Complex networks: The key to systems biology

Genetics and Molecular Biology

Volumn 31, Issue 3, 2008, Pages 591-601

  Costa, Luciano da F ^a   Rodrigues, Francisco A ^a   Cristino, Alexandre S ^a  

^a UNIVERSITY OF SÃO PAULO   (Brazil)

Author keywords

Bioinformatics; Complex networks; Metabolic networks; Protein protein networks; Systems biology; Transcription networks

Indexed keywords

BIOCHEMISTRY; BIOINFORMATICS; CONCEPTUAL FRAMEWORK; DROSOPHILA MELANOGASTER; ESCHERICHIA COLI; HELICOBACTER PYLORI; INFORMATION RETRIEVAL; MEDICAL INFORMATION SYSTEM; MEDICAL LITERATURE; METABOLISM; NONHUMAN; PROCESS DEVELOPMENT; PROCESS MODEL; PROCESS TECHNOLOGY; PROTEIN PROTEIN INTERACTION; REVIEW; SACCHAROMYCES CEREVISIAE; SYSTEMS BIOLOGY; TRANSCRIPTION REGULATION;

EID: 55349111452     PISSN: 14154757     EISSN: 16784685     Source Type: Journal    
DOI: 10.1590/S1415-47572008000400001     Document Type: Review

References (88)

