Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on Boolean network modeling

BMC Bioinformatics

Volumn 8, Issue , 2007, Pages

  Kwon, Yung Keun ^a   Choi, Sun Shim ^b   Cho, Kwang Hyun ^a  

^a Korea Advanced Institute of Science and Technology (KAIST)   (South Korea)

^b Kangwon National University   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

BIOLOGICAL NETWORKS; BOOLEAN NETWORK MODELS; BOOLEAN NETWORKS; CLUSTERING COEFFICIENT; EXTENSIVE SIMULATIONS; POSITIVE CORRELATIONS; SIGNAL TRANSDUCTION NETWORKS; TOPOLOGICAL CHARACTERISTICS;

BOOLEAN ALGEBRA; COMPUTER SIMULATION; SIGNAL TRANSDUCTION; TOPOLOGY;

NEURAL NETWORKS;

BRAIN PROTEIN; PROTEOME;

ARTICLE; BIOLOGICAL MODEL; CONFIDENCE INTERVAL; CONTROLLED STUDY; CORRELATION ANALYSIS; FEEDBACK SYSTEM; HIPPOCAMPUS; INFORMATION SCIENCE; MOUSE; NONHUMAN; PREDICTION; PROTEIN EXPRESSION; PROTEIN FUNCTION; SIGNAL TRANSDUCTION; SIMULATION; ALGORITHM; COMPUTER PROGRAM; COMPUTER SIMULATION; GENE EXPRESSION PROFILING; METABOLISM; METHODOLOGY; PHYSIOLOGY; PROTEIN ANALYSIS; STATISTICAL MODEL;

MUS;

ALGORITHMS; COMPUTER SIMULATION; FEEDBACK; GENE EXPRESSION PROFILING; LOGISTIC MODELS; MODELS, BIOLOGICAL; PROTEIN INTERACTION MAPPING; PROTEOME; SIGNAL TRANSDUCTION; SOFTWARE;

EID: 36849052504     PISSN: None     EISSN: 14712105     Source Type: Journal    
DOI: 10.1186/1471-2105-8-384     Document Type: Article

References (41)

