An overview of cardiac systems biology

Journal of Molecular and Cellular Cardiology

Volumn 44, Issue 3, 2008, Pages 460-469

  Shreenivasaiah, Pradeep Kumar ^a   Rho, Seong Hwan ^a   Kim, Taeyong ^a   Kim, Do Han ^a  

^a Gwangju Institute of Science and Technology (GIST)   (South Korea)

Author keywords

Heart disease; Network biology; Physiomics; Quantitative modeling; Signal transduction

Indexed keywords

ACTION POTENTIAL; CARDIOVASCULAR FUNCTION; CARDIOVASCULAR SYSTEM; COMPUTER PROGRAM; DATA BASE; HEART MUSCLE CELL; HIGH THROUGHPUT SCREENING; MATHEMATICAL COMPUTING; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEOMICS; REVIEW;

ANIMALS; COMPUTER SIMULATION; HEART; HEART DISEASES; HUMANS; MODELS, CARDIOVASCULAR;

EID: 40849142030     PISSN: 00222828     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.yjmcc.2007.12.005     Document Type: Review

References (128)

1. Ng A., Bursteinas B., Gao Q., Mollison E., and Zvelebil M. Resources for integrative systems biology: from data through databases to networks and dynamic system models. Brief Bioinform 7 (2006) 318-330
2. Kitano H. Systems biology: a brief overview. Science 295 (2002) 1662-1664
3. Kitatno H. Computational systems biology. Nature 420 (2002) 206-210
4. Barabasi A.L., and Bonabeau E. Scale-free networks. Sci Amer 288 (2003) 60-69
5. Barabási A.L., and Oltvai Z.N. Network biology: understanding the cell's functional organization. Nat Rev Genet 5 (2004) 101-113
6. Barabasi A.L., and Albert R. Emergence of scaling in random networks. Science 286 (1999) 509-512
7. Booch G. Object Oriented Analysis and Design. 2nd ed. (1994), Benjamin/Cummings, Calif
8. Liew C.C., and Dzau V.J. Molecular genetics and genomics of heart failure. Nat Rev Genet 5 (2004) 811-825
9. Barrans J.D., and Liew C.C. Chipping away at heart failure. Methods Mol Med 126 (2006) 157-169
10. Donahue M.P., Marchuk D.A., and Rockman H.A. Redefining heart failure: the utility of genomics. J Amer Coll Cardiol 48 (2006) 1289-1298
11. Winslow R.L., and Boguski M.S. Genome informatics: current status and future prospects. Circ Res 92 (2003) 953-961
12. McGregor E., and Dunn M.J. Proteomics of the heart: unraveling disease. Circ Res 98 (2006) 309-321
13. Van Eyk J.E. Proteomics: unraveling the complexity of heart disease and striving to change cardiology. Curr Opin Mol Therapeu 3 (2001) 546-553
14. Scobioala S., Klocke R., Michel G., Kuhlmann M., and Nikol S. Proteomics: state of the art and its application in cardiovascular research. Curr Med Chem 11 (2004) 3203-3218
15. Arrell D.K., Neverova I., and Van Eyk J.E. Cardiovascular proteomics: evolution and potential. Circ Res 88 (2001) 763-773
16. Vasan R.S. Biomarkers of cardiovascular disease: molecular basis and practical considerations. Circulation 113 (2006) 2335-2362
17. White M.Y., and Van Eyk J.E. Cardiovascular proteomics: past, present, and future. Mol Diagn Ther 11 (2007) 83-95
18. Matt P., Carrel T., White M., Lefkovits I., and Van Eyk J. Proteomics in cardiovascular surgery. J Thorc Cardiovasc Surg 133 (2007) 210-214
19. Griffin J. Metabolic profiles to define the genome: can we hear the phenotypes?. Philos Trans R Soc Lond B Biol Sci 359 (2004) 857-871
20. David G.J. Metabolite profiling and cardiovascular disease. In: Lindon J., Nicholson J., and Holmes E. (Eds). The Hand book of Metabonomics and Metabolomics (2006), Elsevier
