PlantTFDB
Plant Transcriptional Regulatory Map




Introduction
Transcriptional regulatory interactions between TFs and their target genes provide directly clues to investigate the functional mechanisms of transcriptional regulatory systems. With the aim to provide a comprehensive, high-quality resource for the study of transcriptional regulation in plants, we developed PlantRegMap. It includes multiple types of regulatory elements derived from high-throughput assays for six species(cis-map) and genome-wide regulatory interacttions for 132 species (network) currently. To take full advantage of our enrich data and pipelines, we set up four webservers for regulation prediction and functional enrichment analyses. We wish our data and tools can promote users to explore the functional mechanisms and evolutionary features of plant transcriptional regulatory system.
In addition, Users can access the TF repertoires and annotation, TF binding motifs, and TF prediction server at PlantTFDB, and the architectures and evolutionary features of plant transcription regulatory networks at ATRM.

Features
  1. 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.
  2. Genome-wide regulatory interactions integrated from literature mining, TF ChIP-seq and prediction combined TF binding motifs and regulatory elements.
  3. Systemic GO annotation for 165 species by integrating GO annotation from TAIR and UniProtKB, predicted by InterProScan and transferred from RBHs in other species (see methods, download).
  4. A set of tools for regulation prediction and functional enrichment analyses, including binding site prediction, regulation prediction, GO enrichment and TF enrichment.

How To Cite
  1. Jin JP, Tian F, Yang DC, Meng YQ, Kong L, Luo JC and Gao G. (2016). PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research, doi: 10.1093/nar/gkw982. [full text]
  2. 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]
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)
Publications
  1. Jin JP, Tian F, Yang DC, Meng YQ, Kong L, Luo JC and Gao G. (2016). PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research, doi: 10.1093/nar/gkw982. [full text]
  2. 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]
  3. 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]
  4. 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]
  5. 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]
  6. 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]
  7. 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]
  8. 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]
  9. 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]
  10. 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]
  11. 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.