GenoBase: comprehensive resource database of Escherichia coli K-12.
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.
Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.
Yuta
Y
Otsuka
Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.
Ai
A
Muto
Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.
Rikiya
R
Takeuchi
Mitsubishi Space Software Co., LTD., 5-4-36 Tsukaguchihonnmachi, Amagasaki, Hyougo 661-0001, Japan.
Chihiro
C
Okada
Mitsubishi Space Software Co., LTD., 5-4-36 Tsukaguchihonnmachi, Amagasaki, Hyougo 661-0001, Japan.
Motokazu
M
Ishikawa
Mitsubishi Space Software Co., LTD., 5-4-36 Tsukaguchihonnmachi, Amagasaki, Hyougo 661-0001, Japan.
Koichiro
K
Nakamura
Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.
Natsuko
N
Yamamoto
Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.
Hitomi
H
Dose
Institute of Advanced Biosciences, Keio University, Tsuruoka 997-0017, Japan.
Kenji
K
Nakahigashi
Mitsubishi Space Software Co., LTD., 5-4-36 Tsukaguchihonnmachi, Amagasaki, Hyougo 661-0001, Japan.
Shigeki
S
Tanishima
Axiohelix, Okinawa Sangyo Shien Center, 502,1831-1, Oroku, Naha-shi, Okinawa 901-0152, Japan.
Sivasundaram
S
Suharnan
Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.
Wataru
W
Nomura
Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan.
Toru
T
Nakayashiki
Department of Computer Science, Purdue University, 305 N. University Street, West Lafayette, IN 47907-2107, USA.
Walid G
WG
Aref
Biolog, Inc., Hayward, CA 94545, USA.
Barry R
BR
Bochner
Department of Microbiology and Plant Biology, University of Oklahoma, Norman, OK 73019-0245, USA.
Tyrrell
T
Conway
Department of Biological Sciences, Purdue University, 915 W. State Street, West Lafayette, IN 47907-2054, USA.
Michael
M
Gribskov
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.
Daisuke
D
Kihara
Department Biochemistry and Molecular Biology, University of Miami, P.O. Box 016129, Miami, FL 33101-6129, USA.
Kenneth E
KE
Rudd
Department of Bioinformatics, Ritsumeikan University, 1-1-1 Nojihigashi, Kusatsu, Shiga 525-8577, Japan.
Yukako
Y
Tohsato
Department of Microbiology and Immunobiology, Harvard Medical School, Boston, MA 02115, USA blwanner@genetics.med.harvard.edu.
Barry L
BL
Wanner
Graduate School of Biological Sciences, Nara Institute of Science and Technology, Ikoma, Nara 630-0101, Japan hmori@gtc.naist.jp.
Hirotada
H
Mori
D030541:Databases, Genetic; D048168:Escherichia coli K12 / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000378:metabolism; D005798:Genes, Bacterial; D016680:Genome, Bacterial; D020407:Internet; D058977:Molecular Sequence Annotation; D009154:Mutation
D029968:Escherichia coli Proteins