Disease-aging network reveals significant roles of aging genes in connecting genetic diseases

PLoS Computational Biology

Volumn 5, Issue 9, 2009, Pages

  Wang, Jiguang ^a,b   Zhang, Shihua ^a   Wang, Yong ^a   Chen, Luonan ^c,d   Zhang, Xiang Sun ^a  

^a CHINESE ACADEMY OF SCIENCES   (China)

^b UNIVERSITY OF CHINESE ACADEMY OF SCIENCES   (China)

^c SHANGHAI UNIVERSITY   (China)

^d OSAKA SANGYO UNIVERSITY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ASSOCIATION REACTIONS; CLASSIFICATION (OF INFORMATION); GRAPH THEORY; PROTEINS;

AGEING PROCESS; AGING NETWORKS; BIOLOGY AND MEDICINE; DISEASE GENES; GENE ASSOCIATIONS; GENETIC DISEASE; HUMAN DISEASE; MOLECULAR MECHANISM; PROTEIN-PROTEIN INTERACTION NETWORKS; TYPE II;

GENES;

AGING; ARTICLE; GENETIC ASSOCIATION; GENETIC DISORDER; HOUSEKEEPING GENE; HUMAN; PROTEIN PROTEIN INTERACTION; THEORETICAL STUDY; BIOLOGICAL MODEL; BIOLOGY; CHROMOSOME MAP; CLUSTER ANALYSIS; GENERAL ASPECTS OF DISEASE; GENETIC PREDISPOSITION; GENETICS; METHODOLOGY; PROTEIN ANALYSIS;

AGING; CHROMOSOME MAPPING; CLUSTER ANALYSIS; COMPUTATIONAL BIOLOGY; DISEASE; GENETIC PREDISPOSITION TO DISEASE; HUMANS; MODELS, GENETIC; PROTEIN INTERACTION MAPPING;

EID: 70349653568     PISSN: 1553734X     EISSN: 15537358     Source Type: Journal    
DOI: 10.1371/journal.pcbi.1000521     Document Type: Article

References (49)

