The ID of transcription factor collected in PlantTFDB. The TF ID consists of three characters which represent the species (e.g. Ath represent ) and 6 figures.

The gene coding for this transcription factor.

The ID of gene model, which was extracted from the original data source. Gene model ID can be searched in quick search or advanced search page.

The type of gene model. There are four types of gene model in PlantTFDB:

'genome' -- gene models came from genome annotation;

'refseq' -- gene models came from Refseq mRNA;

'PU_ref' -- gene models came from PlantGDB and Unigene, and they were selected as a representation of a cluster of PUTs and Unigene;

'PU_unref' -- gene models came from PlantGDB and Unigene, but they were not selected as a representation of a cluster of PUTs and Unigene;

The source where gene model was got

The Domain used to identify and classify transcription factors.

Domain and other features identified by InterProScan.

Gene ontology for this transcription factor predicted by InterProScan.

Nucleic Localization signal (NLS) predicted by predictnls.

The best Blast hit from PDB.

The best Blast hit from UniGene, GEO, ArrayExpress and GeneVestigator.

The best Blast hit from EMBL, Refseq, SwissProt, TrEMBL, TransFac and STRING.

Orthologous groups predicted by OrthoMCL in 29 species with genomic sequences.

The links to other web sites.

Publications related to the corresponding TF

Multiple sequence alignment for full length transcription factors was inferred using T-Coffee.

Multiple sequence alignment for domain was constructed through Hidden Markov Model-guided method.

Phylogenetic trees for TFs of a family from one species are inferred using MrBayes (v3.2) based on Dayhoff model for 50,000 generations from Dn, and the result tree is an unrooted tree.

Phylogenetic trees for TFs of a family from all species are inferred using FastTree (v2.1.3) with 100 times bootstraps, and the result tree is an unrooted tree.

In quick search box, you can search the TF using TF ID, gene model ID or common name.

In advanced search, you can query by basic information, properties, expression location and annotations in selected species and families. A customized dispaly of result is supported, and you can choose columns you'd like to see in result. And you can also export results in various formats.

A Web service is a software system designed to support interoperable machine-to-machine interaction over a network. It has an interface described in a machine-processable format (specifically WSDL). Other systems interact with the Web service in a manner prescribed by its description using SOAP-messages, typically conveyed using HTTP with an XML serialization in conjunction with other Web-related standards.

PlantTFDB provides a web service for users to retrieve data from PlantTFDB. Web Service can be visited by http://planttfdb.cbi.pku.edu.cn/webservice/server.php. and WSDL file can be visited by http://planttfdb.cbi.pku.edu.cn/webservice/server.php?wsdl. And the document for the data structure and interface method of PlantTFDB webservcie can be downloaded here.

A PHP client for PlantTFDB Web Service can be downloaded here. And you can include this file in your web page to visit PlantTFDB through Web Service. Example can be visited here.