The effects of feedback loops on disease comorbidity in human signaling networks

Bioinformatics

Volumn 27, Issue 8, 2011, Pages 1113-1120

  Le, Duc Hau ^a   Kwon, Yung Keun ^a  

^a University of Ulsan   (South Korea)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMORBIDITY; FEEDBACK SYSTEM; GENERAL ASPECTS OF DISEASE; GENETICS; HUMAN; SIGNAL TRANSDUCTION;

COMORBIDITY; DISEASE; FEEDBACK, PHYSIOLOGICAL; HUMANS; SIGNAL TRANSDUCTION;

EID: 79954503846     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btr082     Document Type: Article

References (52)

1. Albert,R. (2004) Boolean modeling of genetic regulatory networks. Lect. Notes Phys., 650, 459-481.
2. Awan,A. et al. (2007) Regulatory network motifs and hotspots of cancer genes in a mammalian cellular signalling network. IET Syst. Biol., 1, 292-297.
3. Barabasi,A.L. and Albert,R. (1999) Emergence of scaling in random networks. Science, 286, 509-512.
4. Bhalla,U.S. et al. (2002) MAP kinase phosphatase as a locus of flexibility in a mitogenactivated protein kinase signaling network. Science, 297, 1018-1023.
5. Calvano,S.E. et al. (2005) A network-based analysis of systemic inflammation in humans. Nature, 437, 1032-1037.
6. Caughey,G. et al. (2008) Prevalence of comorbidity of chronic diseases in Australia. BMC Public Health, 8, 221.
7. Claire,M.-E. (2004) Kinetic logic: a tool for describing the dynamics of infectious disease behavior. J. Cell. Mol. Med., 8, 269-281.
8. Cui,Q. et al. (2007) A map of human cancer signaling. Mol. Syst. Biol., 3, 152.
9. Faure,A. et al. (2006) Dynamical analysis of a generic Boolean model for the control of the mammalian cell cycle. Bioinformatics, 22, e124-e131.
10. Ferrell,J.E. Jr and Machleder,E.M. (1998) The biochemical basis of an all-or-none cell fate switch in Xenopus oocytes. Science, 280, 895-898.
11. Gabriel,S. and Michaud, K. (2009) Epidemiological studies in incidence, prevalence, mortality, and comorbidity of the rheumatic diseases. Arthritis Res. Ther., 11, 229.
12. Goehler,H. et al. (2004) A protein interaction network links GIT1, an enhancer of huntingtin aggregation, to Huntington's disease. Mol. Cell, 15, 853-865.
13. Goh,K.-I. et al. (2007) The human disease network. Proc. Natl Acad. Sci. USA, 104, 8685-8690.
14. Gupta,S. et al. (2007) Boolean network analysis of a neurotransmitter signaling pathway. J. Theor. Biol., 244, 463-469.
15. Helikar,T.Å. et al. (2008) Emergent decision-making in biological signal transduction networks. Proc. Natl Acad. Sci. USA, 105, 1913-1918.
16. Hidalgo,C.S.A. et al. (2009) A dynamic network approach for the study of human phenotypes. PLoS Comput. Biol., 5, e1000353.
17. Huang,S. and Ingber,D.E. (2000) Shape-dependent control of cell growth, differentiation, and apoptosis: switching between attractors in cell regulatory networks. Exp. Cell Res., 261, 91-103.
18. Kauffman,S. et al. (2003) Random Boolean network models and the yeast transcriptional network. Proc. Natl Acad. Sci.USA, 100, 14796-14799.
19. Kauffman,S. et al. (2004) Genetic networks with canalyzing Boolean rules are always stable. Proc. Natl Acad. Sci.USA, 101, 17102-17107.
20. Kelli,L.D. et al. (2005) Comparison of three comorbidity measures for predicting health service use in patients with osteoarthritis. Arthritis Care Res., 53, 666-672.
21. Kwon,Y.-K. and Cho,K.-H. (2007) Boolean dynamics of biological networks with multiple coupled feedback loops. Biophys. J., 92, 2975-2981.
22. Kwon,Y.-K. and Cho,K.-H. (2008) Quantitative analysis of robustness and fragility in biological networks based on feedback dynamics. Bioinformatics, 24, 987-994.
23. Kwon,Y.-K. et al. (2007) Investigations into the relationship between feedback loops and functional importance of a signal transduction network based on Boolean network modeling. BMC Bioinformatics, 8, 384.
24. Lee,D.S. et al. (2008) The implications of human metabolic network topology for disease comorbidity. Proc. Natl Acad. Sci. USA, 105, 9880-9885.