1. Karni S, Soreq H, Sharan R (2009) A Network-Based Method for Predicting Disease-Causing Genes. Journal of Computational Biology 16: 181-189.
2. Ozgur A, Vu T, Erkan G, Radev DR (2008) Identifying gene-disease associations using centrality on a literature mined gene-interaction network. Bioinformatics 24: i277. (Pubitemid 351911683)
3. Kitano H (2002) Systems biology: A brief overview: Systems biology. Science 295: 1662-1664.
4. Friedman A, Perrimon N (2007) Genetic Screening for Signal Transduction in the Era of Network Biology. Cell 128: 225-231. (Pubitemid 46123521)
5. Hasty J, McMillen D, Isaacs F, Collins JJ (2001) Computational studies of gene regulatory networks: in numero molecular biology. Nature Reviews Genetics 2: 268-279. (Pubitemid 33674775)
6. Ravasz E, Somera AL, Mongru DA, Oltvai ZN, Barabasi AL (2002) Hierarchical Organization of Modularity in Metabolic Networks. Science. pp 1551-1555. (Pubitemid 34971002)
7. Stelzl U, Worm U, Lalowski M, Haenig C, Brembeck FH, et al. (2005) A Human Protein-Protein Interaction Network: A Resource for Annotating the Proteome. Cell 122: 957-968. (Pubitemid 41345212)
8. Tu Z, Wang L, Xu M, Zhou X, Chen T, et al. (2006) Further understanding human disease genes by comparing with housekeeping genes and other genes. BMC Genomics 7: 31. (Pubitemid 43380728)
9. Jonsson PF, Bates PA (2006) Global topological features of cancer proteins in the human interactome. Bioinformatics 22: 2291.
10. Ideker T, Sharan R (2008) Protein networks in disease. Genome Research 18: 644.
11. Goh KI, Cusick ME, Valle D, Childs B, Vidal M, et al. (2007) The human disease network. Proceedings of the National Academy of Sciences 104: 8685.
12. Feldman I, Rzhetsky A, Vitkup D (2008) Network properties of genes harboring inherited disease mutations. Proceedings of the National Academy of Sciences 105: 4323. (Pubitemid 351754379)
13. Jiang X, Liu B, Jiang J, Zhao H, Fan M, et al. (2008) Modularity in the genetic disease-phenotype network. FEBS letters 582: 2549-2554.
14. Spiro Z, Kovacs IA, Csermely P (2008) Drug-therapy networks and the prediction of novel drug targets. Journal of Biology 7: 20.
15. Li Y, Agarwal P (2009) A Pathway-Based View of Human Diseases and Disease Relationships. PLoS ONE 4.
16. Osiewacz HD (1997) Genetic regulation of aging. Journal of Molecular Medicine 75: 715-727.
17. Harman D (1981) The Aging Process. Proceedings of the National Academy of Sciences 78: 7124-7128.
18. Kiss HJ, Mihalik A, Nánási T, Ory B, Spiró Z, et al. (2009) Ageing as a price of cooperation and complexity: self-organization of complex systems causes the gradual deterioration of constituent networks. BioEssays: news and reviews in molecular, cellular and developmental biology 31: 651.
19. Kowald A, Kirkwood TBL (1996) A network theory of ageing: the interactions of defective mitochondria, aberrant proteins, free radicals and scavengers in the ageing process. Mutation Research DNAging 316: 209-236.
20. Kriete A, Sokhansanj BA, Coppock DL, West GB (2006) Systems approaches to the networks of aging. Ageing Research Reviews 5: 434-448.
21. Soti C, Csermely P (2007) Aging cellular networks: chaperones as major participants. Exp Gerontol 42: 113-119. (Pubitemid 44937822)
22. Vasto S, Candore G, Balistreri CR, Caruso M, Colonna-Romano G, et al. (2007) Inflammatory networks in ageing, age-related diseases and longevity. Mechanisms of Ageing and Development 128: 83-91. (Pubitemid 46073064)
23. Xue H, Xian B, Dong D, Xia K, Zhu S, et al. (2007) A modular network model of aging. Molecular Systems Biology 3: 147.
24. Managbanag JR, Witten TM, Bonchev D, Fox LA, Tsuchiya M, et al. (2008) Shortest-Path Network Analysis Is a Useful Approach toward Identifying Genetic Determinants of Longevity. PLoS ONE 3.
25. Budovsky A, Abramovich A, Cohen R, Chalifa-Caspi V, Fraifeld V (2007) Longevity network: Construction and implications. Mechanisms of Ageing and Development 128: 117-124.
26. Budovsky A, Tacutu R, Yanai H, Abramovich A, Wolfson M, et al. (2008) Common gene signature of cancer and longevity. Mech Ageing Dev 130: 33-39.
27. Wolfson M, Budovsky A, Tacutu R, Fraifeld V (2008) The signaling hubs at the crossroad of longevity and age-related disease networks. International Journal of Biochemistry and Cell Biology: 516-520.
28. de Magalhaes JP, Budovsky A, Lehmann G, Costa J, Li Y, et al. (2009) The Human Ageing Genomic Resources: online databases and tools for biogerontologists. Aging Cell 8: 65-72.
29. Hayflick L (2004) Debates The Not-So-Close Relationship Between Biological Aging and Age-Associated Pathologies in Humans. Journals of Gerontology Series A: Biological and Medical Sciences 59: 547-550.
30. Peri S, Navarro JD, Amanchy R, Kristiansen TZ, Jonnalagadda CK, et al. (2003) Development of Human Protein Reference Database as an Initial Platform for Approaching Systems Biology in Humans. Genome Research 13: 2363-2371. (Pubitemid 37266003)
31. Brandes U (2001) A faster algorithm for betweenness centrality. Journal of Mathematical Sociology 25: 163-177.
32. Barabasi AL, Oltvai ZN (2004) Network biology: understanding the cell's functional organization. Nature Reviews Genetics 5: 101-113.
33. Albert R, Jeong H, Barabasi AL (2000) Error and attack tolerance of complex networks. Nature 406: 378-382. (Pubitemid 30625551)
34. Han JDJ, Bertin N, Hao T, Goldberg DS, Berriz GF, et al. (2004) Evidence for dynamically organized modularity in the yeast protein-protein interaction network. Nature 430: 88-93. (Pubitemid 38915230)
35. Jin G, Zhang S, Zhang X, Chen L (2007) Hubs with Network Motifs Organize Modularity Dynamically in the Protein-Protein Interaction Network of Yeast. PLoS ONE 2: e1207. (Pubitemid 351638149)
36. Newman MEJ (2005) A measure of betweenness centrality based on random walks. Social Networks 27: 39-54. (Pubitemid 40272648)
37. Watts DJ, Strogatz SH (1998) Collective dynamics of 'small-world' networks. Nature 393: 440-442.
38. Wu X, Jiang R, Zhang MQ, Li S (2008) Network-based global inference of human disease genes. Molecular Systems Biology 4: 189. (Pubitemid 351655223)
39. Ishunina T, Swaab D (2001) Increased expression of estrogen receptor alpha and beta in the nucleus basalis of Meynert in Alzheimer's disease. Neurobiol Aging 22: 417-426. (Pubitemid 32510914)
40. Zuppan P, Hall JM, Lee MK, Ponglikitmongkol M, King MC (1991) Possible linkage of the estrogen receptor gene to breast cancer in a family with late-onset disease. American Journal of Human Genetics 48: 1065. (Pubitemid 21903068)
41. Kirkwood TBL (2002) Evolution of ageing. Mechanisms of Ageing and Development 123: 737-745.
42. de Magalhaes JP, Costa J, Toussaint O (2005) HAGR: the Human Ageing Genomic Resources. Nucleic Acids Research 33: D537. (Pubitemid 40207932)
43. Bell R, Hubbard A, Chettier R, Chen D, Miller JP, et al. (2009) A Human Protein Interaction Network Shows Conservation of Aging Processes between Human and Invertebrate Species. PLoS Genetics 5: e1000414.
44. Cui Q, Purisima EO, Wang E (2009) Protein evolution on a human signaling network. BMC Systems Biology 3.
45. Maslov S, Sneppen K (2002) Specificity and Stability in Topology of Protein Networks. Science 296: 910-913. (Pubitemid 34464896)
46. Kondor RI, Lafferty J (2002) Diffusion Kernels on Graphs and Other Discrete Input Spaces. Proceedings of the Nineteenth International Conference on Machine Learning: 315-322.
47. Lanckriet GRG, Deng M, Cristianini N, Jordan MI, Noble WS (2004) Kernel-based data fusion and its application to protein function prediction in yeast. Proceedings of the Pacific Symposium on Biocomputing 2004: 300-311.
48. Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, et al. (2003) Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks. Cold Spring Harbor Lab. pp 2498-2504.
49. Maere S, Heymans K, Kuiper M (2005) BiNGO: a Cytoscape plugin to assess overrepresentation of Gene Ontology categories in Biological Networks. Bioinformatics 21: 3448-3449. (Pubitemid 41222459)