Network-based functional modeling of genomics, transcriptomics and metabolism in bacteria

被引：20

作者：

Cloots, Lore ^{[1
]}

Marchal, Kathleen ^{[1
,2
]}

机构：

[1] Katholieke Univ Leuven, Dept Microbial & Mol Syst, B-3001 Louvain, Belgium

[2] Univ Ghent, Dept Plant Biotechnol & Bioinformat, B-9052 Ghent, Belgium

来源：

CURRENT OPINION IN MICROBIOLOGY | 2011年 / 14卷 / 05期

基金：

比利时弗兰德研究基金会;

关键词：

PROTEIN-PROTEIN INTERACTION; SIGNAL-TRANSDUCTION NETWORKS; ESCHERICHIA-COLI; HIGH-THROUGHPUT; GENETIC INTERACTIONS; REGULATORY NETWORKS; BACILLUS-SUBTILIS; INTERACTION MAP; REVEALS; RECONSTRUCTION;

D O I：

10.1016/j.mib.2011.09.003

中图分类号：

Q93 [微生物学];

学科分类号：

071005 [微生物学];

摘要：

Molecular entities present in a cell (mRNA, proteins, metabolites, ...) do not act in isolation, but rather in cooperation with each other to define an organisms form and function. Their concerted action can be viewed as networks of interacting entities that are active under certain conditions within the cell or upon certain environmental signals. A main challenge in systems biology is to model these networks, or in other words studying which entities interact to form cellular systems or accomplish similar functions. On the contrary, viewing a single entity or an experimental dataset in the light of an interaction network can reveal previous unknown insights in biological processes. In this review we give an overview of how integrated networks can be reconstructed from multiple omics data and how they can subsequently be used for network-based modeling of cellular function in bacteria.

引用

页码：599 / 607

页数：9

共 88 条

[1]

Large-scale identification of protein-protein interaction of Escherichia coli K-12 [J].

Arifuzzaman, M ;

Maeda, M ;

Itoh, A ;

Nishikata, K ;

Takita, C ;

Saito, R ;

Ara, T ;

Nakahigashi, K ;

Huang, HC ;

Hirai, A ;

Tsuzuki, K ;

Nakamura, S ;

Altaf-Ul-Amin, M ;

Oshima, T ;

Baba, T ;

Yamamoto, N ;

Kawamura, T ;

Ioka-Nakamichi, T ;

Kitagawa, M ;

Tomita, M ;

Kanaya, S ;

Wada, C ;

Mori, H .

GENOME RESEARCH, 2006, 16 (05) :686-691

[2]

Babu M, 2009, MOL BIOSYST, V5, P1439, DOI [10.1039/b907407d, 10.1039/B907407d]

[3]

Finding undetected protein associations in cell signaling by belief propagation [J].

Bailly-Bechet, M. ;

Borgs, C. ;

Braunstein, A. ;

Chayes, J. ;

Dagkessamanskaia, A. ;

Francois, J. -M. ;

Zecchina, R. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2011, 108 (02) :882-887

[4]

Functional maps of protein complexes from quantitative genetic interaction data [J].

Bandyopadhyay, Sourav ;

Kelley, Ryan ;

Krogan, Nevan J. ;

Ideker, Trey .

PLOS COMPUTATIONAL BIOLOGY, 2008, 4 (04)

[5]

Rewiring Cells: Synthetic Biology as a Tool to Interrogate the Organizational Principles of Living Systems [J].

Bashor, Caleb J. ;

Horwitz, Andrew A. ;

Peisajovich, Sergio G. ;

Lim, Wendell A. .

ANNUAL REVIEW OF BIOPHYSICS, VOL 39, 2010, 39 :515-537

[6]

PathFinder: mining signal transduction pathway segments from protein-protein interaction networks [J].

Bebek, Gurkan ;

Yang, Jiong .

BMC BIOINFORMATICS, 2007, 8 (1)

[7]

A predictive model for transcriptional control of physiology in a free living cell [J].

Bonneau, Richard ;

Facciotti, Marc T. ;

Reiss, David J. ;

Schmid, Amy K. ;

Pan, Min ;

Kaur, Amardeep ;

Thorsson, Vesteinn ;

Shannon, Paul ;

Johnson, Michael H. ;

Bare, J. Christopher ;

Longabaugh, William ;

Vuthoori, Madhavi ;

Whitehead, Kenia ;

Madar, Aviv ;

Suzuki, Lena ;

Mori, Tetsuya ;

Chang, Dong-Eun ;

DiRuggiero, Jocelyne ;

Johnson, Carl H. ;

Hood, Leroy ;

Baliga, Nitin S. .

CELL, 2007, 131 (07) :1354-1365

[8]

The Inferelator:: an algorithm for learning parsimonious regulatory networks from systems-biology data sets de novo [J].

Bonneau, Richard ;

Reiss, David J. ;

Shannon, Paul ;

Facciotti, Marc ;

Hood, Leroy ;

Baliga, Nitin S. ;

Thorsson, Vesteinn .

GENOME BIOLOGY, 2006, 7 (05)

[9]

eSGA:: E. coli synthetic genetic array analysis [J].

Butland, Gareth ;

Babu, Mohan ;

Diaz-Mejia, J. Javier ;

Bohdana, Fedyshyn ;

Phanse, Sadhna ;

Gold, Barbara ;

Yang, Wenhong ;

Li, Joyce ;

Gagarinova, Alla G. ;

Pogoutse, Oxana ;

Mori, Hirotada ;

Wanner, Barry L. ;

Lo, Henry ;

Wasniewski, Jas ;

Christopoulos, Constantine ;

Ali, Mehrab ;

Venn, Pascal ;

Safavi-Naini, Anahita ;

Sourour, Natalie ;

Caron, Simone ;

Choi, Ja-Yeon ;

Laigle, Ludovic ;

Nazarians-Armavil, Anaies ;

Deshpande, Avnish ;

Joe, Sarah ;

Datsenko, Kirill A. ;

Yamamoto, Natsuko ;

Andrews, Brenda J. ;

Boone, Charles ;

Ding, Huiming ;

Sheikh, Bilal ;

Moreno-Hagelsieb, Gabriel ;

Greenblatt, Jack F. ;

Emili, Andrew .

NATURE METHODS, 2008, 5 (09) :789-795

[10]

Probabilistic integrative modeling of genome-scale metabolic and regulatory networks in Escherichia coli and Mycobacterium tuberculosis [J].

Chandrasekaran, Sriram ;

Price, Nathan D. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2010, 107 (41) :17845-17850

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