ArticleBMC genomics2010
wDBTF: an integrated database resource for studying wheat transcription factor families.
Article in BMC genomics, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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Who cites it
9 citing papers in PubMed, 29 citations in OpenAlex.
- Genome-Wide Sequence and Expression Analysis of the NAC Transcription Factor Family in Polyploid Wheat.G3 (Bethesda, Md.) · 2017Article
- PlantTFDB 4.0: toward a central hub for transcription factors and regulatory interactions in plants.Nucleic acids research · 2017Article
- Transcription factors involved in drought tolerance and their possible role in developing drought tolerant cultivars with emphasis on wheat (Triticum aestivum L.).TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2016Review
- Genome-wide characterization of developmental stage- and tissue-specific transcription factors in wheat.BMC genomics · 2015Article
- Changes in the nuclear proteome of developing wheat (Triticum aestivum L.) grain.Frontiers in plant science · 2015Article
- PlantTFDB 3.0: a portal for the functional and evolutionary study of plant transcription factors.Nucleic acids research · 2014Article
- dbWFA: a web-based database for functional annotation of Triticum aestivum transcripts.Database : the journal of biological databases and curation · 2013Article
- Comparative analyses of nuclear proteome: extending its function.Frontiers in plant science · 2013Article
- Genomic repertoires of DNA-binding transcription factors across the tree of life.Nucleic acids research · 2010Review
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Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTranscription 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.
resultsWe 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.
conclusionswDBTF 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.
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