21. Grainger D.J. Metabolic profiling in heart disease. Heart Metab [serial online] 32 (2006) 22-25. http://www.heartandmetabolism.org/issues/HM32/HM32newtherape.asp Available from: URL:http://www.heartandmetabolism.org/issues/HM32/HM32newtherape.asp
22. Jenuth J.P. The NCBI. Publicly available tools and resources on the Web. Methods Mol Biol 132 (2000) 301-312
23. Edgar R., and Barrett T. NCBI GEO standards and services for microarray data. Nat Biotechnol 24 (2006) 1471-1472
24. Barrett T., Troup D.B., Wilhite S.E., Ledoux P., Rudnev D., Evangelista C., et al. NCBI GEO: mining tens of millions of expression profiles-database and tools update. Nucleic Acids Res 35 (2007) D760-D765 (Database issue)
25. Park I., Hong S.E., Kim T.W., Lee J., Oh J., Choi E., et al. Comprehensive identification and characterization of novel cardiac genes in mouse. J Mol Cell Cardiol 43 (2007) 93-106
26. White S.M., Constantin P.E., and Claycomb W.C. Cardiac physiology at the cellular level: use of cultured HL-1 cardiomyocytes for studies of cardiac muscle cell structure and function. Am J Physiol Heart Circ Physiol 286 (2004) H823-H829
27. Mcculloch A.D., and Paternostro G. Cardiac systems biology. Ann NY Acad Sci 1047 (2005) 283-295
28. Paternostro G., Vignola C., Bartsch D., Omens J.H., McCulloch A.D., and Reed J.C. Age-associated cardiac dysfunction in Drosophila melanogaster. Circ Res 88 (2001) 1053-1058
29. Hu N., Sedmera D., Yost H.J., and Clark E.B. Structure and function of the developing Zebrafish Heart. THE ANATOMICAL RECORD 260 (2000) 148-157
30. Joyce A.R., and Palsson B.O. The model organism as a system: integrating '-omics' data sets. Nat Rev Mol Cell Biol 7 (2006) 198-210
31. Mayr M., Madhu B., and Xu Q. Proteomics and metabolomics combined in cardiovascular research. Trends in cardiovasc Med 17 (Feb 2007) 43-48
32. Hwang D., Rust A.G., Ramsey S., Smith J.J., Leslie D.M., Weston A.D., et al. A data integration methodology for systems biology. Proc Natl Acad Sci U S A 102 (2005) 17296-17301
33. Hwang D., Smith J.J., Leslie D.M., Weston A.D., Rust A.G., Ramsey S., et al. A data integration methodology for systems biology: experimental verification. Proc Natl Acad Sci U S A 102 (2005) 17302-17307
34. Benson D.A., Karsch-Mizrachi I., Lipman D.J., Ostell J., and Wheeler D.L. GenBank. Nucleic Acids Res 35 (2007) D21-D25 (Database issue)
35. Wheeler D.L., Barrett T., Benson D.A., Bryant S.H., Canese K., Chetvernin V., et al. Database resources of the National Center for Biotechnology Information. Nucleic Acids Res 35 (2007) D5-D12 (Database issue)
36. The Universal Protein Resource (UniProt). Nucleic Acids Res 35 (2007) D193-D197 (Database issue)
37. Couto F.M., Silva M.J., Lee V., Dimmer E., Camon E., Apweiler R., et al. GO annotator: linking protein GO annotations to evidence text. J Biomed Discov Collab 1 (2006) 1-19
38. Mulder N.J., Apweiler R., Attwood T.K., Bairoch A., Bateman A., Binns D., et al. New developments in the InterPro database. Nucleic Acids Res 35 (2007) D224-D228 (Database issue)
39. Mishra G.R., Suresh M., Kumaran K., Kannabiran N., Suresh S., Bala P., et al. Human protein reference database-2006 update. Nucleic Acids Res 34 (2006) D411-D414 (Database issue)
40. Kanehisa M., Goto S., Kawashima S., Okuno Y., and Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 32 (2004) D277-D280 (Database issue)
41. Safran M., Solomon I., Shmueli O., Lapidot M., Shen-Orr S., Adato A., et al. GeneCards 2002: towards a complete, object-oriented, human gene compendium. Bioinformatics 18 (2002) 1542-1543
