DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information

By Nicolas Sierro, Yuko Makita, M. D. de Hoon, Kenta Nakai. Nucleic Acids Res., 2007

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DBTBS, first released in 1999, is a reference database on transcriptional regulation in Bacillus subtilis, summarizing the experimentally characterized transcription factors, their recognition sequences and the genes they regulate. Since the previous release, the original content was extended by the addition of the data contained in 569 new publications, the total of which now reaches 947. The number of B. subtilis promoters annotated in the database was more than doubled to 1475. In addition, 463 experimentally validated B. subtilis operons and their terminators have been included. Given the increase in the number of fully sequenced bacterial genomes, we decided to extend the usability of DBTBS in comparative regulatory genomics. We therefore created a new section on the conservation of the upstream regulatory sequences between homologous genes in 40 Gram-positive bacterial species, as well as on the presence of overrepresented hexameric motifs that may have regulatory functions. DBTBS can be accessed at: http://dbtbs.hgc.jp.

Subfields: Genetics, Molecular Biology

View Paper: https://www.semanticscholar.org/paper/a5ec679fbf5f02c290bc13f0d5b64108d13a8d79

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Citations in the corpus

DOOR: a database for prokaryotic operons (2008, methodology): “The DOOR system provides a number of procedures for calculating various operon-related statistics for a specified genome, including (i) the distribution of the number of genes across all operons in the genome; (ii) the distributions of inter-genic distances between operons and between genes, respect”
Condition-Dependent Transcriptome Reveals High-Level Regulatory Architecture in Bacillus subtilis (2012, background): “In this tree built independently of DNA sequence information, the DNA binding sites for different RNAP sigma subunits (11) are clustered (Figure 2B), highlighting the prominent role of sigma factor–mediated promoter recognition in differential gene expression.”
RegPrecise 3.0 – A resource for genome-scale exploration of transcriptional regulation in bacteria (2013, methodology): “We are planning to incorporate supportive experimental evidences for reconstructed regulons and effectors using information from literature and other databases on microbial regulation including RegTransBase [25], RegulonDB [26], DBTBS [27], and CoryneRegNet [24].”