Prediction of methylation CpGs and their methylation degrees in human DNA sequences

Computers in Biology and Medicine

Volumn 42, Issue 4, 2012, Pages 408-413

  Zhou, Xuan ^a,b   Li, Zhanchao ^a   Dai, Zong ^a   Zou, Xiaoyong ^a  

^a SUN YAT SEN UNIVERSITY   (China)

^b GUANGDONG PHARMACEUTICAL UNIVERSITY   (China)

Author keywords

DNA methylation; Support vector machine; Trinucleotide composition

Indexed keywords

CORRELATION COEFFICIENT; DINUCLEOTIDES; DNA METHYLATION; DNA MODIFICATION; EXPERIMENTAL METHODS; FEATURE VECTORS; PREDICTION METHODS; PREDICTION RESEARCH; ROOT-MEAN-SQUARE ERRORS; SUPPORT VECTOR MACHINE (SVM); TRINUCLEOTIDES;

DNA SEQUENCES; FORECASTING; GENE EXPRESSION; IMAGE RETRIEVAL; METHYLATION; NUCLEOTIDES; SUPPORT VECTOR MACHINES;

ALKYLATION;

DNA; TRINUCLEOTIDE;

ACCURACY; ANALYTICAL ERROR; ARTICLE; CORRELATION COEFFICIENT; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; HUMAN; JACKKNIFE TEST; MOLECULAR MODEL; PREDICTION; PRIORITY JOURNAL;

BASE COMPOSITION; COMPUTATIONAL BIOLOGY; CPG ISLANDS; DNA; DNA METHYLATION; HUMANS; MODELS, GENETIC; MODELS, STATISTICAL; REPRODUCIBILITY OF RESULTS; SUPPORT VECTOR MACHINES;

EID: 84858159518     PISSN: 00104825     EISSN: 18790534     Source Type: Journal    
DOI: 10.1016/j.compbiomed.2011.12.008     Document Type: Article

References (35)

