Predicting methylation status of CpG islands in the human brain

Fang, F., Fan, S., Zhang, X., Zhang, M. Q. (2006) Predicting methylation status of CpG islands in the human brain. Bioinformatics, 22 (18). pp. 2204-2209. ISSN 13674803

URL: http://bioinformatics.oxfordjournals.org/cgi/conte...
DOI: 10.1093/bioinformatics/btl377

Abstract

Motivation: Over 50% of human genes contain CpG islands in their 5?-regions. Methylation patterns of CpG islands are involved in tissue-specific gene expression and regulation. Mis-epigenetic silencing associated with aberrant CpG island methylation is one mechanism leading to the loss of tumor suppressor functions in cancer cells. Large-scale experimental detection of DNA methylation is still both labor-intensive and time-consuming. Therefore, it is necessary to develop in silico approaches for predicting methylation status of CpG islands. Results: Based on a recent genome-scale dataset of DNA methylation in human brain tissues, we developed a classifier called MethCGI for predicting methylation status of CpG islands using a support vector machine (SVM). Nucleotide sequence contents as well as transcription factor binding sites (TFBSs) are used as features for the classification. The method achieves specificity of 84.65% and sensitivity of 84.32% on the brain data, and can also correctly predict about two-third of the data from other tissues reported in the MethDB database. © 2006 Oxford University Press.

Item Type: Paper
Subjects: bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA methylation
bioinformatics > genomics and proteomics > Mapping and Rendering > Sequence Rendering
organs, tissues, organelles, cell types and functions > organs types and functions > brain
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > CpG islands
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > genes, structure and function > gene silencing
bioinformatics > genomics and proteomics > genetics & nucleic acid processing > protein structure, function, modification > protein types > transcription factor
CSHL Authors:
Communities: CSHL labs > Zhang lab
Depositing User: CSHL Librarian
Date Deposited: 15 Dec 2011 17:47
Last Modified: 15 Dec 2011 17:47
URI: http://repository.cshl.edu/id/eprint/22788

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