GenoBase: comprehensive resource database of Escherichia coli K-12

Yuta Otsuka; Ai Muto; Rikiya Takeuchi; Chihiro Okada; Motokazu Ishikawa; Koichiro Nakamura; Natsuko Yamamoto; Hitomi Dose; Kenji Nakahigashi; Shigeki Tanishima; Sivasundaram Suharnan; Wataru Nomura; Toru Nakayashiki; Walid G Aref; Barry R Bochner; Tyrrell Conway; Michael Gribskov; Daisuke Kihara; Kenneth E Rudd; Yukako Tohsato; Barry L Wanner; Hirotada Mori

doi:10.1093/nar/gku1164

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GenoBase: comprehensive resource database of Escherichia coli K-12

Journal article

Open access

Peer reviewed

GenoBase: comprehensive resource database of Escherichia coli K-12

Yuta Otsuka, Ai Muto, Rikiya Takeuchi, Chihiro Okada, Motokazu Ishikawa, Koichiro Nakamura, Natsuko Yamamoto, Hitomi Dose, Kenji Nakahigashi, Shigeki Tanishima, …

Nucleic acids research, Vol.43(Database issue), pp.D606-D617

2015-01

DOI: https://doi.org/10.1093/nar/gku1164

PMCID: PMC4383962

PMID: 25399415

Abstract

Databases, Genetic

Escherichia coli K12 - genetics

Escherichia coli Proteins - metabolism

Genes, Bacterial

Genome, Bacterial

Internet

Molecular Sequence Annotation

Mutation

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.

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 1 Clinical & Life Sciences; 1.42 Bacteriology; 1.42.131 RNA Polymerase
Web Of Science research areas: Biochemistry & Molecular Biology
ESI research areas: Biology & Biochemistry

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Title: GenoBase: comprehensive resource database of Escherichia coli K-12
Creators: Yuta Otsuka - Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
Ai Muto - Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
Rikiya Takeuchi - Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
Chihiro Okada - Mitsubishi Space Software Co., LTD., 5-4-36 Tsukaguchihonnmachi, Amagasaki, Hyougo 661-0001, Japan
Motokazu Ishikawa - Mitsubishi Space Software Co., LTD., 5-4-36 Tsukaguchihonnmachi, Amagasaki, Hyougo 661-0001, Japan
Koichiro Nakamura - Mitsubishi Space Software Co., LTD., 5-4-36 Tsukaguchihonnmachi, Amagasaki, Hyougo 661-0001, Japan
Natsuko Yamamoto - Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
Hitomi Dose - Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
Kenji Nakahigashi - Institute of Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan
Shigeki Tanishima - Mitsubishi Space Software Co., LTD., 5-4-36 Tsukaguchihonnmachi, Amagasaki, Hyougo 661-0001, Japan
Sivasundaram Suharnan - Axiohelix, Okinawa Sangyo Shien Center, 502,1831-1, Oroku, Naha-shi, Okinawa 901-0152, Japan
Wataru Nomura - Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
Toru Nakayashiki - Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan
Walid G Aref - Department of Computer Science, Purdue University, 305 N. University Street, West Lafayette, IN 47907-2107, USA
Barry R Bochner - Biolog, Inc., Hayward, CA 94545, USA
Tyrrell Conway - Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019-0245, USA
Michael Gribskov - Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA
Daisuke Kihara - Department 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
Kenneth E Rudd - Department Biochemistry and Molecular Biology, University of Miami, P.O. Box 016129, Miami, FL 33101-6129, USA
Yukako Tohsato - Department of Bioinformatics, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan
Barry L Wanner - Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA blwanner@genetics.med.harvard.edu
Hirotada Mori - Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan hmori@gtc.naist.jp
Publication Details: Nucleic acids research, Vol.43(Database issue), pp.D606-D617
Grant note: U24 GM077905 / NIGMS NIH HHS R01 GM117324 / NIGMS NIH HHS RC1 GM092047 / NIGMS NIH HHS R01 GM075004 / NIGMS NIH HHS
Academic Unit: Miller School of Medicine; Biochemistry & Molecular Biology Research
Language: English
Resource Type: Journal article
PMID: 25399415
PMCID: PMC4383962
Record Identifier: 991031620058802976