DBTBS


17962296	DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. [PMID: 17962296] Sierro N, Makita Y, de Hoon M, Nakai K. Abstract 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. Nucleic Acids Res. 2008:36(Database issue) \| 242 Citations (from Europe PMC, 2025-03-29)
14992510	Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information. [PMID: 14992510] De Hoon MJ, Imoto S, Kobayashi K, Ogasawara N, Miyano S. Abstract We predict the operon structure of the Bacillus subtilis genome using the average operon length, the distance between genes in base pairs, and the similarity in gene expression measured in time course and gene disruptant experiments. By expressing the operon prediction for each method as a Bayesian probability, we are able to combine the four prediction methods into a Bayesian classifier in a statistically rigorous manner. The discriminant value for the Bayesian classifier can be chosen by considering the associated cost of misclassifying an operon or a non-operon gene pair. For equal costs, an overall accuracy of 88.7% was found in a leave-one-out analysis for the joint Bayesian classifier, whereas the individual information sources yielded accuracies of 58.1%, 83.1%, 77.3%, and 71.8% respectively. The predicted operon structure based on the joint Bayesian classifier is available from the DBTBS database (http://dbtbs.hgc.jp). Pac Symp Biocomput. 2004:() \| 19 Citations (from Europe PMC, 2025-03-29)
14681362	DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. [PMID: 14681362] Makita Y, Nakao M, Ogasawara N, Nakai K. Abstract DBTBS (http://dbtbs.hgc.jp) was originally released in 1999 as a reference database of published transcriptional regulation events in Bacillus subtilis, one of the best studied bacteria. It is essentially a compilation of transcription factors with their regulated genes as well as their recognition sequences, which were experimentally characterized and reported in the literature. Here we report its major update, which contains information on 114 transcription factors, including sigma factors, and 633 promoters of 525 genes. The number of references cited in the database has increased from 291 to 378. It also supports a function to find putative transcription factor binding sites within input sequences by using our collection of weight matrices and consensus patterns. Furthermore, though preliminarily, DBTBS now aims to contribute to comparative genomics by showing the presence or absence of potentially orthologous transcription factors and their corresponding cis-elements on the promoters of their potentially orthologously regulated genes in 50 eubacterial genomes. Nucleic Acids Res. 2004:32(Database issue) \| 93 Citations (from Europe PMC, 2025-03-29)
11125112	DBTBS: a database of Bacillus subtilis promoters and transcription factors. [PMID: 11125112] Ishii T, Yoshida K, Terai G, Fujita Y, Nakai K. Abstract With the completion of the determination of its entire genome sequence, one of the next major targets of Bacillus subtilis genomics is to clarify the whole gene regulatory network. To this end, the results of systematic experiments should be compared with the rich source of individual experimental results accumulated so far. Thus, we constructed a database of the upstream regulatory information of B.subtilis (DBTBS). The current version was constructed by surveying 291 references and contains information on 90 binding factors and 403 promoters. For each promoter, all of its known cis-elements are listed according to their positions, while these cis-elements are aligned to illustrate their consensus sequence for each transcription factor. All probable transcription factors coded in the genome were classified with the Pfam motifs. Using this database, we compared the character of B.subtilis promoters with that of Escherichia coli promoters. Our database is accessible at http://elmo.ims.u-tokyo.ac.jp/dbtbs/. Nucleic Acids Res. 2001:29(1) \| 44 Citations (from Europe PMC, 2025-03-29)

DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. [PMID: 17962296]

Sierro N, Makita Y, de Hoon M, Nakai K.

Abstract

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.

Nucleic Acids Res. 2008:36(Database issue) | 242 Citations (from Europe PMC, 2025-03-29)

Predicting the operon structure of Bacillus subtilis using operon length, intergene distance, and gene expression information. [PMID: 14992510]

De Hoon MJ, Imoto S, Kobayashi K, Ogasawara N, Miyano S.

