Mining and predicting CpG islands

Christopher Previti, Oscar Harari, Coral Del Val

Research output: Chapter in Book/Report/Conference proceedingConference contribution

1 Scopus citations

Abstract

A DNA sequence can be described as a string composed of four symbols: A, T, C and G. Each symbol represents a chemically distinct nucleotide molecule. Combinations of two nucleotides are called dinucleotides and CpG islands represent regions of a DNA sequence, certain substrings, which are enriched in CpG dinucleotides (C followed by G). CpG islands represent a prominent and enigmatic feature of vertebrate genomes. They are associated with the promoters of more than 60% of all human genes and represent a critical target for transcriptional control. Mcthylation of these CpG islands leads to structural changes in the DNA that stops the expression of any associated gene (genesilencing). The factors that provoke or impede mcthylation are currently all but unknown. In general, the maintenance of a particular pattern of methylated CpG dinucleotides represents a critical regulatory system during a host of normal developmental processes, but the erroneous methylation of CpG islands and the resulting gene-silencing can lead to the development of cancer. In this work, we present a novel unsupervised machine learning method that is capable of distinguishing biologically significant classes of CpG islands, including the separation of methylated and unmethylated CpG islands. This method represents an important novel approach that will aid in the computational prediction of methylation, which is commonly used in the pre-selection of worthwhile sequences for methylation experiments.

Original languageEnglish
Title of host publication2007 IEEE International Conference on Fuzzy Systems, FUZZY
DOIs
StatePublished - Dec 1 2007
Externally publishedYes
Event2007 IEEE International Conference on Fuzzy Systems, FUZZY - London, United Kingdom
Duration: Jul 23 2007Jul 26 2007

Publication series

NameIEEE International Conference on Fuzzy Systems
ISSN (Print)1098-7584

Conference

Conference2007 IEEE International Conference on Fuzzy Systems, FUZZY
CountryUnited Kingdom
CityLondon
Period07/23/0707/26/07

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