation of these unpublished genomes, please follow the usage policy of data providers.
This work was supported by the National Natural Science Foundation of China [1470330]. The work of Ge Gao was supported partly by the National Outstanding Youth Talent Initiative Program. The work of Jinpu Jin was supported partly by the China Postdoctoral Science Foundation Grant [2014M560017, 2015T80015] and the Postdoctoral Fellowship at Peking-Tsinghua Center for Life Sciences.