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Characterization of the Alzheimer's disease-related network based on the dynamic network approach
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 Title & Authors
Characterization of the Alzheimer's disease-related network based on the dynamic network approach
Kim, Man-Sun; Kim, Jeong-Rae;
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 Abstract
Biological networks have been handled with the static concept. However, life phenomena in cells occur depending on the cellular state and the external environment, and only a few proteins and their interactions are selectively activated. Therefore, we should adopt the dynamic network concept that the structure of a biological network varies along the flow of time. This concept is effective to analyze the progressive transition of the disease. In this paper, we applied the proposed method to Alzheimer's disease to analyze the structural and functional characteristics of the disease network. Using gene expression data and protein-protein interaction data, we constructed the sub-networks in accordance with the progress of disease (normal, early, middle and late). Based on this, we analyzed structural properties of the network. Furthermore, we found module structures in the network to analyze the functional properties of the sub-networks using the gene ontology analysis (GO). As a result, it was shown that the functional characteristics of the dynamics network is well compatible with the stage of the disease which shows that it can be used to describe important biological events of the disease. Via the proposed approach, it is possible to observe the molecular network change involved in the disease progression which is not generally investigated, and to understand the pathogenesis and progression mechanism of the disease at a molecular level.
 Keywords
Protein-protein interaction network;Alzheimer's disease;Dynamic network analysis;Systems biology;
 Language
Korean
 Cited by
 References
1.
Barabasi AL, Oltvai ZN, "Network biology: understanding the cell's functional organization." Nature reviews Genetics, 5(2):101-113, 2004. crossref(new window)

2.
Jeong H, Tombor B, Albert R, Oltvai ZN, Barabasi AL, "The large-scale organization of metabolic networks." Nature, 407(6804):651-654, 2000. crossref(new window)

3.
Kim TH, Kim J, Heslop-Harrison P, Cho KH, "Evolutionary design principles and functional characteristics based on kingdom-specific network motifs." Bioinformatics, 27(2):245-251, 2011. crossref(new window)

4.
Seo CH, Kim JR, Kim MS, Cho KH,"Hub genes with positive feedbacks function as master switches in developmental gene regulatory networks." Bioinformatics, 25(15):1898-1904, 2009. crossref(new window)

5.
Kim MS, Kim JR, Cho KH, "Dynamic network rewiring determines temporal regulatory functions in Drosophila melanogaster development processes." BioEssays : news and reviews in molecular, cellular and developmental biology, 32(6):505-513, 2010.

6.
Kim MS, Kim JR, Kim D, Lander AD, Cho KH, "Spatiotemporal network motif reveals the biological traits of developmental gene regulatory networks in Drosophila melanogaster." BMC systems biology, 6:31, 2012. crossref(new window)

7.
Faisal FE, Milenkovic T, "Dynamic networks reveal key players in aging." Bioinformatics, 30(12):1721-1729, 2014. crossref(new window)

8.
Liang D, Han G, Feng X, Sun J, Duan Y, Lei H, "Concerted perturbation observed in a hub network in Alzheimer's disease." PloS one, 7(7):e40498, 2012. crossref(new window)

9.
Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT et al, "Gene ontology: tool for the unification of biology. The Gene Ontology Consortium." Nature genetics, 25(1):25-29, 2000. crossref(new window)

10.
Carbon S, Ireland A, Mungall CJ, Shu S, Marshall B, Lewis S, Ami GOH, Web Presence Working G, "AmiGO: online access to ontology and annotation data." Bioinformatics, 25(2):288-289, 2009. crossref(new window)

11.
Guimera R, Nunes Amaral LA, "Functional cartography of complex metabolic networks." Nature, 433(7028):895-900, 2005. crossref(new window)

12.
Barabasi AL, "Scale-free networks: a decade and beyond." Science, 325(5939):412-413, 2009. crossref(new window)

13.
Talwar P, Silla Y, Grover S, Gupta M, Agarwal R, Kushwaha S, Kukreti R, "Genomic convergence and network analysis approach to identify candidate genes in Alzheimer's disease." BMC genomics, 15:199, 2014. crossref(new window)

14.
Com E, Clavreul A, Lagarrigue M, Michalak S, Menei P, Pineau C, "Quantitative proteomic Isotope-Coded Protein Label (ICPL) analysis reveals alteration of several functional processes in the glioblastoma." Journal of proteomics, 75(13):3898-3913, 2012. crossref(new window)

15.
Kim T, Hinton DJ, Choi DS, "Protein kinase C-regulated abeta production and clearance." International journal of Alzheimer's disease, 2011:857368, 2011.

16.
Rogev A, Bandyopadhyay S, Zofall M, Zhang K, Fischer T, Collins SR, Qu H, Shales M, Park HO, Hayles J et al, "Conservation and rewiring of functional modules revealed by an epistasis map in fission yeast." Science, 322(5900):405-410, 2008. crossref(new window)

17.
Crary JF, Trojanowski JQ, Schneider JA, Abisambra JF, Abner EL, Alafuzoff I, Arnold SE, Attems J, Beach TG, Bigio EH et al, "Primary age-related tauopathy (PART): a common pathology associated with human aging." Acta neuropathologica, 128(6):755-766, 2014. crossref(new window)

18.
Choi SW, Lee CH, "Disease Classification using Random Subspace Method based on Gene Interaction Information and mRMR Filter", Journal of the Korean Institute of Intelligent Systems, 22(2):192-197, 2012. crossref(new window)

19.
Lee SA, Lee KM, Lee SJ, Kim WJ, Kim YJ, Bae SC, "Gene filtering based on fuzzy pattern matching for whole genome microarray data analysis", Journal of the Korean Institute of Intelligent Systems, 18(4):471-475, 2008. crossref(new window)

20.
Ha KS, Lim JM, Kim HG, "Integrated Model Design of Microarray Data Using miRNA, PPI, Disease Information", Journal of the Korean Institute of Intelligent Systems, 22(6):786-792, 2012. crossref(new window)