PNNL

Abstract

Shewanella oneidensis MR-1 is an important model organism for environmental research as it has an exceptional metabolic and respiratory versatility regulated by a complex regulatory network. We have developed a database to collect experimental and computational data relating to regulation of gene and protein expression and a visualization environment that enables integration of these data types. The regulatory information in the database was collected from the published literature and different Internet resources. It includes predictions of DNA regulator binding sites, sigma factor binding sites, transcription units, operons, promoters, and RNA regulators including non-coding RNAs, riboswitches, and different types of terminators. A visualization environment based on GBrowser was developed for accessing the collected information and for its overlaying with experimental data (experimental results from studies employing microarrays, proteomics, and/or gene mutagenesis) and other genome annotations.