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 TohsatoBarry L. Wanner, Hirotada Mori

Research output: Contribution to journalArticle

10 Citations (Scopus)

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 longterm 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.

Original languageEnglish (US)
Pages (from-to)D606-D617
JournalNucleic Acids Research
Volume43
Issue numberD1
DOIs
StatePublished - Jan 28 2015
Externally publishedYes

Fingerprint

Quality Control
Clone Cells
Databases
Escherichia coli
Genomics
Genes
Datasets

ASJC Scopus subject areas

  • Genetics

Cite this

Otsuka, Y., Muto, A., Takeuchi, R., Okada, C., Ishikawa, M., Nakamura, K., ... Mori, H. (2015). GenoBase: Comprehensive resource database of Escherichia coli K-12. Nucleic Acids Research, 43(D1), D606-D617. https://doi.org/10.1093/nar/gku1164

GenoBase : Comprehensive resource database of Escherichia coli K-12. / Otsuka, Yuta; Muto, Ai; Takeuchi, Rikiya; Okada, Chihiro; Ishikawa, Motokazu; Nakamura, Koichiro; Yamamoto, Natsuko; Dose, Hitomi; Nakahigashi, Kenji; Tanishima, Shigeki; Suharnan, Sivasundaram; Nomura, Wataru; Nakayashiki, Toru; Aref, Walid G.; Bochner, Barry R.; Conway, Tyrrell; Gribskov, Michael; Kihara, Daisuke; Rudd, Kenneth E.; Tohsato, Yukako; Wanner, Barry L.; Mori, Hirotada.

In: Nucleic Acids Research, Vol. 43, No. D1, 28.01.2015, p. D606-D617.

Research output: Contribution to journalArticle

Otsuka, Y, Muto, A, Takeuchi, R, Okada, C, Ishikawa, M, Nakamura, K, Yamamoto, N, Dose, H, Nakahigashi, K, Tanishima, S, Suharnan, S, Nomura, W, Nakayashiki, T, Aref, WG, Bochner, BR, Conway, T, Gribskov, M, Kihara, D, Rudd, KE, Tohsato, Y, Wanner, BL & Mori, H 2015, 'GenoBase: Comprehensive resource database of Escherichia coli K-12', Nucleic Acids Research, vol. 43, no. D1, pp. D606-D617. https://doi.org/10.1093/nar/gku1164
Otsuka Y, Muto A, Takeuchi R, Okada C, Ishikawa M, Nakamura K et al. GenoBase: Comprehensive resource database of Escherichia coli K-12. Nucleic Acids Research. 2015 Jan 28;43(D1):D606-D617. https://doi.org/10.1093/nar/gku1164
Otsuka, Yuta ; Muto, Ai ; Takeuchi, Rikiya ; Okada, Chihiro ; Ishikawa, Motokazu ; Nakamura, Koichiro ; Yamamoto, Natsuko ; Dose, Hitomi ; Nakahigashi, Kenji ; Tanishima, Shigeki ; Suharnan, Sivasundaram ; Nomura, Wataru ; Nakayashiki, Toru ; Aref, Walid G. ; Bochner, Barry R. ; Conway, Tyrrell ; Gribskov, Michael ; Kihara, Daisuke ; Rudd, Kenneth E. ; Tohsato, Yukako ; Wanner, Barry L. ; Mori, Hirotada. / GenoBase : Comprehensive resource database of Escherichia coli K-12. In: Nucleic Acids Research. 2015 ; Vol. 43, No. D1. pp. D606-D617.
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