Decomposing complex reaction networks using random sampling, principal component analysis and basis rotation

BMC Systems Biology

Volumn 3, Issue , 2009, Pages

  Barrett, Christian L ^a   Herrgard, Markus J ^b   Palsson, Bernhard ^a  

^a UNIVERSITY OF CALIFORNIA   (United States)

^b Synthetic Genomics Inc   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; ESCHERICHIA COLI; GENE REGULATORY NETWORK; GENETICS; METABOLISM; METHODOLOGY; MONTE CARLO METHOD; PRINCIPAL COMPONENT ANALYSIS; SYSTEMS BIOLOGY;

ESCHERICHIA COLI; GENE REGULATORY NETWORKS; METABOLIC NETWORKS AND PATHWAYS; MONTE CARLO METHOD; PRINCIPAL COMPONENT ANALYSIS; SYSTEMS BIOLOGY;

EID: 65349142617     PISSN: None     EISSN: 17520509     Source Type: Journal    
DOI: 10.1186/1752-0509-3-30     Document Type: Article

References (39)

1. Reed JL Famili I Thiele I Palsson BO Towards multidimensional genome annotation Nat Rev Genet 2006, 7(2):130-141. 10.1038/nrg1769 16418748
2. Price ND Reed JL Palsson BO Genome-scale models of microbial cells: evaluating the consequences of constraints Nat Rev Microbiol 2004, 2(11):886-897. 10.1038/nrmicro1023 15494745
3. Jeong H Tombor B Albert R Oltvai ZN Barabasi AL The large-scale organization of metabolic networks Nature 2000, 407(6804):651-654. 10.1038/35036627 11034217
4. Ravasz E Somera AL Mongru DA Oltvai ZN Barabasi AL Hierarchical organization of modularity in metabolic networks Science 2002, 297(5586):1551-1555. 10.1126/science.1073374 12202830
5. Ma HW Zeng AP The connectivity structure, giant strong component and centrality of metabolic networks Bioinformatics 2003, 19(11):1423-1430. 10.1093/bioinformatics/btg177 12874056
6. Newman ME Modularity and community structure in networks Proc Natl Acad Sci USA 2006, 103(23):8577-8582. 1482622 16723398 10.1073/pnas.0601602103
7. Guimera R Nunes Amaral LA Functional cartography of complex metabolic networks Nature 2005, 433(7028):895-900. 2175124 15729348 10.1038/ nature03288
8. Stelling J Klamt S Bettenbrock K Schuster S Gilles ED Metabolic network structure determines key aspects of functionality and regulation Nature 2002, 420:190-193. 10.1038/nature01166 12432396
9. Almaas E Kovacs B Vicsek T Oltvai ZN Barabasi AL Global organization of metabolic fluxes in the bacterium Escherichia coli Nature 2004, 427(6977):839-843. 10.1038/nature02289 14985762
10. Covert M Palsson BO Constraints-based models: Regulation of gene expression reduces the steady-state solution space J theor Biol 2003, 221(3):309-325. 10.1006/jtbi.2003.3071 12642111
11. Covert MW Schilling CH Palsson B Regulation of gene expression in flux balance models of metabolism J theor Biol 2001, 213(1):73-88. 10.1006/ jtbi.2001.2405 11708855
12. Barrett CL Herring CD Reed JL Palsson BO The global transcriptional regulatory network for metabolism in Escherichia coli attains few dominant functional states Proc Natl Acad Sci USA 2005, 102(52):19103-19108. 1323155 16357206 10.1073/pnas.0505231102
13. Covert MW Knight EM Reed JL Herrgard MJ Palsson BO Integrating high-throughput and computational data elucidates bacterial networks Nature 2004, 429(6987):92-96. 10.1038/nature02456 15129285
14. Wiback SJ Famili I Greenberg HJ Palsson BO Monte Carlo Sampling Can Be Used to Determine the Size and Shape of the Steady State Flux Space J theor Biol 2004, 228(4):437-447. 10.1016/j.jtbi.2004.02.006 15178193
15. Price ND Schellenberger J Palsson BO Uniform Sampling of Steady State Flux Spaces: Means to Design Experiments and to Interpret Enzymopathies Biophysical Journal 2004, 87(4):2172-2186. 1304643 15454420 10.1529/ biophysj.104.043000
16. Barrett CL Price ND Palsson BO Network-level analysis of metabolic regulation in the human red blood cell using random sampling and singular value decomposition BMC Bioinformatics 2006, 7:132. 1421444 16533395 10.1186/1471-2105-7-132
17. Thiele I Price ND Vo TD Palsson BO Candidate metabolic network states in human mitochondria: Impact of diabetes, ischemia, and diet J Biol Chem 2005, 280(12):11683-11695. 10.1074/jbc.M409072200 15572364
