Das, R., Dimitrova, N., Xuan, Z. Y., Rollins, R. A., Haghighi, F., Edwards, J. R., Ju, J. Y., Bestor, T. H., Zhang, M. Q. (July 2006) Computational prediction of methylation status in human genomic sequences. Proc Natl Acad Sci U S A, 103 (28). pp. 10713-6. ISSN 0027-8424 (Print)
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Abstract
Epigenetic effects in mammals depend largely on heritable genomic methylation patterns. We describe a computational pattern recognition method that is used to predict the methylation landscape of human brain DNA. This method can be applied both to CpG islands and to non-CpG island regions. It computes the methylation propensity for an 800-bp region centered on a CpG dinucleotide based on specific sequence features within the region. We tested several classifiers for classification performance, including K means clustering, linear discriminant analysis, logistic regression, and support vector machine. The best performing classifier used the support vector machine approach. Our program (called hdfinder) presently has a prediction accuracy of 86%, as validated with CpG regions for which methylation status has been experimentally determined. Using hdfinder, we have depicted the entire genomic methylation patterns for all 22 human autosomes.
| Item Type: | Paper |
|---|---|
| Uncontrolled Keywords: | Algorithms Computational Biology DNA chemistry metabolism DNA Methylation Genome Human Humans Predictive Value of Tests |
| Subjects: | bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > DNA methylation bioinformatics > genomics and proteomics > databases > database construction bioinformatics > computational biology bioinformatics > genomics and proteomics > computers > computer software bioinformatics > genomics and proteomics > genetics & nucleic acid processing > DNA, RNA structure, function, modification > CpG islands bioinformatics > genomics and proteomics > databases > databases |
| CSHL Authors: | |
| Communities: | CSHL labs > Zhang lab |
| Depositing User: | CSHL Librarian |
| Date: | 11 July 2006 |
| Date Deposited: | 20 Dec 2011 16:38 |
| Last Modified: | 09 Nov 2017 16:09 |
| PMCID: | PMC1502297 |
| Related URLs: | |
| URI: | https://repository.cshl.edu/id/eprint/22779 |
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