Plant Transcription Factor Database
v4.0Previous version: v1.0, v2.0, v3.0
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Based on the family assignment rules, we identified
320,370transcription factors from
165species and classified them into
58families. Species included in PlantTFDB 4.0 covers the main lineages of green plants, providing genomic TF repertoires across green plants.
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).
Updates in v4.0
- PlantTFDB 4.0 includes 165 species, with 89 newly sequenced species added, covering the main lineages across the green plants.
- Re-collection or annotation of pre-existing types of abundant functional and evolutionary annotation for all identified TFs.
- Re-construction of the orthologous groups for all 156 species with genome sequences, 17 representative species, and clades of chlorophytae, monocots, asterids, fabids and malvids, respectively, and identification of RBHs for every pairs of 156 species to transfer high-quality annotation interspecies (download).
- Systemic GO annotation for 165 species by integrating GO annotation from TAIR and UniProtKB, predicted by InterProScan and transferred from RBHs in other species (download).
- A set of high-quality, non-redundant TF binding motifs, which were projected to 156 species based on the RBHs in the same family (download).
- Multiple types of regulatory elements (e.g., DNase I hypersensitive site, genomic TF footprints, TF binding peaks, histone modifications and nucleosome position) derived from high-throughput assays (PlantRegMap).
- Genome-wide regulatory interactions integrated from literature mining, TF ChIP-seq and prediction combined TF binding motifs and regulatory elements (PlantRegMap).
- Upgraded TF prediction server to support for inputting nucleic acid sequences and larger files (up to 100M), and set up four novel tools for regulation prediction and functional enrichment tools (PlantRegMap).
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 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)
- 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]
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 . 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.