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http://dx.doi.org/10.5762/KAIS.2012.13.9.3952

Detecting cell cycle-regulated genes using Self-Organizing Maps with statistical Phase Synchronization (SOMPS) algorithm  

Kang, Yong-Seok (Department of Vehicle Engineering, Korea Polytechnics)
Bae, Cheol-Soo (Department of Biomedical Engineering, Kwandong University)
Publication Information
Journal of the Korea Academia-Industrial cooperation Society / v.13, no.9, 2012 , pp. 3952-3961 More about this Journal
Abstract
Developing computational methods for identifying cell cycle-regulated genes has been one of important topics in systems biology. Most of previous methods consider the periodic characteristics of expression signals to identify the cell cycle-regulated genes. However, we assume that cell cycle-regulated genes are relatively active having relatively many interactions with each other based on the underlying cellular network. Thus, we are motivated to apply the theory of multivariate phase synchronization to the cell cycle expression analysis. In this study, we apply the method known as "Self-Organizing Maps with statistical Phase Synchronization (SOMPS)", which is the combination of self-organizing map and multivariate phase synchronization, producing several subsets of genes that are expected to have interactions with each other in their subset (Kim, 2008). Our evaluation experiments show that the SOMPS algorithm is able to detect cell cycle-regulated genes as much as one of recently reported method that performs better than most existing methods.
Keywords
Cell cycle-regulated genes; DNA microarray; SOMPS;
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1 Ik-Hyun Lee, Tae-Sun Choi, "Shape From Focus Algorithm with Optimization of Focus Measure for Cell Image" Journal of Korea Institute of Information, Electronics, and Communication Technology, Vol.3, No.3, pp.8-13, 2010.
2 Albert,B., Bray,D., Lewis,J., Raff,M., Roberts,K. and Watson,J.D. Molecular Biology of the Cell. Garland Publishing, New York & London.
3 Allefeld,C. and Kurths,J. An approach to multivariate phase synchronization analysis and its application to event-related potentials., Int. J. Bifurcation and Chaos, 14, pp.417-426. 2004.   DOI
4 Bhattacharya,J."Reduced degree of long-range phase synchrony in pathological human brain",, Acta Neurobiol. Exp., 61, 309-318.2001.
5 Cho,R.J., Campbell,M.Jm, Winzeler,E.A., Steinmetz,L., Conway,A., Wodicka,L., Wolfsberg,T.G., Gabrielian,A.E., Landsman,D., Lockhart,D.J., et al."A genome-wide transcriptional analysis of the mitotic cell cycle"., Mol. Cell, 2, 65-73.1998.   DOI   ScienceOn
6 Cho,R.J., Huang,M., Campbell,M.J., Dong,H., Steinmetz,L., Sapinoso,L., Hampton,G., Elledge,S.J., Davis,R.W. and Lockhart,D.J. "Transcriptional regulation and function during the human cell cycle"., Nat. Genet., 27, 48-54. 2001.
7 de Lichtenberg,U., Jensen,L.J., Fausboll,A., Jensen,T.S., Bork,P. and Brunak,S. "Comparison of computational methods for the identification of cell cycle-regulated genes"., Bioinformatics, 21, 1164-1171.2005.   DOI
8 Gabor,D. Theory of communication., JIEE (London), 93, 429-457.1946.
9 Huygens,Ch.Horologium Oscillatorium. Apud F. Muguet, Parisiis, France.
10 Johannson,D., Lindgren,P., and Berglund,A. "A multivariate approach applied to microarray data for identification of genes with cell cycle-coupled transcriptio"n., Bioinformatics, 19, 467-473. 2003.   DOI
11 Kim, C.S. "Self-Organizing Maps with Statistical Phase Synchronization (SOMPS) for analyzing cell cycle-specific gene expression data., Statistical Applications in Genetics and Molecular Biology", 7:Iss. 1, Article 1.2008.
