BacillusRegNet

Project Description

BacillusRegNet is a cross-species analysis platform for the gene regulatory networks of Bacillus species. The system is built upon RegNet and is able to construct gene regulatory networks for closely-related, non-model Bacillus species using data about the model organism B. subtilis. Experimentally-known information about transcription factors (TFs) and their binding sequences, together with protein homologies is used to predict gene regulation relationships for the target organisms.

bacillusregnet

BacillusRegNet is available as a website. Currently, we have 13 Bacillus and 2 GeoBacillus species in addition to the model organism B. subtilis, and the list can be extended. The website has two sections: Experimental and predicted. The former includes known TFs, operons, promoter and binding sequences for B. subtilis. In addition, nucleotide and amino acid sequences for all organisms, and operon predictions for non-model organisms are available. The latter includes additional information such as the homology of CDSs and proteins, and predicted sequences of promoters and binding sites for non-model organisms from the database.

The homology information is used in a comparative genomics approach in order to identify orthogonal TFs with known binding sequences for Bacillus species. These orthogonal TF-binding sequence pairs can be used to construct novel regulatory networks.

Funding

  1. BB/F529038/1: Systems approaches to biological research training grant
  2. BB/F006063/1: From data to knowledge / the ONDEX System for integrating Life Sciences data sources