SRI International and a group of collaborators propose to further develop the EcoCyc database (DB). The DB is accessible to scientists through the World Wide Web via a user-friendly graphical interface. EcoCyc describes the gene and metabolic pathways to E. coli, and its transporters and transcriptional regulation machinery. It serves as a general reference source for E. coli, and is particularly well suited for use in the analysis of microbial genomes. This project will create new DB modules for several pathogenic E. coli strains whose complete DNA sequence will soon be in the public domain. This addition will facilitate comparative analyses of these strains. EcoCyc is a unique resource for analysis of large gene-expression datasets because it couples an extensive collection of data on transcriptional regulatory mechanisms with a unique program for displaying expression datasets on a full pathway map of the cell. When used as a basis for analyzing newly sequenced microbial genomes, EcoCyc contributes to the identification within those genomes of metabolic pathways that may serve as targets for drug design. Pharmaceutical companies are seeking targets within metabolic pathways as one strategy for developing next-generation drugs against antibiotic-resistant bacteria. EcoCyc is also used for teaching biochemistry by colleges and Universities. SRI further proposes to develop new bioinformatics methods for comparative genomics, and for predicting nutritional requirements and essential genes of an organism form its metabolic network.
| Paley, Suzanne M; Karp, Peter D (2006) The Pathway Tools cellular overview diagram and Omics Viewer. Nucleic Acids Res 34:3771-8 |
| Green, M L; Karp, P D (2006) The outcomes of pathway database computations depend on pathway ontology. Nucleic Acids Res 34:3687-97 |
| Junker, Bjorn H; Koschutzki, Dirk; Schreiber, Falk (2006) Exploration of biological network centralities with CentiBiN. BMC Bioinformatics 7:219 |
| Salgado, Heladia; Gama-Castro, Socorro; Peralta-Gil, Martin et al. (2006) RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions. Nucleic Acids Res 34:D394-7 |
| Salgado, Heladia; Santos-Zavaleta, Alberto; Gama-Castro, Socorro et al. (2006) The comprehensive updated regulatory network of Escherichia coli K-12. BMC Bioinformatics 7:5 |
| Caspi, Ron; Foerster, Hartmut; Fulcher, Carol A et al. (2006) MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 34:D511-6 |
| Keseler, Ingrid M; Collado-Vides, Julio; Gama-Castro, Socorro et al. (2005) EcoCyc: a comprehensive database resource for Escherichia coli. Nucleic Acids Res 33:D334-7 |
| Green, M L; Karp, P D (2005) Genome annotation errors in pathway databases due to semantic ambiguity in partial EC numbers. Nucleic Acids Res 33:4035-9 |
| Krieger, Cynthia J; Zhang, Peifen; Mueller, Lukas A et al. (2004) MetaCyc: a multiorganism database of metabolic pathways and enzymes. Nucleic Acids Res 32:D438-42 |
| Salgado, Heladia; Gama-Castro, Socorro; Martinez-Antonio, Agustino et al. (2004) RegulonDB (version 4.0): transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res 32:D303-6 |
Showing the most recent 10 out of 40 publications