42. Lenhard B., Hayes W.S., and Wasserman W.W. GeneLynx: a gene-centric portal to the human genome. Genome Res 11 (2001) 2151-2157
43. Lenhard B., Wahlestedt C., and Wasserman W.W. GeneLynx mouse: integrated portal to the mouse genome. Genome Res 13 (2003) 1501-1504
44. Frezal J. Genatlas database, genes and development defects. C R Acad Sci III 321 (1998) 805-817
45. Hubbard T.J., Aken B.L., Beal K., Ballester B., Caccamo M., Chen Y., et al. Ensembl 2007. Nucleic Acids Res 35 (2007) D610-D617 (Database issue)
46. Wittig U., Golebiewski M., Kania R., Krebs O., Mir S., Weidemann A., et al. Integration and curation of reaction kinetics data. proceedings of the 3rd International workshop on Data Integration in the Life Sciences 4075 (2006) 9-103
47. Cotter D., Guda P., Fahy E., and Subramaniam S. MitoProteome: mitochondrial protein sequence database and annotation system. Nucleic Acids Res 32 (2004) D463-D467 (Database issue)
48. Zhang Q., Lu M., Shi L., Rui W., Zhu X., Chen G., et al. Cardio: a web-based knowledge resource of genes and proteins related to cardiovascular disease. Int J Cardiol 97 (2004) 245-249
49. Hong S.E., Rho S.H., Yeom Y.I., and Kim D.H. HCNet: a database of heart and calcium functional network. Bioinformatics 22 (2006) 2053-2054
50. CIDMS:Cardiac Integrated Database Managment System, version 1.0. [Online] Available from: URL: http://cidms.org
51. Akman V., and Surav M. Steps toward formalizing context. AI Magazine 17 (1996)
52. Burek P., Hoehndorf R., Loebe F., Visagie J., Herre H., and Kelso J. A top-level ontology of functions and its application in the Open Biomedical Ontologies. Bioinformatics 22 (2006) 66-73
53. Ashburner M., Ball C.A., Blake J.A., Botstein D., Butler H., Cherry J.M., et al. Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25 (2000) 25-29
54. Rosse C., and Mejino Jr. J.L. A reference ontology for biomedical informatics: the foundational model of anatomy. J Biomed Inform 36 (2003) 478-500
55. Berner-Lee T., and Hendler J. Publishing on the semantic web. Nature (2001) 1023-1024
56. Summary Report: W3C Workshop on Semantic Web for Life Sciences. [Online] (Nov 22 2004) Available from: URL:http//www.w3.org/2004/10/swls-workshop-report.html
57. In: Baker C.J.O., and Cheung H. (Eds). Semantic Web: revolutionizing knowledge discovery in the life sciences (2007), Springer, New York
58. Wang X., Gorlitsky R., and Almeida J.S. From XML to RDF: how semantic web technologies will change the design of '-omic' standards. Nat Biotechnol 23 (2005) 1099-1103
59. Bratsas C.H., Quaresma P., Pangalos G., and Maglaveras N. Using ontologies to build a knowledge base of cardiology problems and algorithms. Proceedings 31st annual meeting of CinC; Chicago, USA (2004)
60. Gedzelman S., Simonet M., Bernhard D., Diallo G., and Palmer P. Building an ontology of cardio-vascular diseases for concept-based information retrieval. Proceedings 32nd annual meeting of CinC; Lyon, France (2005)
61. Stromback L., Hall D., and Lambrix P. A review of standards for data exchange within systems biology. Proteomics 7 (2007) 857-867
62. Klipp E., Liebermeister W., Helbig A., Kowald A., and Schaber J. Systems biology standards-the community speaks. Nat Biotechnol 25 (2007) 390-391
63. Brazma A., Krestyaninova M., and Sarkans U. Standards for systems biology. Nat Rev Genet 7 (2006) 593-605
64. Bard J.B., and Rhee S.Y. Ontologies in biology: design, applications and future challenges. Nat Rev Genet 5 (2004) 213-222
