PlantTFDB: a comprehensive plant transcription factor database

Abstract

Transcription factors (TFs) play key roles in controlling gene expression. Systematic identification and annotation of TFs, followed by construction of TF databases may serve as useful resources for studying the function and evolution of transcription factors. We developed a comprehensive plant transcription factor database PlantTFDB (http://planttfdb.cbi.pku.edu.cn), which contains 26,402 TFs predicted from 22 species, including five model organisms with available whole genome sequence and 17 plants with available EST sequences. To provide comprehensive information for those putative TFs, we made extensive annotation at both family and gene levels. A brief introduction and key references were presented for each family. Functional domain information and cross-references to various well-known public databases were available for each identified TF. In addition, we predicted putative orthologs of those TFs among the 22 species. PlantTFDB has a simple interface to allow users to search the database by IDs or free texts, to make sequence similarity search against TFs of all or individual species, and to download TF sequences for local analysis.

Figure 1.

The annotation information of a typical entry of the PlantTFDB showing the rich annotation of a bread wheat MADS box transcription factor (PTTa00615.1). The annotation contains four major categories: (A) Basic information; (B) Annotation; (C) Sequence; (D) Protein sequence feature details. Some of the annotations were tailored since the screen dump of the actual web page is too large to fit. The actual layout and content of the web page could be slightly different, since we keep developing and updating the database with new data available.