MethylSig: A whole genome DNA methylation analysis pipeline

Bioinformatics

Volumn 30, Issue 17, 2014, Pages 2414-2422

  Park, Yongseok ^a,d   Figueroa, Maria E ^b   Rozek, Laura S ^a   Sartor, Maureen A ^a,c  

^a Department of Computational Medicine and Bioinformatics ^*  (United States)

^b Departments of Pathology   (United States)

^c UNIVERSITY OF MICHIGAN   (United States)

^d UNIVERSITY OF PITTSBURGH GRADUATE SCHOOL OF PUBLIC HEALTH   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

HYDROGEN SULFITE; SULFITE;

ACUTE MYELOBLASTIC LEUKEMIA; COMPUTER PROGRAM; CPG ISLAND; DNA METHYLATION; DNA SEQUENCE; GENETICS; GENOMICS; HUMAN; PROCEDURES;

CPG ISLANDS; DNA METHYLATION; GENOMICS; HUMANS; LEUKEMIA, MYELOID, ACUTE; SEQUENCE ANALYSIS, DNA; SOFTWARE; SULFITES;

EID: 84907033475     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/btu339     Document Type: Article

References (37)

1. Akalin, A. et al. (2012a) Base-pair resolution DNA methylation sequencing reveals profoundly divergent epigenetic landscapes in acute myeloid leukemia. PLoS Genet., 8, e1002781.
2. Akalin, A. et al. (2012b) methylkit: a comprehensive R package for the analysis of genome-wide DNA methylation profiles. Genome Biol., 13, R87.
3. Clark, S.J. et al. (2006) DNA methylation: bisulphite modification and analysis. Nat. Protoc., 1, 2353-2364.
4. Fan, J. et al. (2001) Generalized likelihood ratio statistics and Wilks phenomenon. Ann Stat., 29, 153-193.
5. Feng, H. et al. (2014) A bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic Acids Res., 42, e69.
6. Figueroa, M.E. et al. (2010a) Leukemic IDH1 and IDH2 mutations result in a hypermethylation phenotype, disrupt TET2 function, and impair hematopoietic differentiation. Cancer Cell, 18, 553-567.
7. Figueroa, M.E. et al. (2010b) DNA methylation signatures identify biologically distinct subtypes in acute myeloid leukemia. Cancer Cell, 17, 13-27.
8. Griffiths, D.A. (1973) Maximum likelihood estimation for the beta-binomial distribution and an application to the household distribution of the total number of cases of a disease. Biometrics, 29, 637-648.
9. Gu, H. et al. (2010) Genome-scale DNA methylation mapping of clinical samples at single-nucleotide resolution. Nat. Methods, 7, 133-136.
10. Gu, H. et al. (2011) Preparation of reduced representation bisulfite sequencing libraries for genome-scale DNA methylation profiling. Nat. Protoc., 6, 468-481.
11. Hansen, K.D. et al. (2011) Increased methylation variation in epigenetic domains across cancer types. Nat. Genet., 43, 768-775.
12. Hansen, K.D. et al. (2012) BSmooth: from whole genome bisulfite sequencing reads to differentially methylated regions. Genome Biol., 13, R83.
13. Izzo, A. and Schneider, R. (2010) Chatting histone modifications in mammals. Brief. Funct. Genomics, 9, 429-443.
14. Jeddeloh, J. et al. (2008) Reduced-representation methylation mapping. Genome Biol., 9, 231.
15. Kassner, I. et al. (2013) Crosstalk between SET7/9-dependent methylation and ARTD1-mediated ADP-ribosylation of histone H1.4. Epigenetics Chromatin, 6, 1.
16. Ko, M. et al. (2010) Impaired hydroxylation of 5-methylcytosine in myeloid cancers with mutant TET2. Nature, 468, 839-843.
17. Krueger, F. and Andrews, S.R. (2011) Bismark: a flexible aligner and methylation caller for Bisulfite-seq applications. Bioinformatics, 27, 1571-1572.
18. Kulis, M. and Esteller, M. (2010) DNA methylation and cancer. Adv. Genet., 70, 27-56.
19. Laird, P.W. (2010) Principles and challenges of genome-wide DNA methylation analysis. Nat. Rev. Genet., 11, 191-203.
20. Lim, D.H. and Maher, E.R. (2010) DNA methylation: a form of epigenetic control of gene expression. Obstet. Gynaecol., 12, 37-42.
21. Lister, R. and Ecker, J.R. (2009) Finding the fifth base: genome-wide sequencing of cytosine methylation. Genome Res., 19, 959-966.
22. Lister, R. et al. (2009) Human DNA methylomes at base resolution show widespread epigenomic differences. Nature, 462, 315-322.
23. Meissner, A. et al. (2005) Reduced representation bisulfite sequencing for comparative high-resolution DNA methylation analysis. Nucleic Acids Res., 33, 5868-5877.
24. Nordlund, J. et al. (2013) Genome-wide signatures of differential DNA methylation in pediatric acute lymphoblastic leukemia. Genome Biol., 14, r105.
25. Patel, K.P. et al. (2011) Acute myeloid leukemia with IDH1 or IDH2 mutation frequency and clinicopathologic features. Am. J. Clin. Pathol., 135, 35-45.
26. Petrie, K. and Zelent, A. (2007) AML1/ETO, a promiscuous fusion oncoprotein. Blood, 109, 4109-4110.
27. Sharma, S. et al. (2010) Epigenetics in cancer. Carcinogenesis, 31, 27-36.
28. Shen, H. and Laird, P.W. (2013) Interplay between the cancer genome and epigenome. Cell, 153, 38-55.
29. Sun, D. et al. (2014) MOABS: model based analysis of bisulfite sequencing data. Genome Biol., 15, R38.
30. Tomlins, S.A. et al. (2005) Recurrent fusion of TMPRSS2 and ETS transcription factor genes in prostate cancer. Science, 310, 644-648.
31. Tripathi, R.C. et al. (1994) Estimation of parameters in the beta binomial model. Ann. Inst. Stat. Math., 46, 317-331.
32. Vaissiere, T. et al. (2008) Epigenetic interplay between histone modifications and DNA methylation in gene silencing. Mutat. Res., 659, 40-48.
33. van Vlodrop, I.J.H. et al. (2011) Analysis of promoter CpG island hypermethylation in cancer: location, location, location! Clin. Cancer Res., 17, 4225-4231.
34. Wang, T. et al. (2013) RRBS-Analyser: a comprehensive web server for reduced representation bisulfite sequencing data analysis. Hum. Mutat., 34, 1606-1610.
35. Widschwendter, M. et al. (2006) Epigenetic stem cell signature in cancer. Nat. Genet., 39, 157-158.
36. Xu, W. et al. (2011) Oncometabolite 2-hydroxyglutarate is a competitive inhibitor of -ketoglutarate-dependent dioxygenases. Cancer Cell, 19, 17-30.
37. Yang, X. et al. (2010) Targeting DNA methylation for epigenetic therapy. Trends Pharmacol. Sci., 31, 536-546.