65. Soldatova L.N., and King R.D. Are the current ontologies in biology good ontologies?. Nat Biotechnol 23 (2005) 1095-1098
66. Quackenbush J. Data standards for '-omic' science. Nat Biotechnol 22 (2004) 613-614
67. Bhalla U.S., and Iyengar R. Emergent properties of networks of biological signaling pathways. Science 283 (1999) 381-387
68. Davidenko J.M., Pertsov A.V., Salomonsz R., Baxter W., and Jalife J. Stationary and drifting spiral waves of excitation in isolated cardiac muscle. Nature 355 (1992) 349-351
69. Kitano H., Funahashi A., Matsuoka Y., and Jouraku A. Using process diagrams for the graphical representation of biological networks. Nat Biotechnol 23 (2005) 961-966
70. Funahashi A., Matsuoka Y., Jouraku A., and Kitano H. Celldesigner: a modeling tool for biochemical networks. Proceedings of the 2006 Winter Simulation Conference (2006) 1707-1712
71. Suderman M., and Hallett M.i.c.h.a.e.l. Tools for visually exploring biological networks. Bioinformatics 23 (2007) 2651-2659
72. Zhu X., Gerstein M., and Snyder M. Getting connected: analysis and principles of biological networks. Genes Dev 21 (2007) 1010-1024
73. Papin J.A., Reed J.L., and Palsson B.O. Hierarchical thinking in network biology: the unbiased modularization of biochemical networks. Trends Biochem Sci 2912 (2004) 641-647
74. Lee N.H. Genomic approaches for reconstructing gene networks. Pharmacogenomics 6 (2005) 245-258
75. Piano F., Kristin G.C., Hill D.E., and Vidal M.C. Elegans network biology: a beginning. WormBookorg [serial online] (2006). http://www.wormbook.org/chapters/www_networkbio/networkbio.html Availabe from: URL: http://www.wormbook.org/chapters/www_networkbio/networkbio.html
76. Xia Y., Yu H., Jansen R., Seringhaus M., Baxter S., Greenbaum D., et al. Analyzing cellular biochemistry in terms of molecular networks. Annu Rev Biochem 73 (2004) 1051-1087
77. Albert R. Scale-free networks in cell biology. J Cell Sci 118 (2005) 4947-4957
78. Bansal M., Belcastro V., Ambesi-Impiombato A., and di Bernardo D. How to infer gene networks from expression profiles. Mol Syst Biol 3 (2007) 78-88
79. Weiss J.N., Yang L., and Qu Z. Systems biology approaches to metabolic and cardiovascular disorders: network perspectives of cardiovascular metabolism. J Lipid Res 47 (2006) 2355-2366
80. Drake T.A., Schadt E.E., and Lusis A.J. Integrating genetic and gene-expression data: application to cardiovascular and metabolic traits in mice. Mamm Genome 17 (2006) 466-479
81. Ashley E.A., Ferrara R., King J.Y., Vailaya A., Kuchinsky A., He X., et al. Network analysis of human in-stent restenosis. Circulation 114 (2006) 2644-2654
82. Ghazalpour A., Doss S., Yang X., Aten J., Toomey E.M., Van Nas A., et al. Thematic review series: the pathogenesis of atherosclerosis. Toward a biological network for atherosclerosis. J Lipid Res 45 (2004) 1793-1805
83. Kitano H. Biological robustness. Nat Rev Genet 5 (2004) 826-837
84. Ge H., Walhout A.J., and Vidal M. Integrating '-omic' information: a bridge between genomics and systems biology. Trends Genet 19 (2003) 551-560
85. Noble D. Systems biology and the heart. Biosystems 83 (2006) 75-80
86. Ideker T., and Lauffenburger D. Building with a scaffold: emerging strategies for high- to low-level cellular modeling. Trends Biotechnol 21 (2003) 255-262
87. Rual J.F., Venkatesan K., Hao T., Hirozane-Kishikawa T., Dricot A., Li N., et al. Towards a proteome-scale map of the human protein-protein interaction network. Nature 437 (2005) 1173-1178
