NDLI: Correlating CpG islands, motifs, and sequence variants in human chromosome 21.

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Correlating CpG islands, motifs, and sequence variants in human chromosome 21.

Content Provider	Europe PMC
Author	Spontaneo, Leah Cercone, Nick
Copyright Year	2011
Abstract	BackgroundCpG islands are important regions in DNA. They usually appear at the 5’ end of genes containing GC-rich dinucleotides. When DNA methylation occurs, gene regulation is affected and it sometimes leads to carcinogenesis. We propose a new detection program using a hidden-markov model alongside the Viterbi algorithm.MethodsOur solution provides a graphical user interface not seen in many of the other CGI detection programs and we unify the detection and analysis under one program to allow researchers to scan a genetic sequence, detect the significant CGIs, and analyze the sequence once the scan is complete for any noteworthy findings.ResultsUsing human chromosome 21, we show that our algorithm finds a significant number of CGIs. Running an analysis on a dataset of promoters discovered that the characteristics of methylated and unmethylated CGIs are significantly different. Finally, we detected significantly different motifs between methylated and unmethylated CGI promoters using MEME and MAST.ConclusionsDeveloping this new tool for the community using powerful algorithms has shown that combining analysis with CGI detection will improve the continued research within the field of epigenetics.
Journal	BMC Genomics
Volume Number	12 Suppl 2
PubMed Central reference number	PMC3194231
Issue Number	Suppl 2
PubMed reference number	21989037
e-ISSN	14712164
DOI	10.1186/1471-2164-12-s2-s10
Language	English
Publisher	BioMed Central
Publisher Date	2011-07-27
Access Restriction	Open
Rights License	This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Copyright ©2011 Spontaneo and Cercone; licensee BioMed Central Ltd.
Content Type	Text
Resource Type	Article
Subject	Biotechnology Genetics

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