Studying protein-protein interaction networks: A systems view on diseases

Briefings in Functional Genomics

Volumn 11, Issue 6, 2012, Pages 497-504

  Jord́n, Ferenc ^a   Nguyen, Thanh Phuong ^a   Liu, Wei chung ^a  

^a UNIVERSITY OF TRENTO   (Italy)

Author keywords

Centrality; Disease; Network analysis; PPI network

Indexed keywords

ANALYSIS; ARTICLE; CELL FUNCTION; NETWORK ANALYSIS; PROTEIN PROTEIN INTERACTION; SIGNAL TRANSDUCTION; SYSTEMS BIOLOGY;

ANIMALS; COMPUTATIONAL BIOLOGY; DISEASE; HUMANS; PROTEIN INTERACTION MAPS;

EID: 84870316384     PISSN: 20412649     EISSN: 20412657     Source Type: Journal    
DOI: 10.1093/bfgp/els035     Document Type: Article

References (66)

1. Patten BC. An introduction to the cybernetics of the ecosystem: the trophic-dynamic aspect. Ecology 1959;40: 221-31.
2. Barabási AL, Oltvai ZN. Network biology: understanding the cell's functional organization. Nat Rev Genet 2004;5: 101-13.
3. Zhu D, Qin ZS. Structural comparison of metabolic networks in selected single cell organisms. BMC Bioinformatics 2005;6:8.
4. Aggarwal K, Lee KH. Functional genomics and proteomics as a foundation for systems biology. Brief Funct Genomic Proteomic 2003;2:175-84.
5. de Jong H, Geiselmann J, Hernandez C, et al. Genetic Network Analyzer: qualitative simulation of genetic regulatory networks. Bioinformatics 2003;19:336-44.
6. Hopkins AL. Network pharmacology: the next paradigm in drug discovery. Nat ChemBiol 2008;4:682-90.
7. González-Couto E. Functional and systems biology approaches to Huntington's disease. Brief Funct Genomics 2011;10:109-14.
8. Vidal M, Cusick ME, Barabási AL. Interactome networks and human disease. Cell 2011;144:986-98.
9. Ng SK, Tan SH. Discovering protein-protein interactions. J Bioinform Comput Biol 2003;1:711-41.
10. Ito T, Chiba T, Ozawa R, et al. A comprehensive twohybrid analysis to explore the yeast protein interactome. ProcNatl Acad SciUSA 2001;98:4569-74.
11. Uetz P, Giot L, Mansfield TA, et al. A comprehensive analysis of protein-protein interactions in saccharomyces cerevisiae. Nature 2000;403:623-7.
12. Smith GP. Filamentous fusion phage: Novel expression vectors that display cloned antigens on the virion surface. Science 1985;228:1315-7.
13. Bauer A, Kuster B. Affinity purification-mass spectrometry: Powerful tools for the characterization of protein complexes. EurJ Biochem 2003;270:570-8.
14. Bockler BS, Bateman A. Protein interactions in human genetic diseases. Genome Biol 2008;9:R9.1-9.12.
15. Jansen R, Yu H, Greenbaum D, et al. A Bayesian networks approach for predicting protein-protein interactions from genomic data. Science 2003;302:449-53.
16. Ben-Hur A, Noble WS. Kernel methods for predicting protein-protein interactions. Bioinformatics 2005;21:i38-46.
17. Zhang L, Wong S, King O, et al. Predicting co-complexed protein pairs using genomic and proteomic data integration. BMC Bioinformatics 2004;5:38.
18. Bui QC, Katrenko S, Sloot PMA. A hybrid approach to extract protein-protein interactions. Bioinformatics 2011;27: 259-65.
19. Ideker T, Sharan R. Protein networks in disease. Genome Res 2008;18:644-52.
20. Navlakha S, Kingsford C. The power of protein interaction networks for associating genes with diseases. Bioinformatics 2010;26:1057-63.
21. Park J, Lee DS, Christakis NA, et al. The impact of cellular networks on disease comorbidity. Mol Syst Biol 2009;5:262.
22. Kann M. Protein interactions and disease: computational approaches to uncover the etiology of diseases. Brief Bioinform 2007;8:333-46.
23. Oti M, Snel B, Huynen M, etal. Predicting disease genes using protein-protein interactions. JMedGenet 2006;43:691-8.
24. Jeong H, Tombor B, Albert R, et al. The large-scale organization of metabolic networks. Nature 2000;407:651-4.
25. Stelling J, Klamt S, Battenbrock K, et al. Metabolic network structure determines key aspects of functionality and regulation. Nature 2002;420:190-3.
26. Lemke N, Heredia F, Barcellos CK, et al. Essentiality and damage in metabolic networks. Bioinformatics 2004;20: 115-9.
27. Margalef R. Perspectives in Ecological Theory. Chicago: University of Chicago Press, 1968.
28. Wassermann S, Faust K. SocialNetworkAnalysis. Cambridge, United Kingdom: Cambridge University Press, 1994.
29. Potapov A, Voss N, Sasse N, et al. Topology of mammalian transcription networks. Genome Inform 2005;14:270-8.
30. Vazquez A, Dobrin R, Sergi D, et al. The topological relationship between the large-scale attributes and local interaction patterns of complex networks. Proc Natl Acad SciUSA 2004;101:17940-5.
31. Junker BH, Schreiber F. Analysis of Biological Networks. Hoboken, New Jersey, USA: Wiley Interscience, 2008.
32. Milo S, Shen-Orr S, Itzkovitz S, et al. Network motifs: simple building blocks of complex networks. Science 2002; 298:824-7.
