about DBTBS

Database Description
With the entire genome sequence of Bacillus subtilis now determined, one of the next major targets of B. subtilis genomics is to elucidate its complete 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. We therefore constructed the DBTBS database, containing a collection of experimentally validated gene regulatory relations and the corresponding transcription factor binding sites upstream of B. subtilis genes. Its current version is constructed by surveying 947 references and contains the information of 120 binding factors and 1475 gene regulatory relations. For each promoter, all of its known cis-elements are listed according to their positions, while these cis-elements are aligned to illustrate the consensus sequence for each transcription factor. All probable transcription factors coded in the genome were classified using Pfam motifs.

Recent Developments
The DBTBS database was recently reorganized to show operons instead of individual genes as the building blocks of gene regulatory networks. DBTBS now contains 463 experimentally known operons, as well as their terminator sequences if identifiable. In addition, 517 transcriptional terminators were identified computationally. (De Hoon, M.J.L. et al., PLoS Comput. Biol. 1, e25 (2005)).
A new section was added under 'Motif conservation',which presents hexameric motifs found to be conserved to different extents between upstream intergenic regions of genus-specific subgroups of homologous proteins.

Ishii, T., Yoshida, K., Terai, G., Fujita, Y., Nakai, K.
DBTBS: a database of Bacillus subtilis promoters and transcription factors. Nucleic Acids Res., 29,278-280 (2001) (NAR online).
Makita Y., Nakao M., Ogasawara N., Nakai K.
DBTBS: database of transcriptional regulation in Bacillus subtilis and its contribution to comparative genomics. Nucleic Acids Res., 32,D75-77 (2004) (NAR online).
Sierro N., Makita Y., de Hoon M.J.L., Nakai K.
DBTBS: a database of transcriptional regulation in Bacillus subtilis containing upstream intergenic conservation information. Nucleic Acids Res., 36,D93-96 (2008) (NAR online).

Version History
Oct. 25, 1999: Recovery of the server at U. Tokyo
Sep. 1, 2000: First Public Release
Nov. 6, 2000: Release 2.0 (search function; extensive updates of data)
Nov. 7, 2000: Release 2.1 (new promoter table)
Sep. 6, 2001: Release 2.2 (list of predicted regulons)
Aug. 26, 2003: Release 3 (Phylogenetic profile)
Feb. 29, 2004: Release 3.1 (Move the tables of phylogenetic profile and minor data update)
Oct. 31, 2004: Release 3.2 (Data update)
Dec. 14, 2004: Release 3.3 (Fixed some data mistakes)
Jan. 14, 2005: Release 3.4 (Fixed some data mistakes)
May 5, 2005: Release 4 (Added operon and terminator data)
Nov 30, 2005: Release 4.1 (Update Genbank file to 04-OCT-2005 version)
Spe 15, 2007: Release 5 (Addition of hexameric motif conservation between Gram-positive bacteria)

We are grateful to Naotake Ogasawara for useful comments, and Takahiro Ishii, Ken-ichi Yoshida, Goro Terai, Mitsuteru Nakao and Yasutaro Fujita, who have contributed to earlier versions of this database. This work was partly supported by a Grant-in Aid for Scientific Research on Priority Areas 'Genome Information Science' from the Ministry of Education, Culture, Sports, Science and Technology of Japan.

Copyright: Human Genome Center, Inst. Med. Sci., Univ. Tokyo; 1999-2007
Contact: Kenta Nakai