Bioinformatics Advance Access originally published online on July 12, 2006
Bioinformatics 2006 22(18):2204-2209; doi:10.1093/bioinformatics/btl377
| ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Predicting methylation status of CpG islands in the human brain
1 Bioinformatics Division, TNLIST, Department of Automation, Tsinghua University 100084 China
2 Cold Spring Harbor Laboratory, Cold Spring Harbor NY 11274, USA
*To whom correspondence should be addressed.
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.
Availability: An online predictor based on MethCGI is available at http://166.111.201.7/MethCGI.html
Contact: mzhang{at}cshl.edu
Supplementary Information: Supplementary data available at Bioinformatics online and http://166.111.201.7/help.html
Received on May 29, 2006; revised on June 24, 2006; accepted on July 5, 2006
CiteULike 
Connotea 
Del.icio.us What's this?
This article has been cited by other articles:
|
|
 |
|
  C. Bock, J. Walter, M. Paulsen, and T. Lengauer Inter-individual variation of DNA methylation and its implications for large-scale epigenome mapping Nucleic Acids Res., June 1, 2008; 36(10): e55 - e55. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 S. Hannenhalli Eukaryotic transcription factor binding sites--modeling and integrative search methods Bioinformatics, June 1, 2008; 24(11): 1325 - 1331. [Abstract] [Full Text] [PDF]
|
|
|
|
|
|
C. Bock and T. Lengauer Computational epigenetics Bioinformatics, January 1, 2008; 24(1): 1 - 10. [Abstract] [Full Text] [PDF]
|
|
|
|
 |
|
 R. M. Brena and J. F. Costello Genome-epigenome interactions in cancer Hum. Mol. Genet., April 15, 2007; 16(R1): R96 - R105. [Abstract] [Full Text] [PDF]
|
|