Romeuf et al. BMC Genomics 2010, 11:185 http://www.biomedcentral.com/1471-2164/11/185 D A T A B A S E Open Access wDBTF: an integrated database resource for studying wheat transcription factor families Isabelle Romeuf1, Dominique Tessier2, Mireille Dardevet1, Gérard Branlard1, Gilles Charmet1, Catherine Ravel1* Abstract Background: Transcription factors (TFs) regulate gene expression by interacting with promoters of their target genes and are classified into families based on their DNA-binding domains. Genes coding for TFs have been identified in the sequences of model plant genomes. The rice (Oryza sativa spp. japonica) genome contains 2,384 TF gene models, which represent the mRNA transcript of a locus, classed into 63 families. Results: We have created an extensive list of wheat (Triticum aestivum L) TF sequences based on sequence homology with rice TFs identified and classified in the Database of Rice Transcription Factors (DRTF). We have identified 7,112 wheat sequences (contigs and singletons) from a dataset of 1,033,960 expressed sequence tag and mRNA (ET) sequences available. This number is about three times the number of TFs in rice so proportionally is very similar if allowance is made for the hexaploidy of wheat. Of these sequences 3,820 encode gene products with a DNA-binding domain and thus were confirmed as potential regulators. These 3,820 sequences were classified into 40 families and 84 subfamilies and some members defined orphan families. The results were compiled in the Database of Wheat Transcription Factor (wDBTF), an inventory available on the web http://wwwappli.nantes.inra.fr:8180/wDBFT/. For each accession, a link to its library source and its Affymetrix identification number is provided. The positions of Pfam (protein family database) motifs were given when known. Conclusions: wDBTF collates 3,820 wheat TF sequences validated by the presence of a DNA-binding domain out of 7,112 potential TF sequences identified from publicly available gene expression data. We also incorporated in silico expression data on these TFs into the database. Thus this database provides a major resource for systematic studies of TF families and their expression in wheat as illustrated here in a study of DOF family members expressed during seed development. Background Gene expression at the level of mRNA transcription from DNA is regulated through different mechanisms, the most widely studied being regulation by transcription factors (TFs). These DNA-binding proteins control gene expres- sion by interacting with cis-regulatory elements (CREs) in the promoters of their target genes. DNA-binding domains are in general highly conserved among species so their characteristics are used to classify TFs into families. Transcriptional control of gene expression influences many biological processes such as responses to the envir- onment or stress and regulation of metabolic pathways. * Correspondence: Catherine.Ravel@clermont.inra.fr 1Institut National de la Recherche Agronomique (INRA), UMR1095, Génétique, Diversité et Ecophysiologie des Céréales, 234 avenue du Brézet, Clermont-Ferrand, F-63100 France; Université Blaise-Pascal, UMR1095, Campus des Cézeaux, F-63170 Aubière, France The sequencing of model plant genomes has allowed many genes coding for TFs to be identified. A total of 1,533 TFs were identified in the Arabidopsis thaliana genome [1] and classified into 34 families. Comparing these with TF genes in other eukaryotic genomes, i.e., of Drosophila, Caenorhabditis elegans, and Saccharomyces cerevisiae, the size of TF families differs considerably across the eukaryote kingdoms and about 45% of Arabi- dopsis TFs are from families specific to plants [2]. In Oryza sativa spp. japonica, Xiong et al. [3] identified 1,611 TF genes belonging to 37 gene families. Most TF families are of similar size in rice and in Arabidopsis [3]. Information on the TFs of model species has been organized into databases. Arabidopsis TF sequences were compiled and classified into families by several groups: the Riechmann group, the Sheen group http:// genetics.mgh.harvard.edu/sheenweb/AraTRs.html, © 2010 Romeuf et al; licensee BioMed Central Ltd. This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.