Matrix formalism to describe functional states of transcriptional regulatory systems

PLoS Computational Biology

Volumn 2, Issue 8, 2006, Pages 0902-0917

  Gianchandani, Erwin P ^a   Papin, Jason A ^a   Price, Nathan D ^b,d   Joyce, Andrew R ^c   Palsson, Bernhard O ^b  

^a University of Virginia   (United States)

^b UNIVERSITY OF CALIFORNIA SAN DIEGO   (United States)

^c UNIVERSITY OF CALIFORNIA   (United States)

^d INSTITUTE FOR SYSTEMS BIOLOGY   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

MATRIX ALGEBRA;

COMPLEX REGULATORY NETWORK; ENVIRONMENTAL CUES; FUNCTIONAL STATE; MATRIX; MATRIX FORMALISM; NETWORK-CONTROL; REGULATORY RULES; REGULATORY SIGNALS; TRANSCRIPTIONAL REGULATORY NETWORKS; TRANSCRIPTIONAL REGULATORY SYSTEM;

TRANSCRIPTION;

ARTICLE; ESCHERICHIA COLI; GENE EXPRESSION; GENETIC ANALYSIS; GENETIC TRANSCRIPTION; GENOME; LACTOSE OPERON; STOICHIOMETRY; TRANSCRIPTION REGULATION; BIOLOGICAL MODEL; BIOLOGY; GENE EXPRESSION REGULATION; GENETICS; GENOMICS; METHODOLOGY;

COMPUTATIONAL BIOLOGY; ESCHERICHIA COLI; GENE EXPRESSION REGULATION; GENOME; GENOMICS; LAC OPERON; MODELS, GENETIC; TRANSCRIPTION, GENETIC;

EID: 33748049119     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.0020101     Document Type: Article

References (38)

