Publication: Comparison of CpG island distribution in human neuron- and myocyte-specific genes with housekeeping genes using bioinformatics and artificial neural networks
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2011-10-06
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2-s2.0-80053408123
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Mahidol University
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SCOPUS
Bibliographic Citation
Proceedings - 2011 7th International Conference on Natural Computation, ICNC 2011. Vol.1, (2011), 556-560
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Permphan Dharmasaroja Comparison of CpG island distribution in human neuron- and myocyte-specific genes with housekeeping genes using bioinformatics and artificial neural networks. Proceedings - 2011 7th International Conference on Natural Computation, ICNC 2011. Vol.1, (2011), 556-560. doi:10.1109/ICNC.2011.6022068 Retrieved from: https://repository.li.mahidol.ac.th/handle/123456789/11769
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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
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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. © 2011 IEEE.