PlantTFDB
Plant Transcriptional Regulatory Map




Introduction
Systematical identification of transcription factors (TFs), regulatory elements and interactions between them is essential for investigating the functional mechanisms and evolution 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 TF repertoires and comprehensive annotation, multiple types of regulatory elements and genome-wide regulatory interactions derived from literature, high-throughput assays and/or genome comparison, as well as the architectures and evolutionary features of plant transcription regulatory systems. To take full advantage of our enrich data and pipelines, we set up multiple webservers for TF identification, 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.
What's new

  Update in July 2019

  1. Updated annotations for the collected TFs.
  2. Set up a module "extended TF repertoires" to release the TF repertoires of newly sequenced species or previous collected species with new gene annotation in time.
  3. Established the genome-wide, base-resolution conservation landscapes (conserved elements, PhastCons and PhyloP scores) based on the whole genome alignments for 63 plants in seven lineages, covering main lineages of angiosperms (download), and set up a genome browser for users to navigate them (cis-map).
  4. Developed a new algorithm (FunTFBS) to screen for functional TF binding sites by employing the evolutionary footprints from base-varied binding affinities of TFs. The assessment showed that our algorithm is significantly superior to existing methods in accuracy.
  5. Using FunTFBS and the conservation landscapes established above, we further identified over 21,997,501 million functional TFBSs (download) and 2,196,397 regulatory interactions (download), charting the functional regulatory maps for the 63 plants for the first time.
  6. Updated the set of tools for transcriptional regulatory analyses using the newly released algorithm and resources (Regulation Prediction / TF Enrichment).
Features
Regulatory landscape
  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.
Conservation landscape
  1. Orthologous groups and RBHs for all genes of 156 plant species.
  2. A set of pairwise and multiple genome alignments, as well as genome-wide conserved elements and conservation scores (PhastCons and PhyloP) for 63 plant species (download).
Prediction and analysis
  1. 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).
  2. A new algorithm (FunTFBS) and 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.