88. Ramani A.K., Bunescu R.C., Mooney R.J., and Marcotte E.M. Consolidating the set of known human protein-protein interactions in preparation for large-scale mapping of the human interactome. Genome Biol 6 (2005) R40.0-R40.12
89. Oda K., Matsuoka Y., Funahashi A., and Kitano H. A comprehensive pathway map of epidermal growth factor receptor signaling. Mol Syst Biol 1 (2005) 2005.0010
90. Futschik M.E., Chaurasia G., and Herzel H. Comparison of human protein-protein interaction maps. Bioinformatics 23 (2007) 605-611
91. Luo R.Y., Liao S., Tao G.Y., Li Y.Y., Zeng S., Li Y.X., et al. Dynamic analysis of optimality in myocardial energy metabolism under normal and ischemic conditions. Mol Syst Biol 2 (2006) 2006.0031
92. Nobel D. Cardiac action and pace maker potentials based on the Hodgkin-Huxley equations. Nature 188 (1960) 495-497
93. Noble D., and Rudy Y. Models of cardiac ventricular action potentials: iterative interaction between experiment and simulation. Philos Trans: Mats, Phys and Engi Sci 359 (2001) 1127-1142
94. DiFrancesco D., and Nobel D. A model of cardiac electical activity incorporating ionic pumps and concentration changes. Philos Trans R Soc B Biol Sci 307 (1985) 353-398
95. McCulloch A.D. Functionally and structurally integrated computational modeling of ventricular physiology. Jpn J Physiol 54 (2004) 531-539
96. Nobel D. The future: putting Humpty-Dumpty together again. Biochem Soc Trans 31 (2003) 156-158
97. Smith N.P., Crampin E.J., Niederer S.A., Bassingthwaighte J.B., and Beard D.A. Computational biology of cardiac myocytes: proposed standards for the physiome. J Exp Biol 210 (2007) 1576-1583
98. Hunter P., and Nielsen P. A strategy for integrative computational physiology. Physiology (Bethesda, Md) 20 (2005) 316-325
99. Hunter P., Smith N., Fernandez J., and Tawhai M. Integration from proteins to organs: the IUPS Physiome Project. Mech Ageing Dev 126 (2005) 187-192
100. Winslow R.L., and Greenstein J.L. The ongoing journey to understand heart function through integrative modeling. Circ Res 95 (2004) 1135-1136
101. Luo C.H., and Rudy Y. A dynamic model of the cardiac ventricular action potential. I. Simulations of ionic currents and concentration changes. Circ Res 74 (1994) 1071-1096
102. 2+ dynamics: the roles of ryanodine receptor adaptation and sarcoplasmic reticulum load. Biophys J 74 (1998) 1149-1168
103. Mazhari R., Greenstein J.L., Winslow R.L., Marban E., and Nuss H.B. Molecular interactions between two long-QT syndrome gene products, HERG and KCNE2, rationalized by in vitro and in silico analysis. Circ Res 89 (2001) 33-38
104. Irvine L.A., Jafri M.S., and Winslow R.L. Cardiac sodium channel Markov model with temperature dependence and recovery from inactivation. Biophys J 76 (1999) 1868-1885
105. Rice J.J., Jafri M.S., and Winslow R.L. Modeling short-term interval-force relations in cardiac muscle. Am J physiol Heart Circ Physiol 278 (2000) H913-H931
106. Rice J.J., Jafri M.S., and Winslow R.L. Modelling short-term interval-force relations in cardiac muscle. Ann NY Acad Sci 853 (1998) 345-349
107. Rice J.J., Jeremy J., Jafri M.S., and Winslow R.L. Computational modeling of short-term interval-force relations in single cardiac myocytes. Ann Biomed Eng 28 SUPPL.1 (2000) S-89
108. Deserranno D., Kassemi M., and Thomas J. Incorporation of myofilament activation mechanics into a lumped model of the human heart. Ann Biomed Eng 35 (2007) 321-336