1. LiuAW, Li D, Zhang J, Zhu Y, He F: SigFlux: a novel network feature to evaluate the importance of proteins in signal transduction networks. BMC Bioinformatics 2006, 27(7):515. 10.1186/1471-2105-7-515
2. Yu H, Greenbaum D, Lu Xin H, Zhu X, Gerstein M: Genomic analysis of essentiality within protein networks. Trends in Genetics 2004, 20(6):227-231. 10.1016/j.tig.2004.04.008 15145574
3. He X, Zhang J: Why do hubs tend to be essential in protein networks?. PLoS Genetics 2006, 2(6):e88. 1473040 16751849 10.1371/ journal.pgen.0020088
4. Balaji S, Iyer L, Aravind L, Babu M: Uncovering a hidden distributed architecture behind scale-free transcriptional regulatory networks. Journal of Molecular Biology 2006, 260:204-212. 10.1016/j.jmb.2006.04.026
5. Albert R, Jeong H, Barabasi A: Error and attack tolerance of complex networks Nature 2000, 406:378-382. 10.1038/35019019 10935628
6. Ma'ayan A, Jenkins S, Neves S, Hasseldine A, Grace E, Dubin-Thaler B, Eungdamrong N, Weng G, Ram P, Rice J, Kershenbaum A, Stolovitzky G, Blitzer R, Iyengar R: Formation of regulatory patterns during signal propagation in a Mammalian cellular network Science. 2005, 30(5737):1078-1083. 10.1126/science.1108876 16099987
7. Vitkup D, Kharchenko P, Wagner A: Influence of metabolic network structure and function on enzyme evolution. Genome Biology 2006, 7(5):R39. 1779518 16684370 10.1186/gb-2006-7-5-r39
8. Barabasi ALU Oltvai ZN: Network biology: understanding the cell's functional organization. Nature Reviews Genetics 2004, 5(2):101-113. 10.1038/nrg1272 14735121
9. Wilhelm T, Behre J, Schuster S: Analysis of structural robustness of metabolic networks. Systems Biology 2004, 1:114-120. 10.1049/sb:20045004 17052121
10. Thomas R, Thieffry D, Kaufman M: Dynamical behaviour of biological regulatory networks-I. Biological role of feedback loops and practical use of the concept of the loop-characteristic state. Bulletin of Mathematical Biology 1995, 57(2):247-276. 7703920
11. Plahte E, Mestl T, Omholt SW: Feedback loops, stability and multi-stationarity in dynamical systems. Journal of Biological Systems 1995, 3:409-413. 10.1142/S0218339095000381
12. Gouzé JL: Positive and negative circuits in dynamical systems. Journal of Biological Systems 1998, 6:11-15. 10.1142/S0218339098000054
13. Snoussi EH: Necessary conditions for multistationarity and stable periodicity. Journal of Biological Systems 1998, 6:3-9. 10.1142/ S0218339098000042
14. Mendoza L, Thieffry D, Alvarez-Buylla ER: Genetic control of flower morphogenesis in Arabidopsis thaliana: A logical analysis. Bioinformatics 1999, 15(7/8):593-606. 10.1093/bioinformatics/15.7.593 10487867
15. Martinet-Adelist C: Kinetic logic: a tool for describing the dynamics of infectious disease behavior. Journal of Cellular and Molecular Medicine 2004, 8(2):269-281. 10.1111/j.1582-4934.2004.tb00283.x
16. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D, Alon U: Network Motifs: Simple Building Blocks of Complex Networks. Science 2002, 298(5594):824-827. 10.1126/science.298.5594.824 12399590
17. Yeger-Lotem E, Sattath S, Kashtan N, Itzkovitz S, Milo R, Pinter R, Alon U, Margalit H: Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proceedings of the National Academy of Sciences, USA 2004, 101(16):5934-5939. 10.1073/ pnas.0306752101
18. Prill R, Iglesias P, Levchenko A: Dynamic Properties of Network Motifs Contribute to Biological Network Organization. PLoS Biology 2005, 3(11):e343. 1239925 16187794 10.1371/journal.pbio.0030343
19. Kauffman S. Peterson C. Samuelsson B, Troein C: Random Boolean network models and the yeast transcriptional network. Proceedings of the National Academy of Sciences, USA 2003, 100:14796-14799. 10.1073/ pnas.2036429100
20. Shmulevich I, Lähdesmäki H, Dougherty ER, Astola, Zhang W: The role of certain Post classes in Boolean network models of genetic networks. Proceedings of the National Academy of Sciences, USA 2003, 100:10734-10739. 10.1073/pnas.1534782100
21. Kauffman S, Peterson C, Samuelsson B, Troein C: Genetic networks with canalyzing Boolean rules are always stable. Proceedings of the National Academy of Sciences, USA 2004, 101(49):17102-17107. 10.1073/ pnas.0407783101
22. Shmulevich I, Kauffman S, Aldana M: Eukaryotic cells are dynamically ordered or critical but not chaotic. Proceedings of the National Academy of Sciences, USA 2005, 102:13439-13444. 10.1073/pnas.0506771102
23. Kwon YK, Cho KH: Boolean dynamics of biological networks with multiple coupled feedback loops. Biophysical Journal 2007, 92(8):2975-2981. 10.1529/biophysj.106.097097 17259267
24. Fraser H, Hirsh A, Steinmetz L, Scharfe C, Feldman M: Evolutionary rate in the protein interaction network. Science 2002, 296(5568):750-752. 10.1126/science.1068696 11976460
25. Wuchty S: Evolution and topology in the yeast protein interaction network. Genome Research 2004. 14(7):1310-1314. 442146 15231746 10.1101/ gr.2300204
26. Ferrell JE Jr., Machleder EM: The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science 1998, 280:895-898. 10.1126/ science.280.5365.895 9572732
27. Bhalla US, Ram PT, Iyengar R: MAP kinase phosphatase as a locus of flexibility in a mitogen-activated protein kinase signaling network. Science 2002, 297:1018-1023. 10.1126/science.1068873 12169734
28. Pomerening JR, Sontag ED, Ferrell JE Jr.: Building a cell cycle oscillator: Hysteresis and bistability in the activation of Cdc2. Nature Cell Biology 2003, 5:346-351. 10.1038/ncb954 12629549
29. Smits WK, Kuipers OP, W VJ: Thenotypic variation in bacteria: the role of feedback regulation. Nature Reviews Microbiology 2006, 4:259-271. 10.1038/nrmicro1381 16541134
30. Sha W, Moore J, Chen K, Lassaletta AD, Yi CS, Tyson JJ, Sible JC; Hysteresis drives cell-cycle transitions in Xenopus laevis egg extracts. Proceedings of the National Academy of Sciences, USA 2003, 100(3):975-980. 10.1073/pnas.0235349100
31. Hirata H, Yoshiura S, Ohtsuka T, Bessho Y, Harada T, Yoshikawa K, Kageyama R: Oscillatory expression of the bHLH factor Hes1 regulated by a negative feedback loop. Science 2002, 298:840-843. 10.1126/ science.1074560 12399594
32. Li F, Long T, Lu Y, Ouyang Q, Tang C: The yeast cell-cycle network is robustly designed. Proceedings of the National Academy of Sciences, USA 2004, 10(14):4781-4786. 10.1073/pnas.0305937101
33. Kitano H: Biological robustness. Nature Reviews Genetics 2004, 5(11):826-837. 10.1038/nrg1471 15520792
34. Ciliberti S, Martin OC, Wagner A: Robustness can evolve gradually in complex regulatory gene networks with varying topology. PLoS Computational Biology 2007, 3(2):e15. 1794322 17274682 10.1371/ journal.pcbi.0030015
35. Huang S, Eichler G, Bar-Yam Y, Ingber DE: Cell fates as high-dimensional attractor states of a complex gene regulatory network. Physical Review Letters 2005, 94(12):128701. 10.1103/PhysRevLett.94.128701 15903968
36. Xiong W, Ferrell J Jr.: A positive-feedback-based bistable 'memory module' that governs a cell fate decision. Nature 2003, 426(6965):460-465. 10.1038/nature02089 14647386
37. Brandman O, Ferrell J Jr., Li R, Meyer T: Interlinked Fast and Slow Positive Feedback Loops Drive Reliable Cell Decisions. Science 2005, 310:496-498. 10.1126/science.1113834 16239477
38. Kauffman SA: Metabolic stability and epigenesis in randomly constructed genetic nets. Journal of Theoretical Biology 1969, 22(3):437-467. 10.1016/0022-5193(69)90015-0 5803332
39. Kauffman SA: The Origins of Order: Self-Organization and Selection in Evolution New York: Oxford Univ. Press 1993.
40. Stern MD: Emergence of homeostasis and "noise imprinting" in an evolution model Proceedings of the National Academy of Sciences, USA 1999, 96(19):10746-10751. 10.1073/pnas.96.19.10746
41. Bhattacharjya A, Liang S: Power-Law Distributions in Some Random Boolean. Networks Physical Review Letters 1996, 77(8):1644-1647. 10.1103/ PhysRevLett.77.1644 10063130