1. Aderem A (2005) Systems biology: Its practice and challenges. Cell 121:511-513.
2. Albert R (2005) Scale-free networks in cell biology. J Cell Sci 118:4947-57.
3. Albert R, Jeong H and Barabási AL (2000) Error and attack tolerance of complex networks. Nature 406:378-382.
4. Alon U (2007) An Introduction to Systems Biology: Design Principles of Biological Circuits. Chapman and Hall, Boca Raton, 320 pp.
5. Babu MM, Luscombe NM, Aravind L, Gerstein M and Teichmann SA (2004) Structure and evolution of transcriptional regulatory networks. Curr Opin Struct Biol 14:283-91.
6. Balazsi G, Barabási AL and Oltvai ZN (2005) Functional organization of transcriptional-regulatory networks. FEBS J 272:103-103.
7. Bar-Joseph Z, Gerber GK, Lee TI, Rinaldi NJ, Yoo JY, Robert F, Gordon DB, Fraenkel E, Jaakkola TS, Young RA, et al. (2003) Computational discovery of gene modules and regulatory networks. Nat Biotechnol 21:1337-42.
8. Barabási AL (2007) Network medicine - From obesity to the "diseasome". N Engl J Med 357:404-407.
9. Barabási AL and Albert R (1999) Emergence of scaling in random networks. Science 286:509-512.
10. Barabási AL and Oltvai ZN (2004) Network biology: Understanding the cell's functional organization. Nat Rev Genet 5:101-113.
11. Barabási AL, Jeong H, Ravasz R, Néda Z, Vicsek T and Schubert A (2002) On the topology of the scientific collaboration networks. Physica A 311:590-614.
12. Berg J, Lässig M and Wagner A (2004) Structure and evolution of protein interaction networks: A statistical model for link dynamics and gene duplications. BMC Evol Biol 4:51.
13. Boccaletti S, Latora V, Moreno Y, Chaves M and Hwang DU (2006) Complex networks: Structure and dynamics. Physics Rep 424:175-308.
14. Bollobás B (1998) Modem Graph Theory, Graduate Texts in Mathematics. Springer, New York, 184 pp.
15. Bork P (1991) Shuffled domains in extracellular proteins. FEBS Lett 286:47-54.
16. Carroll SB (2000) Endless forms: The evolution of gene regulation and morphological diversity. Cell 101:577-580.
17. Chartrand G and Lesniak L (1986) Graphs & Digraphs, Wadsworth Publ. Co., Belmont, 359 pp.
18. Chothia C (1992) One thousand families for the molecular biologist. Nature 357:543-544.
19. Cohen J, Briand F, Newman C and Palka Z (1970) Community Food Webs: Data and Theory Bio-Mathematics. Springer-Verlag, Berlin, 2220 pp.
20. Colizza V, Flammini A, Maritan A and Vespignani A (2005) Characterization and modeling of protein-protein interaction networks. Physica A 352:1-27.
21. Conant GC and Wagner A (2003) Convergent evolution of gene circuits. Nat Genet 34:264-266.
22. Costa LF and Sporns O (2005) Hierarchical features of large-scale cortical connectivity. Eur Phys J B Condensed Matter 48:567-573.
23. Costa LF and Sporns O (2006) Correlating thalamocortical connectivity and activity. Appl Phys Lett 89:013903.
24. Costa LF, Rodrigues FA and Travieso G (2006) Protein domain connectivity and essentiality. Appl Phys Lett 89:174101-1-174101-3.
25. Costa LF, Rodrigues FA, Travieso G and Boas PRV (2007) Characterization of complex networks: A survey of measurements. Adv Physics 56:167-242.
26. Davidson EH, Rast JP, Oliveri P, Ransick A, Calestani C, Yuh CH, Minokawa T, Amore G, Hinman V, Arenas-Mena C, et al. (2002) A genomic regulatory network for development. Science 295:1669-1678.
27. Diestel R (2000) Graph Theory. Springer-Verlag, Heidelberg, 431 pp.
28. Edwards J and Palsson B (2000) The Escherichia coli MG1655 in silico metabolic genotype: Its definition, characteristics, and capabilities. Proc Natl Acad Sci USA 97:5528-5523.
29. Erdös P and Rényi A (1959) On random graphs. Publ Math 6:290-297.
30. Erdös P and Rényi A (1960) On the evolution of random graphs. Publ Math Inst Hung Acad Sci 5:17-61.
31. Faloutsos M, Faloutsos P and Faloutsos C (1999) On power-law relationships of the Internet topology. Comp Commun Rev 29:251-262.
32. Fields S and Song O (1989) A novel genetic system to detect protein-protein interactions. Nature 340:245-246.
33. Flory PJ (1941) Molecular size distribution in three dimensional polymers. II. Trifunctional branching units. J Amer Chem Soc 63:3091-3096.
