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Title: Comparison of CpG island distribution in human neuron- and myocyte-specific genes with housekeeping genes using bioinformatics and artificial neural networks
Authors: Permphan Dharmasaroja
Keywords: CpG island;MLP;PNN;RBF;SVM;tissue-specific
Issue Date: 2011
Publisher: 2011 7th International Conference on Natural Computation, ICNC 2011
Citation: Proceedings - 2011 7th International Conference on Natural Computation, ICNC 2011 1 (2011);556-560
Abstract: CpG islands are cluster of CG-rich DNA sequences that associate with the promoter of many human genes. Previous studies based on the original CpG criteria, as being length > 200 bp, %GC ≥ 50%, and ObsCpG/ExpCpG ≥ 0.60, showed that CpG islands overlap the promoter of all human housekeeping genes and over half of all tissue-specific genes. The present study, using the new and widely accepted criteria defined as length > 500 bp, %GC ≥ 55%, and ObsCpG/ExpCpG ≥ 0.65, showed that CpG islands of ∼60% of housekeeping genes overlap the promoter, suggesting that the previous studies might include Alu repeats in the promoter region. Using artificial neural networks, RBF, MLP, PNN, and SVM identified ObsCpG/ExpCpG of the 5′ region-CpG islands and ratio of exonic CpG island number to total CpGs as important variables for classification of myocytes-specificity, with ObsCpG/ExpCpG < 0.65 being specific. For classification of neuron-specificity, the %GC and ObsCpG/ExpCpG of the 5′ region-CpG islands were important variables.
Description: Scopus
ISSN: 978-142449953-3
Appears in Collections:Anatomy: International Proceedings

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