109. Niederer S.A., Hunter P.J., and Smith N.P. A quantitative analysis of cardiac myocyte relaxation: a simulation study. Biophys J 90 (2006) 1697-1722
110. Winslow R.L., Tanskanen A., Chen M., and Greenstein J.L. Multi-scale modeling of calcium signaling in the cardiac dyad. Ann NY Acad Sci 1080 (2006) 362-375
111. Hinch R., Greenstein J.L., and Winslow R.L. Multi-scale models of local control of calcium induced calcium release. Prog Biophys Mol Biol 90 (2006) 136-150
112. Winslow R.L., and Greenstein J.L. Biophysical models of the cardiovascular system. In: Stephanopoulos I. (Ed). Systems Biology. Networks, Models, and Applications vol. II (2007), University Press, Oxford 265-296
113. Cortassa S., Aon M.A., Marban E., Winslow R.L., and O'Rourke B. An integrated model of cardiac mitochondrial energy metabolism and calcium dynamics. Biophys J 84 (2003) 2734-2755
114. Vo T.D., and Palsson B.O. Building the power house: recent advances in mitochondrial studies through proteomics and systems biology. Am J Physiol Cell Physiol 292 (2007) C164-C177
115. Saucerman J.J., and McCulloch A.D. Mechanistic systems models of cell signaling networks: a case study of myocyte adrenergic regulation. Prog Biophys Mol Biol 85 (2004) 261-278
116. Saucerman J.J., Brunton L.L., Michailova A.P., and McCulloch A.D. Modeling beta-adrenergic control of cardiac myocyte contractility in silico. J Biol Chem 278 (2003) 47997-48003
117. 2+. Biophys J 88 (2005) 2234-2249
118. Saucerman J.J., Zhang J., Martin J.C., Peng L.X., Stenbit A.E., Tsien R.Y., et al. Systems analysis of PKA-mediated phosphorylation gradients in live cardiac myocytes. Proc natl Acad Sci U S A 103 (2006) 12923-12928
119. Cortassa S., Aon M., O'Rourke B., Jacques R., Tseng H.-J., Marban E., et al. A computational model integrating electrophysiology, contraction, and mitochondrial bioenergetics in the ventricular myocyte. Biophys J 91 (2006) 1564-1589
120. Winslow R.L., Cortassa S., and Greenstein J.L. Using models of the myocyte for functional interpretation of cardiac proteomic data. J Physiol 563 (2005) 73-81
121. Swertz M.A., and Jansen R.C. Beyond standardization: dynamic software infrastructures for systems biology. Nat Rev Genet 8 (2007) 235-243
122. Shannon P.T., Reiss D.J., Bonneau R., and Baliga N.S. The Gaggle: an open-source software system for integrating bioinformatics software and data sources. BMC bioinformatics 7 (2006) 176-189
123. Hucka M., Finney A., Sauro H., Bolouri H., Doyle J., and Kitano H. The ERATO Systems Biology Workbench: enabling interaction and exchange between software tools for computational biology. PacSympBiocomput 7 (2002) 450-461
124. Kumar S.P., and Feidler J.C. BioSPICE: a computational infrastructure for integrative biology. Omics 7 (2003) 225-225
125. Stromback L., Jakoniene V., Tan H., and Lambrix P. Representing, storing and accessing molecular interaction data: a review of models and tools. Brief Bioinform 7 (2006) 331-338
126. Puglisi J.L., and Bers D.M. LabHEART: an interactive computer model of rabbit ventricular myocyte ion channels and Ca transport. Am J Physiol Cell Physiol 281 (2001) C2049-C2060
127. Sarai N., Matsuoka S., and Noma A. simBio: a Java package for the development of detailed cell models. Prog Biophys Mol Biol 90 (2006) 360-377
128. Demir S.S. Computational modeling of cardiac ventricular action potentials in rat and mouse: review. Jpn J Physiol 54 (2004) 523-530