34. Franklin D, Godfirey V, O'Brien D, Deng C and Xiong Y (2000) Functional collaboration between different cyclin-dependent kinase inhibitors suppresses tumor growth with distinct tissue specificity. Mol Cell Biol 20:6147-6158.
35. Garlaschelli D (2004) Universality in food webs. Eur Phys J B 38:277-285.
36. Garlaschelli D, Caldarelli G and Pietronero L (2003) Universal scaling relations in food webs. Nature 423:165-168.
37. Gavin A, Boesche M, Krause R, Grandi P, Marzioch M, Bauer A, Schultz J, Rick J, Michon A, Cruciat C, et al. (2002) Functional organization of the yeast proteome by systematic analysis of protein complexes. Nature 415:141-147.
38. Gama-Castro S, Jiménez-Jacinto V, Peralta-Gil M, Santos-Zavaleta A, Peñaloza-Spinola MI, Contreras-Moreira B, Segura-Salazar J, Muniz-Rascado L, Martinez-Flores I, Salgado H, et al. (2008) RegulonDB (version 6.0): Gene regulation model of Escherichia coli K-12 beyond transcription, active (experimental) annotated promoters and textpresso navigation. Nucleic Acids Res. 36:D120-D124.
39. George RA and Heringa J (2002) An analysis of protein domain linkers: Their classification and role in protein folding. Protein Eng 15:871-879.
40. Giot L, Bader J, Brouwer C, Chaudhuri A, Kuang, B, Li Y, Hao Y, Ooi C, Godwin B, Vitols E, et al. (2003) A protein interaction map of Drosophila melanogaster. Science 302:1727-1736.
41. Guelzim N, Bottani S, Bourgine P and Kepes F (2002) Topological and causal structure of the yeast transcriptional regulatory network. Nat Genet 31:60-63.
42. Harbison CT, Gordon DB, Lee TI, Rinaldi NJ, MacIsaac KD, Danford TW, Hannett NM, Tagne JB, Reynolds DB, Yoo J, et al. (2004) Transcriptional regulatory code of a eukaryotic genome. Nature 431:99-104.
43. Hartwell LH, Hopfield JJ, Leibler S and Murray AW (1999) From molecular to modular cell biology. Nature 402:C47-52.
44. Hishigaki H, Nakai K, Ono T, Tanigami A and Takagi T (2001) Assessment of prediction accuracy of protein function from protein-protein interaction data. Yeast 18:523-531.
45. Hormozdiari F, Berenbrink P, Prulj N and Sahinalp SC (2007) Not all scale-free networks are born equal: The role of the seed graph in PPI network evolution. PLoS Comput Biol 3:e118.
46. Huerta AM, Salgado H, Thieffry D and Collado-Vides J (1998) RegulonDB: A database on transcriptional regulation in Escherichia coli. Nucleic Acids Res 26:55-59.
47. Ihmels J, Friedlander G, Bergmann S, Sarig O, Ziv Y and Barkai N (2002) Revealing modular organization in the yeast transcriptional network. Nat Genet 31:370-377.
48. Jeong H, Tombor B, Albert R, Oltvai ZN and Barabási AL (2000) The large-scale organization of metabolic networks. Nature 407:651-654.
49. Jeong H, Mason SP, Barabási AL and Oltvai ZN (2001) Lethality and centrality in protein networks. Nature 411:41-42.
50. Lee TI, Rinaldi NJ, Robert F, Odom DT, Bar-Joseph Z, Gerber GY, Hannett NM, Harbison CT, Thompson CM, Simon I, et al. (2002) Transcriptional regulatory networks in Saccharomyces cerevisiae. Science 298:799-804.
51. Levine M and Tjian R (2003) Transcription regulation and animal diversity. Nature 424:147-51.
52. Lockhart DJ and Winzeler EA (2000) Genomics, gene expression and DNA arrays. Nature 405:27-36.
53. MacIsaac KD, Wang T, Gordon DB, Gifford DK, Stormo GD and Fraenkel E (2006) An improved map of conserved regulatory sites for Saccharomyces cerevisiae. BMC Bioinformatics 7:113.
54. Milo R, Shen-Orr S, Itzkovitz S, Kashtan N, Chklovskii D and Alon U (2002) Network motifs: Simple building blocks of complex networks. Science 298:824-827.
55. Newman MEJ (2001) Scientific collaboration networks. II. Shortest paths, weighted networks, and centrality. Phys Rev E Stat Nonlin Soft Matter Phys 64:016132.
56. Newman MEJ (2002) Assortative mixing in networks. Phys Rev Lett 89:208701.
57. Newman MEJ (2003) Structure and function of complex networks. SIAM Review 45:167-256.
58. Ng S, Zhang Z and Tan S (2003) Integrative approach for computationally inferring protein domain interactions. Bioinformatics 19:923-929.
