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Nucleic Acids Res. 2015 Jan;43(Database issue):D606-17. doi: 10.1093/nar/gku1164. Epub 2014 Nov 15.

GenoBase: comprehensive resource database of Escherichia coli K-12.

Author information

  • 1Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.
  • 2Mitsubishi Space Software Co., LTD., 5-4-36 Tsukaguchihonnmachi, Amagasaki, Hyougo 661-0001, Japan.
  • 3Institute of Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.
  • 4Axiohelix, Okinawa Sangyo Shien Center, 502,1831-1, Oroku, Naha-shi, Okinawa 901-0152, Japan.
  • 5Department of Computer Science, Purdue University, 305 N. University Street, West Lafayette, IN 47907-2107, USA.
  • 6Biolog, Inc., Hayward, CA 94545, USA.
  • 7Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019-0245, USA.
  • 8Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.
  • 9Department of Computer Science, Purdue University, 305 N. University Street, West Lafayette, IN 47907-2107, USA Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.
  • 10Department Biochemistry and Molecular Biology, University of Miami, P.O. Box 016129, Miami, FL 33101-6129, USA.
  • 11Department of Bioinformatics, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan.
  • 12Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA blwanner@genetics.med.harvard.edu.
  • 13Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan hmori@gtc.naist.jp.

Abstract

Comprehensive experimental resources, such as ORFeome clone libraries and deletion mutant collections, are fundamental tools for elucidation of gene function. Data sets by omics analysis using these resources provide key information for functional analysis, modeling and simulation both in individual and systematic approaches. With the long-term goal of complete understanding of a cell, we have over the past decade created a variety of clone and mutant sets for functional genomics studies of Escherichia coli K-12. We have made these experimental resources freely available to the academic community worldwide. Accordingly, these resources have now been used in numerous investigations of a multitude of cell processes. Quality control is extremely important for evaluating results generated by these resources. Because the annotation has been changed since 2005, which we originally used for the construction, we have updated these genomic resources accordingly. Here, we describe GenoBase (http://ecoli.naist.jp/GB/), which contains key information about comprehensive experimental resources of E. coli K-12, their quality control and several omics data sets generated using these resources.

© The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

PMID:
25399415
[PubMed - indexed for MEDLINE]
PMCID:
PMC4383962
Free PMC Article
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