12 Kohonen,T. Self-Organizing Maps. Springer-Verlag, Berlin. 1995.
13 Lee,T.I., Rinaldi,N.J., Robert,F., Odom,D.T., Bar-Joseph,Z., Gerber,G.K., Hannett,N., Harbison,C.T., Thompson,C.M., Simon,I., et al. "Transcriptional regulatory networks in Saccharomyces cerevisiae"., Science, 298, 799-804.2002.   DOI
14 Lu,X., Zhang,W., Qin,Z.S., Kwasi,K.E. and Liu,J.S.Statistical resynchronization and Bayesian detection of peridically expressed genes., Nucleic Acids Res., 32, 447-455. 2004.   DOI
15 Luan,Y. and Li,H. "Model-based methods for identifying periodically expressed genes based on time course microarray gene expression data"., Bioinformatics, 20, 332-339.2004.   DOI
16 Mewes,H.W., Frishman,D., Güldner,U., Mannhaupt,G., Mayer,K., Mokrejs,M., Morgenstern,B., Münsterkoetter,M., Rudd,S. and Weil,B. MIPS: a database for genomes and protein sequences., Nucleic Acids Res., 30, 31-34.
17 Pikovsky,A.S. "On the interaction of strange attractors"., Phys. B, 55, 149-154. 1984a.   DOI   ScienceOn
18 Pikovsky,A.S. "Synchronization and stochastization of the ensemble of autogenerators by external noise"., Radiophys. Quant. Electron, 27, 576-581. 1984b.
19 Pikovsky,A., Rosenblum,M. and Kurths,J. Synchronization: a universal concept in nonlinear science. . Cambridge University Press. 2001.
20 Qian,J., Dolled-Filhart,M., Lin,J., Yu,H. and Gerstein,M. Beyond synexpression relationships: local clustering of time-shifted and inverted gene expression profiles identifies new, biologically relevant interactions., J. Mol. Biol., 314, 1053-1066. 2001.   DOI
21 Rosenblum,M.G., Pikovsky,A.S. and Kurths,J. "Phase synchronization of chaotic oscillators"., Phys. Rev. Lett., 76, 1804-1807. 1996.   DOI   ScienceOn
22 Rustici,G., Mata,J., Kivinen,K., Lió,P., Penkett,C.J., Burns,G., Hayles,J., Brazma,A., Nurse,P. and Bahler,J. Periodic gene expression program of the fission yeast cell cycle., Nat. Genet., 36, 809-817. 2004.   DOI
23 Simon,I., Barnett,J., Hannett,N., Harbison,C.T., Ranaldi,N.J., Volkert,T.L., Wyrick,J.J., Zeitlinger,J., Gifford,D.K., Jaakola,T.S., et al."Serial regulation of transcriptional regulators in the yeast cell cycle"., Cell, 106, 697-708. 2001.   DOI
24 Spellman,P.T., Sherlock,G., Zhang,M.Q., Lyer,V.R., Anders,K., Eisen,M.B., Brown,P.Q., Botstein,D. and Futcher,B. "Comprehensive identification of cell cycle-regulated genes of the yeast S. cerevisiae by microarray hybridization"., Mol. Biol. Cell, 9, 3273-3297. 1998.   DOI   ScienceOn
25 Strogatz,S.H. "From Kuramoto to Crawford: exploring the onset of synchronization in populations of coupled oscillators"., Physica D, 143, 1-20. 2000.   DOI
26 Whitfield, M. L., Sherlock, G., Saldanha, A. J., Murray, J. I., Ball, C. A., Alexander, K. E., Matese, J. C., Perou, C. M., Hurt, M. M., Brown, P. O., et al. "Identification of gene periodically expressed in the human cell cycle and their expression in tumors"., Mol. Biol. Cell, 13, 1977-2000, 2002.   DOI   ScienceOn
27 Zhao,L.P., Prentice,R. and Breeden,L. "Statistical modeling of large microarray data sets to identifying stimulus-response profiles"., Proc. Natl. Acad. Sci. USA, 98, 5631-5636, 2001.   DOI