1. Doerfler W. DNA methylation and gene activity. Ann. Rev. Biochem. 1983, 52:93-124.
2. Hermann A., Gowher H., Jeltsch A. Biochemistry and biology of mammalian DNA methyltransferases. Cell. Mol. Life Sci. 2004, 61:2571-2587.
3. Bird A., Boyes J. The essentials of DNA methylation. Cell 1992, 70:5-8.
4. Jones P.A., Baylin S.B. The fundamental role of epigenetic events in cancer. Nat. Rev. Genet. 2002, 3:415-428.
5. Feng F., Wang H., Han L., Wang S. Fluorescent conjugated polyelectrolyte as an indicator for convenient detection of DNA methylation. J. Am. Chem. Soc. 2008, 130:11338-11343.
6. Song L., James S.R., Kazim L., Karpf A.R. Specific method for the determination of genomic DNA methylation by liquid chromatography-electrospray ionization tandem mass spectrometry. Anal. Chem. 2005, 77:504-510.
7. Wolffe A.P., Matzke M.A. Epigenetics: regulation through repression. Science 1999, 286:481-486.
8. Reik W., Dean W., Walter J. Epigenetic reprogramming in mammalian development. Science 2001, 293:1089-1093.
9. Li E. Chromatin modification and epigenetic reprogramming in mammalian development. Nat. Rev. Genet. 2002, 3:662-673.
10. Hamet P., Tremblay J. Genes of aging. Metabolism 2003, 52:5-9.
11. Ahuja N., Issa J.P. Aging, methylation and cancer. Histol. Histopathol. 2000, 15:835-842.
12. Zhang Z., Deng C., Lu Q., Richardson B., Ahuja N., Issa J.P. Age-dependent DNA methylation changes in the ITGAL (CD11a) promoter. Mech. Ageing Dev. 2002, 123:1257-1268.
13. Scarano M.I., Strazzullo M., Matarazzo M.R., D'Esposito M. DNA methylation 40 years later: its role in human health and disease. J. Cell Physiol. 2005, 204:21-35.
14. Jones P.A., Ahuja N., Issa J.P. DNA methylation and cancer. Oncogene 2002, 21:5358-5360.
15. Clark S.J., Statham A., Stirzaker C., Molloy P.L., Frommer M. DNA methylation: bisulphite modification and analysis. Nat. Protoc. 2006, 1:2353-2364.
16. Okamoto A., Tanabe K., Saito I.J. Site-specific discrimination of cytosine and 5-methylcytosine in duplex DNA by peptide nucleic acids. Am. Chem. Soc. 2002, 124:10262-10263.
17. Gonzalgo M.L., Jones P.A. Rapid quantitation of methylation differences at specific sites using methylation-sensitive single nucleotide primer extension (Ms-SNuPE). Nucleic Acids Res. 1997, 25:2529-2531.
18. Herman J.G., Graff J.R., Myohanen S., Nelkin B.D., Baylin S.B. Methylation-specific PCR: a novel PCR assay for methylation status of CpG islands. Proc. Natl. Acad. Sci. USA 1996, 93:9821-9826.
19. Bhasin M., Zhang H., Reinherza E.L., Rechea P.A. Prediction of methylated CpGs in DNA sequences using a support vector machine. FEBS Lett. 2005, 579:4302-4308.
20. Das R., Dimitrova N., Xuan Z.Y., Rollins R.A., Haghighi F., Edwards J.R. Computational prediction of methylation statuS in human genomic sequences. Proc. Natl. Acad. Sci. USA 2006, 103:10713-10716.
21. Fang F., Fan S.C., Zhang X.G., Zhang M.Q. Predicting methylation status of CpG islands in the human brain. Bioinformatics 2006, 22:2204-2209.
22. Bock C., Paulsen M., Tierling S., Tierling S., Mikeska T., Lengauer T., Walter J. CpG island methylation in human lymphocytes is highly correlated with DNA sequence, repeats, and predicted DNA structure. PLoS Genet. 2006, 2:e26.
23. Grunau C., Renault E., Rosenthal A., Roizes G. MethDB-a public database for DNA methylation data. Nucleic Acids Res. 2001, 29:270-274.
24. Amoreira C., Hindermann W., Grunau C. An improved version of the DNA methylation database (MethDB). Nucleic Acids Res. 2003, 31:75-77.
25. Li W.Z., Godzik A. Cd-hit: a fast program for clustering and comparing large sets of protein or nucleotide sequences. Bioinformatics 2006, 22:1658-1659.
26. Chou K.C. A novel approach to predicting protein structural classes in a 〈20-1〉-D amino acid composition space. Proteins: Struct. Funct. Genet. 1995, 21:319-344.
27. Chou K.C., Elrod D.W. Prediction of enzyme family classes. J. Proteome Res. 2003, 2:183-190.
28. Vapnik V. The Nature of Statistical Learning Theory 1995, Springer, New York.
29. Cristianini N., Shawe T.J. An Introduction to Support Vector Machines and Other Kernel-Based Learning Methods 2000, Cambridge University Press, Cambridge.
30. *cjlin/libsvm.
31. Chou K.C., Zhang C.T. Review: prediction of protein structural classes. Crit. Rev. Biochem. Mol. Biol. 1995, 30:275-349.
32. Cao Y., Liu S., Zhang L., Qin J., Wang J., Tang K. Prediction of protein structural class with rough sets. BMC Bioinform. 2006, 7:20.
33. Chou K.C., Shen H.B. Recent progress in protein subcellular location prediction. Anal. Biochem. 2007, 370:1-16.
34. Swets J.A. Measuring the accuracy of diagnostic systems. Science 1988, 240:1285-1293.
35. Yu C.S., Lin C.J., Huwang J.K. Predicting subcellular localization of proteins for Gram-negative bacteria by support vector machines based on n-peptide compositions. Protein Sci. 2004, 13:1402-1406.