COLOMBOS: an ever expanding collection of bacterial expression compendia.

COLOMBOS is an publically available access portal to comprehensive organism-specific cross-platform expression compendia for bacterial organisms. It provides a suite of tools for exploring, analyzing, and visualizing the data within these compendia. The expression compendia themselves are built based on a propriety methodology that is unique in directly combining the data from different technological platforms. COLOMBOS also incorporate extensive annotations for both genes and experimental conditions; these heterogeneous data are functionally integrated in the analysis tools to interactively browse and query the compendia not only for specific genes or experiments, but also metabolic pathways, transcriptional regulation mechanisms, experimental conditions, biological processes, etc. Several improvements have been made. Content wise, we have invested in the development of a compendia creation and management system that has enabled us to greatly expand existing compendia (Escherichia coli, Bacillus subtilis, and Salmonella Typhimurium) as well as add compendia for other species. Additionally, the current version supports the inclusion of RNAseq data. Functionally, we have revamped the interface with new interactive visualization and analysis tools, a bicluster tree algortihm for discovering complex coexpression patterns around a set of query genes, and inclusion of noise models for measurement errors, enabling analysis of differential expression with measures of statistical significance. This work is relevant to a large community of microbiologists by facilitating the use of publicly available genome-wide expression data to support their research, as well as providing a useful resource for top-down systems biology applications