EcoliNet is a probabilistic functional gene network for Escherichia coli, which is an intensively studied species of bacteria, due to its utility in both exploring the molecular mechanisms underlying fundamental biological processes and manufacturing useful metabolites for the biomedical industry.
Although traditional forward and reverse genetic approaches have played major roles in gene-to-phenotype association mapping in E. coli, a more efficient and sensitive genetics approach would facilitate characterization of the part of the genome whose function is not yet known. Network-assisted predictive genetics is an example of such an approach whose popularity is growing. These days, a tons of omics data for E. coli from experiemntal and computational studies is publicly available. As a result, we were able to use comprehensive information to build EcoliNet that is comprised of 95,520 co-functional links among 4,099 protein coding genes (covers ~99% of all E. coli coding genes).
EcoliNet also provides such network biology tools to (i) find new members of a pathway, (ii) infer functions from network neighbors.
Moreover, EcoliNet provides not only the integrated network but also all data specific networks (~1.3 million functional links), including 54 co-expression and 4 high-throughput PPI networks via freely accessible Download page. Therefore, co-functional gene networks for other bacterial species can be constructed via orthology-based transfer of information from EcoliNet.