title: BacillusRegNet: a transcriptional regulation database and analysis platform for Bacillus species.
abstract: As high-throughput technologies become cheaper and easier to use, raw sequence data and corresponding annotations for many organisms are becoming available. However, sequence data alone is not sufficient to explain the biological behaviour of organisms, which arises largely from complex molecular interactions. There is a need to develop new platform technologies that can be applied to the investigation of whole-genome datasets in an efficient and cost-effective manner. One such approach is the transfer of existing knowledge from well-studied organisms to closely-related organisms. In this paper, we describe a system, BacillusRegNet, for the use of a model organism, Bacillus subtilis, to infer genome-wide regulatory networks in less well-studied close relatives. The putative transcription factors, their binding sequences and predicted promoter sequences along with annotations are available from the associated BacillusRegNet website (http://bacillus.ncl.ac.uk).
authors.affiliation: School of Computing Science, and Centre for Synthetic Biology and Bioexploitation, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
authors.forename: Goksel
authors.initials: G
authors.lastname: Misirli
authors.affiliation: School of Computing Science, and Centre for Synthetic Biology and Bioexploitation, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
authors.forename: Jennifer
authors.initials: J
authors.lastname: Hallinan
authors.affiliation: Department of Mathematics and Computer Science, University of Southern Denmark, Odense, DK-5230, Denmark.
authors.forename: Richard
authors.initials: R
authors.lastname: Röttger
authors.affiliation: Department of Mathematics and Computer Science, University of Southern Denmark, Odense, DK-5230, Denmark.
authors.forename: Jan
authors.initials: J
authors.lastname: Baumbach
authors.affiliation: School of Computing Science, and Centre for Synthetic Biology and Bioexploitation, Newcastle University, Newcastle upon Tyne, NE1 7RU, UK.
authors.forename: Anil
authors.initials: A
authors.lastname: Wipat
mesh_terms: D000465:Algorithms; D001412:Bacillus subtilis / Q000235:genetics* / Q000378:metabolism; D001665:Binding Sites; D019295:Computational Biology / Q000379:methods*; D003198:Computer Simulation; D003199:Computer Systems; D030541:Databases, Genetic; D030562:Databases, Protein; D015964:Gene Expression Regulation, Bacterial; D053263:Gene Regulatory Networks; D016680:Genome, Bacterial; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D011401:Promoter Regions, Genetic; D012984:Software; D049490:Systems Biology; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
chemical_list: D014157:Transcription Factors