Computing Elementary Flux Modes Involving a Set of Target Reactions

被引：9

作者：

David, Laszlo ^{[1
,2
,3
]}

Bockmayr, Alexander ^{[1
,2
]}

机构：

[1] Free Univ Berlin, Dept Math & Comp Sci, D-14195 Berlin, Germany

[2] DFG Res Ctr Matheon, Berlin, Germany

[3] BMS, Berlin, Germany

来源：

IEEE-ACM TRANSACTIONS ON COMPUTATIONAL BIOLOGY AND BIOINFORMATICS | 2014年 / 11卷 / 06期

关键词：

Metabolic networks; constraint-based analysis; elementary flux modes; mixed-integer linear programming; COUPLING ANALYSIS; METABOLIC NETWORKS; PATHWAY ANALYSIS; RECONSTRUCTION; COMPUTATION; TOOL;

D O I：

10.1109/TCBB.2014.2343964

中图分类号：

Q5 [生物化学];

学科分类号：

071010 ; 081704 ;

摘要：

Elementary flux mode (EM) computation is an important tool in the constraint-based analysis of genome-scale metabolic networks. Due to the combinatorial complexity of these networks, as well as the advances in the level of detail to which they can be reconstructed, an exhaustive enumeration of all EMs is often not practical. Therefore, in recent years interest has shifted towards searching EMs with specific properties. We present a novel method that allows computing EMs containing a given set of target reactions. This generalizes previous algorithms where the set of target reactions consists of a single reaction. In the one-reaction case, our method compares favorably to the previous approaches. In addition, we present several applications of our algorithm for computing EMs containing two target reactions in genome-scale metabolic networks. A software tool implementing the algorithms described in this paper is available at https://sourceforge.net/projects/caefm.

引用

页码：1099 / 1107

页数：9

共 31 条

[1] A note on the complexity of finding and enumerating elementary modes [J].

Acuna, Vicente ;

Marchetti-Spaccamela, Alberto ;

Sagot, Marie-France ;

Stougie, Leen .

BIOSYSTEMS, 2010, 99 (03) :210-214

[2] Modes and cuts in metabolic networks: Complexity and algorithms [J].

Acuna, Vicente ;

Chierichetti, Flavio ;

Lacroix, Vincent ;

Marchetti-Spaccamela, Alberto ;

Sagot, Marie-France ;

Stougie, Leen .

BIOSYSTEMS, 2009, 95 (01) :51-60

[3]

[Anonymous], 1998, Theory of linear and integer programming

[4]

[Anonymous], 1994, J BIOL SYSTEMS, DOI DOI 10.1142/S0218339094000131

[5] Flux coupling analysis of genome-scale metabolic network reconstructions [J].

Burgard, AP ;

Nikolaev, EV ;

Schilling, CH ;

Maranas, CD .

GENOME RESEARCH, 2004, 14 (02) :301-312

[6] FFCA: a feasibility-based method for flux coupling analysis of metabolic networks [J].

David, Laszlo ;

Marashi, Sayed-Amir ;

Larhlimi, Abdelhalim ;

Mieth, Bettina ;

Bockmayr, Alexander .

BMC BIOINFORMATICS, 2011, 12

[7] Computing the shortest elementary flux modes in genome-scale metabolic networks [J].

de Figueiredo, Luis F. ;

Podhorski, Adam ;

Rubio, Angel ;

Kaleta, Christoph ;

Beasley, John E. ;

Schuster, Stefan ;

Planes, Francisco J. .

BIOINFORMATICS, 2009, 25 (23) :3158-3165

[8] Can sugars be produced from fatty acids? A test case for pathway analysis tools [J].

de Figueiredo, Luis F. ;

Schuster, Stefan ;

Kaleta, Christoph ;

Fell, David A. .

BIOINFORMATICS, 2008, 24 (22) :2615-2621

[9] Global reconstruction of the human metabolic network based on genomic and bibliomic data [J].

Duarte, Natalie C. ;

Becker, Scott A. ;

Jamshidi, Neema ;

Thiele, Ines ;

Mo, Monica L. ;

Vo, Thuy D. ;

Srivas, Rohith ;

Palsson, Bernhard O. .

PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 2007, 104 (06) :1777-1782

[10] Reconstruction and validation of Saccharomyces cerevisiae iND750, a fully compartmentalized genome-scale metabolic model [J].

Duarte, NC ;

Herrgård, MJ ;

Palsson, BO .

GENOME RESEARCH, 2004, 14 (07) :1298-1309

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