This website serves as the supplement to Large-Scale Mapping and Validation of Escherichia coli Transcriptional Regulation from a Compendium of Expression Profiles, PLoS Biology 2007. Our paper had two major goals. The first was to create a means to determine the relative merits of different network inference algorithms in an unbiased manner on experimental data. The second was to use the network inferred by the best current algorithm to identify novel biology and thereby demonstrate the practical application of network inference software.

Many Microbe Microarrays Database (M3D) is a resource for analyzing and retrieving gene expression data for microbes. The database currently contains Affymetrix expression compendia for Escherichia coli, Saccharomyces cerevisiae, and Shewanella oneidensis.

E. coli protein database (EcoProDB) integrates protein information identified on 2-D gels along with other resources to provide the comparative platform for the expression levels of many heterogeneous proteins under different genetic and environmental conditions using the interactive interface and search mechanism.

ASAP is a relational database and web interface developed to store, update, and distribute genome sequences in conjunction with associated annotations and functional characterization data. It is currently being used to update our E. coli K-12 annotations and to distribute experimental data from our functional genomics project.

GenProtEC is dedicated to the functions encoded by the Escherichia coli K-12 (strain MG1655) genome defined in the GenBank Accession No. NC_000913.2 deposit. Our annotation work includes multiple types of information: 1. Sequence similarity to orthologues as defined by Darwin (start and end of aligned region, identity, and PAM distance). 2. Resolution of fused proteins into modular units with independent functions. 3. Identification of sequence similar protein groups within E. coli that are clustered by transitive relationships. The sequence similarity is limited to PAM 200 and an alignment of at least 83 amino acids. 4. Updated literature references. 5. Classification of gene products by their gene type and by their cellular role(s). The MultiFun classification system for cellular roles is used to assign gene products to one or more roles. MultiFun has been converted to Gene Ontology terms. 6. Familes of proteins related by structure and biochemical reaction mechanisms (work in progress). 7. SCOP superfamily identification and location (e.g. binding site domains) for E. coli proteins.