1. Salgado H, Gama-Castro S, Peralta-Gil M, Díaz-Peredo E, Sánchez-Solano F, et al. (2004) RegulonDB (version 4.0): Transcriptional regulation, operon organization and growth conditions in Escherichia coli K-12. Nucleic Acids Res 32: D303-D306.
2. Friedman N, Linial M, Nachman I, Pe'er D (2000) Using Bayesian networks to analyze expression data. J Comput Biol 7: 601-620.
3. Kauffman S, Peterson C, Samuelsson B, Troein C (2003) Random Boolean network models and the yeast transcriptional network. Proc Natl Acad Sci U S A 100: 14796-14799.
4. Shmulevich I, Dougherty ER, Kim S, Zhang W (2002) Probabilistic Boolean networks: A rule-based uncertainty model for gene regulatory networks. Bioinformatics 18: 261-274.
5. Covert MW, Schilling CH, Palsson B (2001) Regulation of gene expression in flux balance models of metabolism. J Theor Biol 213: 73-88.
6. Thomas R (1973) Boolean formalization of genetic control circuits. J Theor Biol 42: 563-585.
7. McAdams HH, Arkin A (1997) Stochastic mechanisms in gene expression. Proc Natl Acad Sci U S A 94: 814-819.
8. de Jong H (2002) Modeling and simulation of genetic regulatory systems: A literature review. J Comput Biol 9: 67-103.
9. Covert MW, Knight EM, Reed JL, Herrgard MJ, Palsson BO (2004) Integrating high-throughput and computational data elucidates bacterial networks. Nature 429: 92-96.
10. Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, et al. (2004) Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc Natl Acad Sci U S A 101: 5934-5939.
11. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298: 799-804.
12. Davidson EH, et al. (2002) A genomic regulatory network for development. Science 295: 1669-1678.
13. Ideker T, Thorsson V, Ranish JA, Christmas R, Buhler J, et al. (2001) Integrated genomic and proteomic analyses of a systematically perturbed metabolic network. Science 292: 929-934.
14. Chvatal V (1983) Linear programming. New York: W. H. Freeman. 478 p.
15. Reed JL, Famili I, Thiele I, Palsson BO, et al. (2006) Towards multidimensional genome annotation. Nat Rev Genet 7: 130-141.
16. Price ND, Reed JL, Palsson BO (2004) Genome-scale models of microbial cells: Evaluating the consequences of constraints. Nat Rev Microbiol 2: 886-897.
17. von Hippel PH (2004) Biochemistry. Completing the view of transcriptional regulation. Science 305: 350-352.
18. Palsson B (2006) Systems biology: Properties of reconstructed networks. New York: Cambridge University Press. 322 p.
19. Papin JA, Stelling J, Price ND, Klamt S, Schuster S, et al. (2004) Comparison of network-based pathway analysis methods. Trends Biotechnol 22: 400-405.
20. Wiback SJ, Famili I, Greenberg HJ, Palsson BO (2004) Monte Carlo sampling can be used to determine the size and shape of the steady-state flux space. J Theor Biol 228: 437-447.
21. Almaas E, Kovacs B, Vicsek T, Oltvai ZN, Barabasi AL (2004) Global organization of metabolic fluxes in the bacterium Escherichia coli. Nature 427: 839-843.
22. Papp B, et al. (2004) Metabolic network analysis of the causes and evolution of enzyme dispensability in yeast. Nature 429: 661-664.
23. Papin JA, Price ND, Wiback SJ, Fell DA, Palsson BO (2003) Metabolic pathways in the post-genome era. Trends Biochem Sci 28: 250-258.
24. Stelling J, Klamt S, Bettenbrock K, Schuster S, Gilles ED. (2002) Metabolic network structure determines key aspects of functionality and regulation. Nature 420: 190-193.
25. Schilling CH, Letscher D, Palsson BO (2000) Theory for the systemic definition of metabolic pathways and their use in interpreting metabolic function from a pathway-oriented perspective. J Theor Biol 203: 229-248.
26. Wiback SJ, Palsson BO (2002) Extreme pathway analysis of human red blood cell metabolism. Biophys J 83: 808-818.
27. Papin JA, Palsson BO (2004) The JAK-STAT signaling network in the human B cell: An extreme signaling pathway analysis. Biophys J 87: 37-46.
28. Price ND, Papin JA, Palsson BO (2002) Determination of redundancy and systems properties of the metabolic network of Helicobacter pylori using genome-scale extreme pathway analysis. Genome Res 12: 760-769.
29. Lay DC (2003) Linear algebra and its applications. Boston: Addison Wesley. 492 p.
30. Famili I, Mahadevan R, Palsson BO (2005) k-Cone analysis: Determining all candidate values for kinetic parameters on a network scale. Biophys J 88: 1616-1625.
31. Price ND, Schellenberber J, Palsson BO (2004) uniform sampling of steady state flux spaces: Means to design experiments and to interpret enzymopathies. Biophys J 87: 2172-2186.
32. Thiele I, Price ND, Vo TD, Palsson BO (2005) Candidate metabolic network states in human mitochondria. Impact of diabetes, ischemia, and diet. J Biol Chem 280: 11683-11695.
33. Ibarra RU, Edwards JS, Palsson BO (2002) Escherichia coli K-12 undergoes adaptive evolution to achieve in silico predicted optimal growth. Nature 420: 186-189.
34. Fong SL, Palsson BO (2004) Metabolic gene-deletion strains of Escherichia coli evolve to computationally predicted growth phenotypes. Nat Genet 36: 1056-1058.
35. Papin JA, Price ND, Palsson BO (2002) Extreme pathway lengths and reaction participation in genome-scale metabolic networks. Genome Res 12: 1889-1900.
36. Beard DA, Liang SD, Qian H (2002) Energy balance for analysis of complex metabolic networks. Biophys J 83: 79-86.
37. Balazsi G, Barahase AL, Oltvai ZN (2005) Topological units of environmental signal processing in the transcriptional regulatory network of Escherichia coli. Proc Natl Acad Sci U S A 102: 7841-7846.
38. Shen-Orr SS, Milo R, Mangan S, Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31: 64-68.