59. Ohno S (1970) Evolution by Gene Duplication. Springer-Verlag, New York, 160 pp.
60. Phillips DC (1966) The three-dimensional structure of an enzyme molecule. Sci Am 215:78-90.
61. Poyatos J and Hurst L (2004) How biologically relevant are interaction-based modules in protein networks? Genome Biol 5:R93.
62. Rain J, Selig L, De Reuse H, Battaglia V, Reverdy C, Simon S, Lenzen G, Petel F, Wojcik J, Schaechter V, et al. (2001) The protein-protein interaction map of Helicobacter pylori. Nature 409:211-215.
63. Ravasz E, Somera A, Mongru D, Oltvai Z and Barabási A (2002) Hierarchical organization of modularity in metabolic networks. Science 297:1551-1555.
64. Ren B, Robert F, Wyrick JJ, Aparicio O, Jennings EG, Simon I, Zeitlinger J, Schreiber J, Hannett N, Kanin E, et al. (2000) Genome-wide location and function of DNA binding proteins. Science 290:2306-2309.
65. Richardson JS (1981) The anatomy and taxonomy of protein structure. Adv Prot Chem 34:167-339.
66. Schena M, Shalon D, Davis RW and Brown PO (1995) Quantitative monitoring of gene expression patterns with a complementary DNA microarray. Science 270:467-470.
67. Schuster S, Fell D and Dandekar T (2000) A general definition of metabolic pathways useful for systematic organization and analysis of complex metabolic networks. Nat Biotechnol 18:326-332.
68. Schwikowski B, Uetz P and Fields S (2000) A network of protein-protein interactions in yeast. Nat Biotechnol 18:1257-1261.
69. Shen-Orr SS, Milo R, Mangan S and Alon U (2002) Network motifs in the transcriptional regulation network of Escherichia coli. Nat Genet 31:64-68.
70. Sole R and Fernandez P (2003) Modularity "for free" in genome architecture? Arxiv preprint q-bio/0312032.
71. Teichmann SA and Babu MM (2004) Gene regulatory network growth by duplication. Nat Genet 36:492-496.
72. Thieffry D, Huerta AM, Perez-Rueda E and Collado-Vides J (1998) From specific gene regulation to genomic networks: A global analysis of transcriptional regulation in Escherichia coli. Bioessays 20:433-440.
73. Uetz P and Hughes RE (2000) Systematic and large-scale two-hybrid screens. Curr Opin Microbiol 3:303-308.
74. Vázquez A and Moreno Y (2003) Resilience to damage of graphs with degree correlations. Phys Rev E Stat Nonlin Soft Matter Phys 67:015101.
75. Vázquez A, Flammini A, Maritan A and Vespignani A (2003a) Global protein function prediction from protein-protein interaction networks. Nat Biotechnol 21:697-700.
76. Vázquez A, Flammini A, Maritan A and Vespignani A (2003b) Modeling of protein interaction networks. Complexus 1:38-44.
77. Vogelstein B, Lane D and Levine AJ (2000) Surfing the p53 network. Nature 408:307-310.
78. Wagner A (2001) The yeast protein interaction network evolves rapidly and contains few redundant duplicate genes. Mol Biol Evol 18:1283-1292.
79. Wagner A (2003) How the global structure of protein interaction networks evolves. Proc Biol Sci 270:457-466.
80. Wagner A and Fell DA (2001) The small world inside large metabolic networks. Proc Biol Sci 268:1803-1810.
81. Walhout A, Boulton S and Vidal M (2000) Yeast two-hybrid systems and protein interaction mapping projects for yeast and worm. Yeast 17:88-94.
82. Watts DJ and Strogatz SH (1998) Collective dynamics of small-world networks. Nature 393:440-442.
83. West DB (2001) Introduction to Graph Theory. Prentice Hall, Upper Saddle River, 588 pp.
84. Wray GA, Hahn MW, Abouheif E, Balhoff JP, Pizer M, Rockman MV and Romano LA (2003) The evolution of transcriptional regulation in eukaryotes. Mol Biol Evol 20:1377-419.
85. Wuchty S (2001) Scale-free behavior in protein domain networks. Mol Biol Evol 18:1694-1702.
86. Wuchty S (2002) Interaction and domain networks of yeast. Proteomics 2:1715-1723.
87. Wuchty S, Oltvai ZN and Barabási AL (2003) Evolutionary conservation of motif constituents in the yeast protein interaction network. Nat Genet 35:176-179.
88. Yu H, Luscombe NM, Qian J and Gerstein M (2003) Genomic analysis of gene expression relationships in transcriptional regulatory networks. Trends Genet 19:422-427.