Redefining CpG islands using hidden Markov models

Biostatistics

Volumn 11, Issue 3, 2010, Pages 499-514

  Wu, Hao ^a   Caffo, Brian ^a   Jaffee, Harris A ^a   Irizarry, Rafael A ^a   Feinberg, Andrew P ^b  

^a JOHNS HOPKINS UNIVERSITY   (United States)

^b JOHNS HOPKINS UNIVERSITY SCHOOL OF MEDICINE   (United States)

Author keywords

CpG island; Epigenetics; Hidden Markov model; Sequence analysis

Indexed keywords

INVERTEBRATA; MAMMALIA; VERTEBRATA;

ARTICLE; BIOLOGICAL MODEL; CPG ISLAND; GENETIC EPIGENESIS; GENETICS; HUMAN; HUMAN GENOME; PROBABILITY; STATISTICAL MODEL;

CPG ISLANDS; EPIGENESIS, GENETIC; GENOME, HUMAN; HUMANS; MARKOV CHAINS; MODELS, GENETIC; MODELS, STATISTICAL;

EID: 77956627119     PISSN: 14654644     EISSN: 14684357     Source Type: Journal    
DOI: 10.1093/biostatistics/kxq005     Document Type: Article

References (24)

1. AGILENT (2008). http://www.chem.agilent.com/Scripts/PDS.asp?lPage=50884.
2. ALTSCHUL, S., GISH, W., MILLER, W., MYERS, E. AND LIPMAN, D. (1990). Basic local alignment search tool. Journal of Molecular Biology 215, 403-410.
3. BAILEY, T. (1998). Combining evidence using p-values: application to sequence homology searches. Bioinformatics 14, 48-54.
4. BAILEY, T., WILLIAMS, N., MISLEH, C. AND LI, W. (2006). MEME: discovering and analyzing DNA and protein sequence motifs. Nucleic Acids Research 34 (Web Server issue), W369.
5. BIRD, A. (1986). CpG-rich islands and the function of DNA methylation. Nature 321, 209-213.
6. BOYS, R. AND HENDERSON, D. (2004). A Bayesian approach to DNA sequence segmentation. Biometrics 60, 573-581.
7. CHURCHILL, G. A. (1989). Stochastic models for heterogeneous DNA sequences. Bulletin of Mathematical Biology 51, 79-94.
8. DEMPSTER, A., LAIRD, N. AND RUBIN, D. (1977). Maximum likelihood from incomplete data via the EM algorithm. Journal of the Royal Statistical Society, Series B (Methodological) 39, 1-38.
9. DURBIN, R., EDDY, S., KROGH, A. AND MITCHISON, G. (1998). Biological Sequence Analysis: Probabilistic Models of Proteins and Nucleic Acids. Cambridge: Cambridge University Press.
10. FEINBERG, A. P. (2007). Phenotypic plasticity and the epigenetics of human disease. Nature 447, 433-440.
11. GARDINER-GARDEN, M. AND FROMMER, M. (1987). CpG islands in vertebrate genomes. Journal of Molecular Biology 196, 261-282.
12. GLASS, J., THOMPSON, R., KHULAN, B., FIGUEROA, M., OLIVIER, E., OAKLEY, E., VAN ZANT, G., BOUHASSIRA, E., MELNICK, A., GOLDEN, A. and others (2007). CG dinucleotide clustering is a species-specifc property of the genome. Nucleic Acids Research 35, 6798.
13. IRIZARRY, R., LADD-ACOSTA, C., WEN, B., WU, Z., MONTANO, C., ONYANGO, P., CUI, H., GABO, K., RONGIONE, M., WEBSTER, M. and others (2008). Genome-wide methylation analysis of human colon cancer reveals similar hypo-and hypermethylation at conserved tissue-specifc CpG island shores. Nature Genetics 41, 178-186.
14. IRIZARRY, R., WU, H. AND FEINBERG, A. (2009). A species-generalized probabilistic model-based defnition of CpG islands. Mammalian Genome 20, 674-680.
15. KENT, W., SUGNET, C., FUREY, T., ROSKIN, K., PRINGLE, T., ZAHLER, A., HAUSSLER, D. (2002). The human genome browser at UCSC. Genome Research 12, 996-1006.
16. LANDER, E., LINTON, L., BIRREN, B., NUSBAUM, C., ZODY, M., BALDWIN, J., DEVON, K., DEWAR, K., DOYLE, M., FITZHUGH, W. and others (2001). Initial sequencing and analysis of the human genome. Nature 409, 860-921.
17. LYKO, F., RAMSAHOYE, B. AND JAENISCH, R. (2000). Development: DNA methylation in Drosophila melanogaster. Nature 408, 538-540.
18. MEISSNER, A., MIKKELSEN, T., GU, H., WERNIG, M., HANNA, J., SIVACHENKO, A., ZHANG, X., BERNSTEIN, B., NUSBAUM, C., JAFFE, D. and others (2008). Genome-scale DNA methylation maps of pluripotent and differentiated cells. Nature 454, 766-770.
19. MURI, F. (1998). Modelling bacterial genomes using hidden Markov models. In: Payne, R. and Green, P. J. (editors), COMPSTAT '98 Proceedings in Computational Statistics. Heidelberg: Physica, pp. 89-100.
20. NICOLAS, P., BIZE, L., MURI, F., HOEBEKE, M., RODOLPHE, F., EHRLICH, S. D., PRUM, B. AND BESSIÈRES, P. (2002). Mining Bacillus subtilis chromosome heterogeneities using hidden Markov models. Nucleic Acids Research 30, 1418-1426.
21. PRUITT, K., TATUSOVA, T. AND MAGLOTT, D. (2006). NCBI reference sequences (RefSeq): a curated non-redundant sequence database of genomes, transcripts and proteins. Nucleic Acids Research 33(Database issue): D501-4.
22. RABINER, L. (1989). A tutorial on hidden Markov models and selected applications inspeech recognition. Proceedings of the IEEE 77, 257-286.
23. TAKAI, D. AND JONES, P. (2002). Comprehensive analysis of CpG islands in human chromosomes 21 and 22. Proceedings of the National Academy of Sciences of the United States of America 99, 3740.
24. YAGI, S., HIRABAYASHI, K., SATO, S., LI, W., TAKAHASHI, Y., HIRAKAWA, T., WU, G., HATTORI, N., HATTORI, N., OHGANE, J. and others (2008). DNA methylation profle of tissue-dependent and differentially methylated regions (T-DMRs) in mouse promoter regions demonstrating tissue-specifc gene expression. Genome research 18, 1969.