DBD––taxonomically broad transcription factor predictions: new content and functionality

By Derek Wilson, Varodom Charoensawan, Sarah K. Kummerfeld, Sarah A. Teichmann. Nucleic Acids Res., 2007

304 citations recorded by the source corpus.

DNA-binding domain (DBD) is a database of predicted sequence-specific DNA-binding transcription factors (TFs) for all publicly available proteomes. The proteomes have increased from 150 in the initial version of DBD to over 700 in the current version. All predicted TFs must contain a significant match to a hidden Markov model representing a sequence-specific DNA-binding domain family. Access to TF predictions is provided through http://transcriptionfactor.org, where new search options are now provided such as searching by gene names in model organisms, searching for all proteins in a particular DBD family and specific organism. We illustrate the application of this type of search facility by contrasting trends of DBD family occurrence throughout the tree of life, highlighting the clear partition between eukaryotic and prokaryotic DBD expansions. The website content has been expanded to include dedicated pages for each TF containing domain assignment details, gene names, links to external databases and links to TFs with similar domain arrangements. We compare the increase in number of predicted TFs with proteome size in eukaryotes and prokaryotes. Eukaryotes follow a slower rate of increase in TFs than prokaryotes, which could be due to the presence of splice variants or an increase in combinatorial control.

Subfields: Molecular Biology

View Paper: https://www.semanticscholar.org/paper/2edfe5ed17f53bf76fd4684311264599a2ded1da

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In Molecular Biology

Citations in the corpus

A census of human transcription factors: function, expression and evolution (2009, background): “Computational studies have reported TF repertoires by searching for genes containing DNA-binding domains either across all completely sequenced genome”
A Genecentric Human Protein Atlas for Expression Profiles Based on Antibodies* (2008, unknown): “TCDB, Transporter Classification Database; DBD, DNA-binding domain.”
SUPERFAMILY—sophisticated comparative genomics, data mining, visualization and phylogeny (2008, methodology): “Likewise, the DBD database (25) uses a curated subset of the HMMs for the prediction of sequence-speciﬁc transcription factors.”