25. Lee,S.-Y. et al. (2005) Synchronous adenocarcinoma and mucosa-associated lymphoid tissue (MALT) lymphoma in a single stomach. Jpn J. Clin. Oncol., 35, 591-594.
26. Lim,J. et al. (2006) A proteinprotein interaction network for human inherited ataxias and disorders of Purkinje cell degeneration. Cell, 125, 801-814.
27. Ma'ayan,A. et al. (2005) Formation of regulatory patterns during signal propagation in a mammalian cellular network. Science, 309, 1078-1083.
28. Mai,Z. and Liu,H. (2009) Boolean network-based analysis of the apoptosis network: irreversible apoptosis and stable surviving. J. Theor. Biol., 259, 760-769.
29. Mendoza,L. et al. (1999) Genetic control of flower morphogenesis in Arabidopsis thaliana: a logical analysis. Bioinformatics, 15, 593-606.
30. Milo,R. et al. (2002) Network motifs: simple building blocks of complex networks. Science, 298, 824-827.
31. Neil,S. et al. (2009) Synchronous adenocarcinoma and marginal zone B-cell lymphoma of the colon: a case report. 15, 318-322.
32. Nishigami,T. et al. (2010) Concomitant adenocarcinoma and colonic non-Hodgkin's lymphoma in a patient with ulcerative colitis: a case report and molecular analysis. Pathol.- Res. Pract., 206, 846-850.
33. Nishino,N. et al. (1996) Synchronous lymphoma and adenocarcinoma occurring as a collision tumor in the stomach: report of a case. Surg. Today, 26, 508-512.
34. Oldham,M.C. et al. (2006) Conservation and evolution of gene coexpression networks in human and chimpanzee brains. Proc. Natl Acad. Sci. USA, 103, 17973-17978.
35. Park,J. et al. (2009) The impact of cellular networks on disease comorbidity. Mol. Syst. Biol., 5.
36. Pomerening,J.R. et al. (2003) Building a cell cycle oscillator: hysteresis and bistability in the activation of Cdc2. Nat. Cell Biol., 5, 346-351.
37. Prill,R.J. et al. (2005) Dynamic properties of network motifs contribute to biological network organization. PLoS Biol., 3, e343.
38. Pujana,M.A. et al. (2007) Network modeling links breast cancer susceptibility and centrosome dysfunction. Nat. Genet., 39, 1338-1349.
39. Raja,M. and Azzoni, A. (2008) Comorbidity of Asperger's syndrome and bipolar disorder. Clin. Pract. Epidemiol. Ment. Health, 4, 26.
40. Rual,J.-F. et al. (2005) Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437, 1173-1178.
41. Saadatpour,A. et al. (2010) Attractor analysis of asynchronous Boolean models of signal transduction networks. J. Theor. Biol., 266, 641-656.
42. Saez-Rodriguez,J. et al. (2007) A logical model provides insights into T cell receptor signaling. PLoS Comput. Biol., 3, e163.
43. Sahin,O. et al. (2009) Modeling ERBB receptor-regulated G1/S transition to find novel targets for de novo trastuzumab resistance. BMC Syst. Biol., 3, 1.
44. Schlatter,R. et al. (2009) ON/OFF and beyond - a Boolean model of apoptosis. PLoS Comput. Biol., 5, e1000595.
45. Shmulevich,I. et al. (2003) The role of certain post classes in Boolean network models of genetic networks. Proc. Natl Acad. Sci. USA, 100, 10734-10739.
46. Shmulevich,I. et al. (2005) Eukaryotic cells are dynamically ordered or critical but not chaotic. Proc. Natl Acad. Sci. USA, 102, 13439-13444.
47. Snoussi,E.H. (1998) Necessary conditions for multistationarity and stable periodicity. J. Biol. Syst., 6, 3-9.
48. Stelzl,U. et al. (2005) A human protein-protein interaction network: a resource for annotating the proteome. Cell, 122, 957-968.
49. Tang,J. et al. (2008) Performance of comorbidity measures to predict stroke and death in a community-dwelling, hypertensive medicaid population. Stroke, 39, 1938-1944.
50. Tetsche,M. et al. (2008) The impact of comorbidity and stage on ovarian cancer mortality: a nationwide Danish cohort study. BMC Cancer, 8, 31.
51. Ye,Y. et al. (2005) A genome-wide tree- and forest-based association analysis of comorbidity of alcoholism and smoking. BMC Genet., 6, S135.
52. Yeger-Lotem,E. et al. (2004) Network motifs in integrated cellular networks of transcription-regulation and protein-protein interaction. Proc. Natl Acad. Sci. USA, 101, 5934-5939.