33. Lin WH, Liu WC, Hwang MJ. Topological and organizational properties of the products of house-keeping and tissue-specific genes in protein-protein interaction networks. BMCSyst Biol 2009;3:32.
34. Jeong H, Mason SP, Barabási AL, et al. Lethality and centrality in protein networks. Nature 2001;411:41-2.
35. Watts DJ, Strogatz SH. Collective dynamics of 'smallworld' networks. Nature 1998;393:440-2.
36. Albert R, Jeong H, Barabási AL. Error and attack tolerance of complex networks. Nature 2000;406:378-81.
37. He X, Zhang J. Why do hubs tend to be essential in protein networks? PLoS Genet 2006;2:e88.
38. Estrada E, Higham DJ, Hatano N. Communicability betweenness in complex networks. Physica A 2009;388: 764-74.
39. Massa MS, Chiogna M, Romualdi C. Gene set analysis exploiting the topology of a pathway. BMC Syst Biol 2010;4:121.
40. Taylor IW, Linding R, Warde-Farley D, et al. Dynamic modularity in protein interaction networks predicts breast cancer outcome. Nat Biotechnol 2009;27:199-204.
41. Yu H, Kim PM, Sprecher E, et al. The importance of bottlenecks in protein networks: Correlation with gene essentiality and expression dynamics. PLoSComput Biol 2007;3:e59.
42. Jordán F, Liu WC, van Veen FJF. Quantifying the importance of species and their interactions in a host-parasitoid community. Commun Ecol 2003;4:79-88.
43. Csermely P. Strong links are important, but weak links stabilize them. Trends Biochem Sci 2004;29:331-4.
44. Jordán F, Liu WC, Mike A. Trophic field overlap: a new approach to quantify keystone species. EcolModel 2009;220: 2899-907.
45. Nguyen TP, Jordán F. A quantitative approach to study indirect effects among disease proteins in the human protein interaction network. BMCSyst Biol 2010;4:103.
46. Nguyen TP, Liu WC, Jordán F. Inferring pleiotropy by network analysis: linked diseases in the human PPI network. BMCSyst Biol 2011;5:179.
47. Liu WC, Lin WH, Davis AJ, et al. A network perspective on the topological importance of enzymes and their phylogenetic conservation. BMC Bioinformatics 2007;8:121.
48. Szathmáry E, Jordán F, Pál Cs. Can genes explain biological complexity? Science 2001;292:1315-6.
49. Featherstone DE, Broadie K. Wrestling with pleiotropy: Genomic and topological analysis of the yeast gene expression network. BioEssays 2002;24:267-74.
50. Promislow DEL. Protein networks, pleiotropy and the evolution of senescence. ProcRoy SocLondB 2004;271:1225-34.
51. Tyler AL, Asselbergs FW, Williams SM, et al. Shadows of complexity: what biological networks reveal about epistasis and pleiotropy. BioEssays 2009;31:220-7.
52. Brown KR, Jurisica I. Online predicted human interaction database. Bioinformatics 2005;21:2076-82.
53. Hamosh A, Scott AF, Amberger JS, et al. Online Mendelian Inheritance in Man (OMIM), a knowledgebase of human genes and genetic disorders. Nucleic Acids Res 2005;33: D514-7.
54. Patrick DM, Zhang CC, Tao Y, et al. Defective erythroid differentiation in miR-451 mutant mice mediated by 14-3-3_. Genes Dev 2010;24:1614-9.
55. Lin MT. Identification of frequent gains of DNA copy number and characterization of potential novel oncogenes in head and neck squamous cell carcinoma, PhD thesis, The Ohio State University, 2007, pp. 143.
56. Li Y, Zou L, Li Q, et al. Amplification of LAPTM4B and YWHAZ contributes to chemotherapy resistance and recurrence of breast cancer. NatMed 2010;16:214-8.
57. Goravanahally MP, Salem M, Yao J, et al. Differential gene expression in the bovine corpus luteum during transition from early phase to midphase and its potential role in acquisition of luteolytic sensitivity to prostaglandin F2 Alpha. Biol Reprod 2009;80:980-8.
58. Tsui IF, Poh CF, Garnis C, et al. Multiple pathways in the FGF signaling network are frequently deregulated by gene amplification in oral dysplasias. Int J Cancer 2009;125: 2219-28.
59. Avizienyte E, Wyke AW, Jones RJ, et al. Src-induced de-regulation of e-cadherin in colon cancer cells requires integrin signalling. Nat Cell Biol 2002;4:632-8.
60. Ryan DP, Matthews JM. Protein-protein interactions in human disease. Curr Opin Struct Biol 2005;15:441-6.
61. Sam L, Liu Y, Li J, et al. Discovery of protein interaction networks shared by diseases. Pac Symp Biocomput 2007;12: 76-87.
62. Xu J, Li Y. Discovering disease-genes by topological features in human protein-protein interaction network. Bioinformatics 2006;22:2800-5.
63. Liu M, Liberzon A, Kong SW, et al. Network-based analysis of affected biological processes in Type 2 Diabetes models. PLoS Genet 2007;3:e96.
64. Dezso Z, Nikolsky Y, Nikolskaya T, et al. Identifying disease-specific genes based on their topological significance in protein networks. BMCSyst Biol 2009;3:36.
65. Goh KI, Cusick ME, Valle D, et al. The human disease network. ProcNatl Acad SciUSA 2007;104:8685-90.
66. Goñi J, Esteban FJ, Velez de Mendizábal N, et al. A computational analysis of protein-protein interaction networks in neurodegenerative diseases. BMCSyst Biol 2008;2:52.