Escherichia coli Multi-omics Database

presented by the Institute for Advanced Biosciences, Keio University

To understand the highly complex nature of living systems, a comprehensive knowledge of the quantitative information regarding the inner molecular components of cells is necessary. Here at the Institute for Advanced Biosciences, Keio University located in Tsuruoka city of Japan, we are dedicated to a collaborative grand challenge to gather multi-omics data of the model organism Escherichia coli for these purposes.

Please cite the following manuscript:

Multiple high throughput analyses monitor the response of E.coli to perturbations. Science, 2007. 316(5824): 593-597.
Ishi N, Nakahigashi K, Baba T, Robert M, Soga T, Kanai A, Hirasawa T, Naba M, Hirai K, Hoque A, Ho PY, Kakazu Y, Sugawara K, Igarashi S, Harada S, Masuda T, Sugiyama N, Togashi T, Hasegawa M, Takai Y, Yugi K, Arakawa K, Iwata N, Toya Y, Nakayama Y, Nishioka T, Shimizu K, Mori H, Tomita M.

Please Note:

Users of the data should carefully read the original manuscript and supplementary methods and text for additional information about the measurement values, samples and data series, and the normalization methods used and be aware of the limitations before pursuing any analysis using this data. Failure to do so might result in erroneous interpretations and conclusions for which the authors of this study cannot be held responsible. The database is provided "as is" and without warranties of any kind. We do not assume any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed in this web site.

CE-MS metabolome data

Metabolomics, the comprehensive quantitative measurement of low molecular weight intracellular compounds, was conducted by our "state-of-the-art" CE-MS analysis. Click the icon on the right to download the data in Excel format.
Metabolome Data
Metabolome data
CE-TOFMS metabolome raw data (Click here to download MS Excel file)

RT-PCR Transcriptome Data

Transcriptomics, the comprehensive quantitative measurement of intracellular mRNAs, was performed using microarrays and RT-PCR. Click the icon on the right to download the data in Excel format.

RT-PCR Transcriptome Data
RT-PCR data for Wildtype and Mutants
DNA Array
DNA Array data (Click here to download MS Excel file)
DNA Array raw-data (Click here to download zip archive)

Proteome data

Proteomics, the comprehensive quantitative measurement of proteins, was conducted with LC-MS/MS and 2D-DIGE method. Click the icon on the right to download the data in Excel format.

Proteome Data
Absolute protein quantification by LC-MS/MS
2D-DIGE Data
Important additional information for 2D-DIGE data users
Ratio data (Click here to download MS Excel file)
Gel Images
Summary
Mutant data
2D-DIGE Mutant data (Click here to download MS Excel file)

Fluxome data

Fluxomics, the comprehensive quantitative measurement of metabolic flux, was conducted with GC-MS measurement of 13C labeled compounds. Click the icon on the right to download the data in Excel format.

Fluxome Data
Fluxome data
GC-MS Flux (Click here to download MS Excel file)

Version 1.0.0

2007.05.10

First release of version 1 (updated publication information)

Version 0.9.1

2007.03.12

Minor update of the data to v.0.9.1.

Version 0.9.0

2007.03.06

Minor update of the data to v.0.9.0.










Contact:

Prof. Masaru Tomita
Institute for Advanced Biosciences, Keio University
Zip: 997-0035
Address: Baba-cho 14-1, Tsuruoka City, Yamagata, Japan
Tel: +81-235-29-0800
Fax: +81-235-29-0809
Mail: mt at sfc.keio.ac.jp

*for technical questions and comments about the web site, contact Kazuharu Arakawa (gaou at sfc.keio.ac.jp)

Contents

Links

Disclaimer

The database is provided "as is" and without warranties of any kind. We do not assume any legal liability or responsibility for the accuracy, completeness, or usefulness of any information, apparatus, product, or process disclosed in this web site.

Acknowledgement

This work was supported by the New Energy and Industrial Technology Development Organization (NEDO), and by research funds from Tsuruoka City and the Yamagata Prefectural Government..

Copyright

Copyright 2007 Institute for Advanced Biosciences, Keio University. All rights reserved.