Nucleic Acids Research, 2005, Vol. 33, Database issue D329-D333
© 2005, the authors
Nucleic Acids Research, Vol. 33, Database issue © Oxford University Press 2005; all rights reserved
EchoBASE: an integrated post-genomic database for Escherichia coli
Department of Biology (Area 10), University of York, PO Box 373,York, YO10 5YW, UK and 1 Scientific Computing and Mathematical Modelling, GlaxoSmithKline, Gunnels Wood Road, Stevenage, SG1 2NY, UK
* To whom correspondence should be addressed. Tel: +44 1904 328678; Fax: +44 1904 328825; Email: ght2{at}york.ac.uk
Received August 13, 2004; Accepted September 21, 2004
EchoBASE (http://www.ecoli-york.org) is a relational database designed to contain and manipulate information from post-genomic experiments using the model bacterium Escherichia coli K-12. Its aim is to collate information from a wide range of sources to provide clues to the functions of the approximately 1500 gene products that have no confirmed cellular function. The database is built on an enhanced annotation of the updated genome sequence of strain MG1655 and the association of experimental data with the E.coli genes and their products. Experiments that can be held within EchoBASE include proteomics studies, microarray data, protein–protein interaction data, structural data and bioinformatics studies. EchoBASE also contains annotated information on ‘orphan’ enzyme activities from this microbe to aid characterization of the proteins that catalyse these elusive biochemical reactions.
The online version of this article has been published under an open access model. Users are entitled to use, reproduce, disseminate, or display the open access version of this article for non-commercial purposes provided that: the original authorship is properly and fully attributed; the Journal and Oxford University Press are attributed as the original place of publication with the correct citation details given; if an article is subsequently reproduced or disseminated not in its entirety but only in part or as a derivative work this must be clearly indicated. For commercial re-use permissions, please contact journals.permissions{at}oupjournals.org.
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  R. S. P. Horler, A. Muller, D. C. Williamson, J. R. Potts, K. S. Wilson, and G. H. Thomas Furanose-specific Sugar Transport: CHARACTERIZATION OF A BACTERIAL GALACTOFURANOSE-BINDING PROTEIN J. Biol. Chem., November 6, 2009; 284(45): 31156 - 31163. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. S. P. Horler and C. K. Vanderpool Homologs of the small RNA SgrS are broadly distributed in enteric bacteria but have diverged in size and sequence Nucleic Acids Res., September 1, 2009; 37(16): 5465 - 5476. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 L. A. Nahum, S. Goswami, and M. H. Serres Protein families reflect the metabolic diversity of organisms and provide support for functional prediction Physiol Genomics, August 7, 2009; 38(3): 250 - 260. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. S. P. Horler, A. Butcher, N. Papangelopoulos, P. D. Ashton, and G. H. Thomas EchoLOCATION: an in silico analysis of the subcellular locations of Escherichia coli proteins and comparison with experimentally derived locations Bioinformatics, January 15, 2009; 25(2): 163 - 166. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 N. Ruiz Bioinformatics identification of MurJ (MviN) as the peptidoglycan lipid II flippase in Escherichia coli PNAS, October 7, 2008; 105(40): 15553 - 15557. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
N. Ruiz, L. S. Gronenberg, D. Kahne, and T. J. Silhavy Identification of two inner-membrane proteins required for the transport of lipopolysaccharide to the outer membrane of Escherichia coli PNAS, April 8, 2008; 105(14): 5537 - 5542. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
P. D. Karp, I. M. Keseler, A. Shearer, M. Latendresse, M. Krummenacker, S. M. Paley, I. Paulsen, J. Collado-Vides, S. Gama-Castro, M. Peralta-Gil, et al. Multidimensional annotation of the Escherichia coli K-12 genome Nucleic Acids Res., December 3, 2007; 35(22): 7577 - 7590. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 T. Fuhrer, L. Chen, U. Sauer, and D. Vitkup Computational Prediction and Experimental Verification of the Gene Encoding the NAD+/NADP+-Dependent Succinate Semialdehyde Dehydrogenase in Escherichia coli J. Bacteriol., November 15, 2007; 189(22): 8073 - 8078. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
R. M. Watt, J. Wang, M. Leong, H.-f. Kung, K. S.E. Cheah, D. Liu, A. Danchin, and J.-D. Huang Visualizing the proteome of Escherichia coli: an efficient and versatile method for labeling chromosomal coding DNA sequences (CDSs) with fluorescent protein genes Nucleic Acids Res., March 19, 2007; 35(6): e37 - e37. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
T. Inoue, R. Shingaki, S. Hirose, K. Waki, H. Mori, and K. Fukui Genome-Wide Screening of Genes Required for Swarming Motility in Escherichia coli K-12 J. Bacteriol., February 1, 2007; 189(3): 950 - 957. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 J. C. Silva, R. Denny, C. Dorschel, M. V. Gorenstein, G.-Z. Li, K. Richardson, D. Wall, and S. J. Geromanos Simultaneous Qualitative and Quantitative Analysis of theEscherichia coli Proteome: A Sweet Tale Mol. Cell. Proteomics, April 1, 2006; 5(4): 589 - 607. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 H. Ochman and L. M. Davalos The nature and dynamics of bacterial genomes. Science, March 24, 2006; 311(5768): 1730 - 1733. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. D. Prickett, M. Page, A. E. Douglas, and G. H. Thomas BuchneraBASE: a post-genomic resource for Buchnera sp. APS Bioinformatics, March 1, 2006; 22(5): 641 - 642. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
M. Riley, T. Abe, M. B. Arnaud, M. K.B. Berlyn, F. R. Blattner, R. R. Chaudhuri, J. D. Glasner, T. Horiuchi, I. M. Keseler, T. Kosuge, et al. Escherichia coli K-12: a cooperatively developed annotation snapshot--2005 Nucleic Acids Res., January 5, 2006; 34(1): 1 - 9. [Abstract] [Full Text] [PDF]
|
|