CLUSTERING METHODS IMPLEMENTED INTO MICROARRAYTOOL PROGRAM FOR ANALYSIS OF DNA MICROARRAY DATA
DOI:
https://doi.org/10.11603/mie.1996-1960.2008.2.7277Abstract
Microarray technologies (DNA chips) allow to perform a quantitative anlysis of expression of ten thousands genes. In this work a novel Microarraytool program was developed which allows to perform the cluster analysis and to compare the different experiments data by statistical analysis. Several clustering algorithms have been implemented into Microarraytool program: hierarchical clustering, k-means clustering, self-organizing maps (SOM) algorithm and self-organizing tree maps (SOTA) algorithm. The testing of these algorithms was performed using the Stanford Microarray Database for expression of 8613 individual genes in human fibroblasts after stimulation. The testing procedure revealed a correct performance of these algorithms implemented into Microarraytool program.References
Baldi P., Hatfield G.W. DNA Mscroarrays and gene expression : From experiments to data analysis modeling. -Cambridge University Press, 2002.
Soares M.B. Identification and cloning of differentially expressed genes // Curr. Opin. Biotechnol. -1997. - V. 8. - № 5. - P. 542 - 546.
Campbell A.M., Heyer L.J. Discovering genomics, proteomics, and bioinformatics. - CSHL Press, 2003.
Zhang N., Tan H., Yeung E.S. Automated and integrated system for highthroughput DNA genotyping directly from blood // Anal. Chem. - 1999. - V. 71. - P. 1138 -1145.
Raitio M., Lindroos K., Laukkanen M. et al. Y-chromosomal SNPs in Finno-Ugric-speaking populations analyzed by minisequencing on microarrays // Genome Res. - 2001. - V. 11. - № 3. - P. 471 - 482.
Behr M.A., Wilson M.A. Comparative genomics of BCG vacines by whole-genome DNA microarray // Science. -1999. - V. 284. - P. 1520 -1523.
Khan J., Saal L.H., Bittner M.L. et al. 1999. Expressionprofiling in cancer using cDNA microarrays // Electrophoresis. - 1999. - V. 20. - № 2. - P. 223 - 229.
Івахно С., Корнелюк О. Мікроареї: огляд технологій та аналіз даних // Укр. біохім. журн.-2004.-Т. 76, № 2.-С. 5-19.
Heller M. J. DNA Microarray Technology: Devices, Systems, and Applications // Annu. Rev. Biomed. Eng. - 2002. - V. 4. -P. 129 -153.
Zanders E.D. Gene expression analysis as an aid to the
identification of drug targets // Pharmacogenomics. -2000. -V. 1. - № 4. - P. 375 - 384.
Jain A.K., Murty M.N., Flynn P.J.. Data clustering: A review // ACM Computing Surveys. - 1999. -V. 31. - № 3. - P. 264-323.
Jain A. K., Dubes R.C. Algorithms for Clustering Data. Prentice Hall Advanced Reference Series. Prentice Hall, New Jersey, 1988.
Toronen P., Kolehmainen M., Wong G. et al. Analysis of gene expression data using self- organizing maps // FEBS Letters. -1999. - V. 451. - P. 142-146.
Dopazo J., Carazo J.M. Phylogenetic reconstruction using a growing neural network that adopts the topology of a phylogenetic tree // J. Mol. Evol. -1997. - V. 44. - P. 226 - 233.
Fritzke B. Growing cell structures—a self-organizing network for unsupervised and supervised learning // Neural Networks. -1994. - V. 7. - P. 1141 -1160.
Dopazo J., Carazo J.M. Phylogenetic reconstruction using a growing neural network that adopts the topology of a phylogenetic tree // J. Mol. Evol. -1997. - V. 44. - P. 226 - 233.
Fritzke B. Growing cell structures—a self-organizing network for unsupervised and supervised learning // Neural Networks. -1994. - V. 7. - P. 1141 -1160.
Herrero J., Valencia A., Dopazo J. A hierarchical unsupervised growing neural network for clustering gene expression patterns // Bioinformatics. - 2001. - V. 17. - № 2. -P. 126 -136.
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