Abstract

We predict the operon structure of the Bacillus subtilis genome using the average operon length, the distance between genes in base pairs, and the similarity in gene expression measured in time course and gene disruptant experiments. By expressing the operon prediction for each method as a Bayesian probability, we are able to combine the four prediction methods into a Bayesian classifier in a statistically rigorous manner. The discriminant value for the Bayesian classifier can be chosen by considering the associated cost of misclassifying an operon or a non-operon gene pair. For equal costs, an overall accuracy of 88.7% was found in a leave-one-out analysis for the joint Bayesian classifier, whereas the individual information sources yielded accuracies of 58.1%, 83.1%, 77.3%, and 71.8% respectively. The predicted operon structure based on the joint Bayesian classifier is available from the DBTBS database (http://dbtbs.hgc.jp).

Pac Symp Biocomput. 2004:() | 19 Citations (from Europe PMC, 2025-03-29)

DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. [PMID: 14681362]

Makita Y, Nakao M, Ogasawara N, Nakai K.

Abstract

DBTBS (http://dbtbs.hgc.jp) was originally released in 1999 as a reference database of published transcriptional regulation events in Bacillus subtilis, one of the best studied bacteria. It is essentially a compilation of transcription factors with their regulated genes as well as their recognition sequences, which were experimentally characterized and reported in the literature. Here we report its major update, which contains information on 114 transcription factors, including sigma factors, and 633 promoters of 525 genes. The number of references cited in the database has increased from 291 to 378. It also supports a function to find putative transcription factor binding sites within input sequences by using our collection of weight matrices and consensus patterns. Furthermore, though preliminarily, DBTBS now aims to contribute to comparative genomics by showing the presence or absence of potentially orthologous transcription factors and their corresponding cis-elements on the promoters of their potentially orthologously regulated genes in 50 eubacterial genomes.

Nucleic Acids Res. 2004:32(Database issue) | 93 Citations (from Europe PMC, 2025-03-29)

DBTBS: a database of Bacillus subtilis promoters and transcription factors. [PMID: 11125112]

Ishii T, Yoshida K, Terai G, Fujita Y, Nakai K.

Abstract

With the completion of the determination of its entire genome sequence, one of the next major targets of Bacillus subtilis genomics is to clarify the whole gene regulatory network. To this end, the results of systematic experiments should be compared with the rich source of individual experimental results accumulated so far. Thus, we constructed a database of the upstream regulatory information of B.subtilis (DBTBS). The current version was constructed by surveying 291 references and contains information on 90 binding factors and 403 promoters. For each promoter, all of its known cis-elements are listed according to their positions, while these cis-elements are aligned to illustrate their consensus sequence for each transcription factor. All probable transcription factors coded in the genome were classified with the Pfam motifs. Using this database, we compared the character of B.subtilis promoters with that of Escherichia coli promoters. Our database is accessible at http://elmo.ims.u-tokyo.ac.jp/dbtbs/.

Nucleic Acids Res. 2001:29(1) | 44 Citations (from Europe PMC, 2025-03-29)

URL:	http://dbtbs.hgc.jp/
Full name:	Database of Transcriptional Regulation in Bacillus subtilis
Description:	DBTBS is a reference database on transcriptional regulation in Bacillus subtilis, summarizing the experimentally characterized transcription factors, their recognition sequences and the genes they regulate.
Year founded:	2001
Last update:	2015-05-02
Version:
Accessibility:	Unaccessible
Country/Region:	Japan

Data type:	DNA Protein
Data object:
Database category:	Interaction
Major species:
Keywords:	transcription factor transcription factor binding site transcriptional regulation

University/Institution:	University of Tokyo
Address:	4-6-1 Shirokanedai, Minato-ku, Tokyo 108-8639
City:	Tokyo
Province/State:
Country/Region:	Japan
Contact name (PI/Team):	Kenta Nakai
Contact email (PI/Helpdesk):	knakai@ims.u-tokyo.ac.jp

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Database Commons a catalog of worldwide biological databases

a catalog of worldwide biological databases

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DBTBS

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Database Commons
a catalog of worldwide biological databases