The complementary neighborhood patterns and methylation-to-mutation likelihood structures of 15,110 single-nucleotide polymorphisms in the bovine genome

Genetics

Volumn 180, Issue 1, 2008, Pages 639-647

  Jiang, Zhihua ^a   Wu, Xiao Lin ^a,b   Zhang, Ming ^a   Michal, Jennifer J ^a   Wright Jr , Raymond W ^a  

^a WASHINGTON STATE UNIVERSITY   (United States)

^b UNIVERSITY OF WISCONSIN MADISON   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

TRANSITION ELEMENT; COMPLEMENT;

ANIMAL GENETICS; ARTICLE; CATTLE; CPG ISLAND; DNA FLANKING REGION; GENE CONVERSION; GENE MUTATION; METHYLATION; NONHUMAN; PATTERN RECOGNITION; PRIORITY JOURNAL; SINGLE NUCLEOTIDE POLYMORPHISM; ANIMAL; BAYES THEOREM; BIOLOGICAL MODEL; DNA METHYLATION; GENOME; MOLECULAR EVOLUTION; MUTATION; NUCLEIC ACID DATABASE; NUCLEOTIDE SEQUENCE; PROBABILITY; STATISTICAL MODEL;

ANIMALIA; BOS; BOVINAE; MAMMALIA;

ANIMALS; BAYES THEOREM; CATTLE; COMPLEMENT SYSTEM PROTEINS; CPG ISLANDS; DATABASES, NUCLEIC ACID; DNA METHYLATION; DNA MUTATIONAL ANALYSIS; EVOLUTION, MOLECULAR; GENOME; MODELS, GENETIC; MODELS, STATISTICAL; MUTATION; POLYMORPHISM, SINGLE NUCLEOTIDE; PROBABILITY;

EID: 56049085832     PISSN: 00166731     EISSN: 00166731     Source Type: Journal    
DOI: 10.1534/genetics.108.090860     Document Type: Article

References (24)

1. BIRD, A. P., 1986 CpG-rich islands and the function of DNA methylation. Nature 321: 209-213.
2. BOX, G. E., and G. JENKINS, 1976 Time Series Analysis: Forecasting and Control, Ed. 2. Holden-Day, San Francisco.
3. COOPER, D. N., and M. KRAWCZAK, 1990 The mutational spectrum of single base-pair substitutions causing human genetic disease: patterns and predictions. Hum. Genet. 85: 55-74.
4. DU, F. X., A. C. CLUTTER and M. M. LOHUIS, 2007 Characterizing linkage disequilibrium in pig populations. Int. J. Biol. Sci. 3: 166-178.
5. DUNCAN, B. K., and J. H. MILLER, 1980 Mutagenic deamination of cytosine residues in DNA. Nature 287: 560-561.
6. EBERLY, L. E., and B. P. CARLIN, 2000 Identifiability and convergence issues for Markov chain Monte Carlo fitting of spatial models. Stat. Med. 19: 2279-2294.
7. GELMAN, A., J. B. CARLIN, H. S. STERN and D. B. RUBIN, 2004 Bayesian Data Analysis, Ed. 2. Chapman & Hall/CRC, London.
8. GOODMAN, S., 1999 Toward evidence-based medical statistics. 2: The Bayes factor. Ann. Intern. Med. 130: 1005-1013.
9. HARDER, A., M. ROSCHE, D. E. REUSS, N. HOLTKAMP, K. UHLMANN et al., 2004 Methylation analysis of the neurofibromatosis type 1 (NF1) promoter in peripheral nerve sheath tumours. Eur. J. Cancer 40: 2820-2828.
10. HAYES, B., J. K. LAERDAHL, S. LIEN, T. MOEN, P. BERG et al., 2007 An extensive resource of single nucleotide polymorphism markers associated with Atlantic salmon (Salmo salar) expressed sequences. Aquaculture 265: 82-90.
11. JIANG, Z., Z. WANG, T. KUNEJ, G. A. WILLIAMS, J. J. MICHAL et al., 2007 A novel type of sequence variation: multiple-nucleotide length polymorphisms discovered in the bovine genome. Genetics 176: 403-407.
12. KIM, S., and A. MISRA, 2007 SNP genotyping: technologies and biomedical applications. Annu. Rev. Biomed. Eng. 9: 289-320.
13. MORTON, B. R., 1995 Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions. Proc. Natl. Acad. Sci. USA 92: 9717-9721.
14. MORTON, B. R., I. V. BI, M. D. MCM ULLEN and B. S. GAUT, 2006 Variation in mutation dynamics across the maize genome as a function of regional and flanking base composition. Genetics 172: 569-577.
15. RAFALSKI, A., 2002 Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5: 94-100.
16. RAFTERY, A. E., 1995 Bayesian model selection in social research. Sociol. Methodol. 25: 111-163.
17. RILEY, J. H., C. J. ALLAN, E. LAI and A. ROSES, 2000 The use of single nucleotide polymorphisms in the isolation of common disease genes. Pharmacogenomics 1: 39-47.
18. SAUNA, Z. E., C. KIMCHI-SARFATY, S. V. AMBUDKAR and M. M. GOTTESMAN, 2007 Silent polymorphisms speak: how they affect pharmacogenomics and the treatment of cancer. Cancer Res. 67: 9609-9612.
19. SCHWARZ, G., 1978 Estimating the dimension of a model. Ann. Stat. 6: 461-464.
20. WANG, D., A. D. JOHNSON, A. C. PAPP, D. L. KROETZ and W. SADÉE, 2005 Multidrug resistance polypeptide 1 (MDR1, ABCB1) variant 3435C>T affects mRNA stability. Pharmacogenet. Genomics 15: 693-704.
21. YAMAGISHI, M. E., and A. I. SHIMABUKURO, 2008 Nucleotide frequencies in human genome and fibonacci numbers. Bull. Math Biol. 70: 643-653.
22. ZHANG, F., and Z. ZHAO, 2004 The influence of neighboring-nucleotide composition on single nucleotide polymorphisms (SNPs) in the mouse genome and its comparison with human SNPs. Genomics 84: 785-795.
23. ZHAO, Z., and E. BOERWINKLE, 2002 Neighboring- nucleotide effects on single nucleotide polymorphisms: a study of 2.6 million polymorphisms across the human genome. Genome Res. 12: 1679-1686.
24. ZHAO, Z., and F. ZHANG, 2006 Sequence context analysis in the mouse genome: single nucleotide polymorphisms and CpG island sequences. Genomics 87: 68-74.