Plant Transcription Factor Database collected  transcription factors from  species, and they are classified into  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), expression information derived from EST and microarray, and annotations in various databases such as UniProt, RefSeq, TransFac and STRING. 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.

PlantTFDB v2.0 covers 49 species , leading to a more than 100% growth compared with the previous release (22 species). Species collected in PlantTFDB covered green algae (nine species), moss (one species), ferns (one species), gymnosperms (three species), and angiosperms (35 species), covering main lineages of kingdom Plantae.

New method of constructing protein dataset was adopted to get a comprehensive proteome. In PlantTFDB v2.0, protein is the basic unit, and each TF entry is a unique protein. Different gene models (or gene models from different data source) encoding the same protein are treated as one entry.

Rules for identification and classification of TFs have been updated according to recently literatures, GO annotation, TAIR and Uniprot annotations. A more stringent pipeline was adopted to ensure that entries collected are really TF rather than other regulators such as regulation cofactor, remodeling factors, histone demethylases, DNA methyltransferases and histone acetyltransferases.

Phylogenetic trees have been constructed for families across species. And ortholog groups are constructed for species with genome sequences. These will provide convenience for further analysis on TF evolutionary.

Search function has been improved to let user to search TFs with much more flexibility.

Web service has been provided for advanced users to access PlantTFDB 2.0 by programming more efficiently.

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]

Luo Jingchu (luojc at mail.cbi.pku.edu.cn)

Gu Xiaocheng (guxc at lsc.pku.edu.cn)

Gao Ge (gaog at mail.cbi.pku.edu.cn)

Kong Lei (kongl at mail.cbi.pku.edu.cn)

Tang Liang (tangl at mail.cbi.pku.edu.cn)

Zhang He (zhangh at mail.cbi.pku.edu.cn)

Jin Jinpu (jinjp at mail.cbi.pku.edu.cn)

Liu Xiaochuan (liuxc at mail.cbi.pku.edu.cn)

Zhao Yi (zhaoy at mail.cbi.pku.edu.cn)

He Kun (hek at mail.cbi.pku.edu.cn)

Guo Anyuan (guoay at mail.cbi.pku.edu.cn)

Zhu Qihui (zhuqh at mail.cbi.pku.edu.cn)

Chen Xin (chenx at mail.cbi.pku.edu.cn)

We would like to extend our grateful acknowledgments and thanks to JGI for providing genome annotations for 10 genomes unpublished, and thank MGSC for providing genome annotations for Medicago truncatula.

This work was supported by China Ministry of Science and Technology 863 Hi-Tech Research and Development Programs (No. 2007AA02Z165), 973 Basic Research Program (No. 2007CB946904).