18. Wang L Birol I Hatzimanikatis V Metabolic control analysis under uncertainty: Framework development and case studies Biophys J 2004, 87(6):3750-3763. 1304888 15465856 10.1529/biophysj.104.048090
19. Liebermeister W Klipp E Biochemical networks with uncertain parameters IEE Systems Biology 2005, 152(3):97-107. 10.1049/ip-syb:20045033 16986274
20. Gorsuch RL Factor Analysis Hillsdale, New Jersey: Lawrence Erlbaum Associates 2 1983.
21. Sauer U Canonaco F Heri S Perrenoud A Fischer E The soluble and membrane-bound transhydrogenases UdhA and PntAB have divergent functions in NADPH metabolism of Escherichia coli J Biol Chem 2004, 279(8):6613-6619. 10.1074/jbc.M311657200 14660605
22. Aledo JC del Valle AE The ATP paradox is the expression of an economizing fuel mechanism J Biol Chem 2004, 279(53):55372-55375. 10.1074/jbc.M410479200 15509563
23. Yang F Beard DA Thermodynamically based profiling of drug metabolism and drug-drug metabolic interactions: A case study of acetaminophen and ethanol toxic interaction Biophys Chem 2006, 120(2):121-134. 10.1016/ j.bpc.2005.10.013 16314027
24. Henry CS Broadbelt LJ Hatzimanikatis V Thermodynamics-Based Metabolic Flux Analysis Biophys J 2007, 92(5):1792-1805. 1796839 17172310 10.1529/ biophysj.106.093138
25. Famili I Palsson BO The convex basis of the left null space of the stoichiometric matrix leads to the definition of metabolically meaningful pools Biophys J 2003, 85(1):16-26. 1303061 12829460 10.1016/ S0006-3495(03)74450-6
26. Famili I Mahadevan R Palsson BO k-Cone Analysis: Determining All Candidate Values for Kinetic Parameters on a Network Scale Biophys J 2005, 88(3):1616-1625. 1305218 15626710 10.1529/biophysj.104.050385
27. Carlson JM Doyle J Complexity and robustness Proc Natl Acad Sci USA 2002, 99(Suppl 1):2538-2545. 128573 11875207 10.1073/pnas.012582499
28. Stelling J Sauer U Szallasi Z Doyle FJ 3rd Doyle J Robustness of cellular functions Cell 2004, 118(6):675-685. 10.1016/j.cell.2004.09.008 15369668
29. Riley M Abe T Arnaud MB Berlyn MK Blattner FR Chaudhuri RR Glasner JD Horiuchi T Keseler IM Kosuge T et al. Escherichia coli K-12: A cooperatively developed annotation snapshot-2005 Nucleic Acids Res 2006, 34(1):1-9. 1325200 16397293 10.1093/nar/gkj405
30. Keseler IM Collado-Vides J Gama-Castro S Ingraham J Paley S Paulsen IT Peralta-Gil M Karp PD EcoCyc: A comprehensive database resource for Escherichia coli Nucleic Acids Res 2005, 33(Database):D334-337. 540062 15608210
31. Salgado H Gama-Castro S Peralta-Gil M Diaz-Peredo E Sanchez-Solano F Santos-Zavaleta A Martinez-Flores I Jimenez-Jacinto V Bonavides-Martinez C Segura-Salazar J et al. RegulonDB (version 5.0): Escherichia coli K-12 transcriptional regulatory network, operon organization, and growth conditions Nucleic Acids Res 2006, 34(Database):D394-397. 1347518 16381895 10.1093/nar/gkj156
32. Becker SA Feist AM Mo ML Hannum G Palsson BO Herrgard MJ Quantitative prediction of cellular metabolism with constraint-based models: The COBRA Toolbox Nat Protocols 2007, 2(3):727-738. 10.1038/nprot.2007.99
33. Beard DA Liang SD Qian H Energy balance for analysis of complex metabolic networks Biophys J 2002, 83(1):79-86. 1302128 12080101 10.1016/ S0006-3495(02)75150-3
34. Price ND Famili I Beard DA Palsson BO Extreme pathways and Kirchhoff's second law Biophys J 2002, 83(5):2879-2882. 1302372 12425318 10.1016/ S0006-3495(02)75297-1
35. Lovasz L Hit-and-run mixes fast Math Program 1999, 86(3):443-461. 10.1007/s101070050099
36. Smith RL Efficient Monte-Carlo procedures for generating points uniformly distributed over bounded regions Operations Research 1984, 32:1296-1308. 10.1287/opre.32.6.1296
37. Jackson JE A User's Guide to Principal Components John Wiley and Sons, Inc, New York 1991.
38. Strang G Linear Algebra and its Applications Fort Worth: Saunders College Publishing Third 1988.
39. Kaiser HF The varimax criterion for analytic rotation in factor analysis Psychometrika 1958, 23(3):187-200. 10.1007/BF02289233