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. 2011 Jan;39(Database issue):D583-90.
doi: 10.1093/nar/gkq1143. Epub 2010 Nov 21.

EcoCyc: a comprehensive database of Escherichia coli biology

Ingrid M Keseler  1 , Julio Collado-Vides, Alberto Santos-Zavaleta, Martin Peralta-Gil, Socorro Gama-Castro, Luis Muñiz-Rascado, César Bonavides-Martinez, Suzanne Paley, Markus Krummenacker, Tomer Altman, Pallavi Kaipa, Aaron Spaulding, John Pacheco, Mario Latendresse, Carol Fulcher, Malabika Sarker, Alexander G Shearer, Amanda Mackie, Ian Paulsen, Robert P Gunsalus, Peter D Karp
Affiliations

EcoCyc: a comprehensive database of Escherichia coli biology

Ingrid M Keseler et al. Nucleic Acids Res. 2011 Jan.

Abstract

EcoCyc (http://EcoCyc.org) is a comprehensive model organism database for Escherichia coli K-12 MG1655. From the scientific literature, EcoCyc captures the functions of individual E. coli gene products; their regulation at the transcriptional, post-transcriptional and protein level; and their organization into operons, complexes and pathways. EcoCyc users can search and browse the information in multiple ways. Recent improvements to the EcoCyc Web interface include combined gene/protein pages and a Regulation Summary Diagram displaying a graphical overview of all known regulatory inputs to gene expression and protein activity. The graphical representation of signal transduction pathways has been updated, and the cellular and regulatory overviews were enhanced with new functionality. A specialized undergraduate teaching resource using EcoCyc is being developed.

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Figures

Figure 1.
Figure 1.
Growth of experimental GO term annotations in EcoCyc over time. Data is grouped by database version, beginning with release 11.5 (August 2007) and ending with release 14.5 (September 2010). The first three bars in each group report the number of assignments of a GO term from each of the three primary GO categories with an EXP_IDA (inferred by direct assay) evidence code. In contrast, the last two bars report the number of genes that have at least one GO term annotation with an EXP or an EXP-IDA evidence code. EXP includes the EXP-IDA evidence codes as well as others such as EXP-IMP (inferred by mutant phenotype).
Figure 2.
Figure 2.
The Regulation Summary Diagram. Colors indicate the overall effect on the production of the functional protein. (A) Regulation Summary Diagram for the oppD gene. Transcription initiation is influenced by a variety of TFs, which are themselves regulated by small molecules. The operon containing oppD is transcribed by RNA polymerase containing the alternative sigma factor Sigma 28. Translation is regulated by a small molecule, spermidine, the small RNA GcvB, and Hfq. The OppD protein can be part of two different heteromultimeric complexes. (B) Regulation Summary Diagram for the trpA gene. Transcription initiation is regulated by TrpR. In the presence of the charged tryptophanyl-tRNATrp, transcription is attenuated due to formation of a stem-loop structure in the mRNA. Pyridoxal-phosphate is a cofactor for the tryptophan synthase enzyme.
Figure 3.
Figure 3.
New graphic representation of the EvgSA two-component signal transduction pathway.
Figure 4.
Figure 4.
Omics Data Graphing.
See this image and copyright information in PMC

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