The PDF below contains links to articles and R packages used in our analysis.
Bock, C. Analysing and interpreting DNA methylation data. Nat. Rev. Genet. 13, 705-719 (2012).
Chen, D. et al. Genome-wide Association Study of Susceptibility Loci for Cervical Cancer. J. Natl. Cancer Inst. (2013).
Du, P. et al. Comparison of Beta-value and M-value methods for quantifying methylation levels by microarray analysis. BMC Bioinformatics 11, 587-2105-11-587 (2010).
Esteller, M., Corn, P. G., Baylin, S. B. & Herman, J. G. A gene hypermethylation profile of human cancer. Cancer Res. 61, 3225-3229 (2001).
Heyn, H., Moran, S. & Esteller, M. Aberrant DNA methylation profiles in the premature aging disorders Hutchinson-Gilford Progeria and Werner syndrome. Epigenetics 8, 28-33 (2013).
Hinoue, T. et al. Genome-scale analysis of aberrant DNA methylation in colorectal cancer. Genome Res. 22, 271-282 (2012).
Houseman, E. A. et al. Model-based clustering of DNA methylation array data: a recursive- partitioning algorithm for high-dimensional data arising as a mixture of beta distributions. BMC Bioinformatics 9, 365-2105-9-365 (2008).
Hsu, S. H. et al. Methylation of gene encoding the growth suppressor protein tyrosine phosphatase receptor-type O (PTPRO) in human hepatocellular carcinoma and identification of VCP as its bona fide substrate.J. Cell. Biochem. (2013).
Illumina Inc (2012). Infinium® HumanMethylatio450 BeadChip. Pub. No. 270-2010-001
Ley, T. J. et al. DNMT3A mutations in acute myeloid leukemia. N. Engl. J. Med. 363, 2424-2433
(2010).
Sandoval, J. et al. Genome-wide DNA methylation profiling predicts relapse in childhood B-cell
acute lymphoblastic leukaemia. Br. J. Haematol. 160, 406-409 (2013).
Schoofs, T. et al. DNA methylation changes are a late event in acute promyelocytic leukemia
and coincide with loss of transcription factor binding. Blood 121, 178-187 (2013).
Wiemels, J. L. et al. Methylenetetrahydrofolate reductase (MTHFR) polymorphisms and risk of molecularly defined subtypes of childhood acute leukemia. Proc. Natl. Acad. Sci. U. S. A. 98, 4004-4009 (2001).
Yang, W. H., Lan, H. Y., Tai, S. K. & Yang, M. H. Repression of bone morphogenetic protein 4 by let-7i attenuates mesenchymal migration of head and neck cancer cells. Biochem. Biophys. Res. Commun. 433, 24-30 (2013).
R Packages
GEO series Import: GEOquery
Hierarchical clustering:
pvclust
RPMM: Recursively Partitioned Mixture Model IlluminaHumanMethylation450k.db
Teschendorff, A. E. et al. A beta-mixture quantile normalization method for correcting probe design bias in Illumina Infinium 450 k DNA methylation data. Bioinformatics 29, 189-196 (2013).
lme4: Linear mixed-effects models using S4 classes