IMA: An R package for high-throughput analysis of Illumina's 450K Infinium methylation data

Bioinformatics

Volumn 28, Issue 5, 2012, Pages 729-730

  Wang, Dan ^a   Yan, Li ^a   Hu, Qiang ^a   Sucheston, Lara E ^a   Higgins, Michael J ^a   Ambrosone, Christine B ^a   Johnson, Candace S ^a   Smiraglia, Dominic J ^a   Liu, Song ^a  

^a ROSWELL PARK CANCER INSTITUTE   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; COMPUTER PROGRAM; CPG ISLAND; DNA METHYLATION; DNA MICROARRAY; HUMAN; HUMAN GENOME;

CPG ISLANDS; DNA METHYLATION; GENOME, HUMAN; HUMANS; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; SOFTWARE;

EID: 84863230488     PISSN: 13674803     EISSN: 14602059     Source Type: Journal    
DOI: 10.1093/bioinformatics/bts013     Document Type: Article

References (17)

1. Aryee,M.J. et al. (2011) Accurate genome-scale percentage DNAmethylation estimates from microarray data. Biostatistics, 12, 197-210.
2. Barbosa-Morais,N.L. et al. (2010) A re-annotation pipeline for Illumina BeadArrays: improving the interpretation of gene expression data. Nucleic Acids Res., 38, e17.
3. Bibikova,M. et al. (2011) High density DNA methylation array with single CpG site resolution. Genomics, 98, 288-295.
4. Christensen,B.C. et al. (2011) DNA methylation, isocitrate dehydrogenase mutation, and survival in glioma. J. Natl Cancer Inst., 103, 143-153.
5. Du,P. et al. (2008) lumi: a pipeline for processing Illumina microarray. Bioinformatics, 24, 1547-1548.
6. Gentleman,R.C. et al. (2004) Bioconductor: open software development for computational biology and bioinformatics. Genome Biol., 5, R80-R80.
7. Houseman,E.A. et al. (2008) 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.
8. Irizarry,R.A. et al. (2009) The human colon cancer methylome shows similar hypo- and hypermethylation at conserved tissue-specific CpG island shores. Nat. Genet., 41, 178-186.
9. Jones,P.A. and Baylin,S.B. (2007) The epigenomics of cancer. Cell, 128, 683-692.
10. Kuan,P.F. et al. (2010) A statistical framework for Illumina DNA methylation arrays. Bioinformatics, 26, 2849-2855.
11. Laird,P.W. (2010) Principles and challenges of genome-wideDNAmethylation analysis. Nat. Rev. Genet., 11, 191-203.
12. Marsit,C.J. et al. (2011) DNA methylation array analysis identifies profiles of bloodderived DNA methylation associated with bladder cancer. J. Clin. Oncol., 29, 1133-1139.
13. Maunakea,A.K. et al. (2010) Conserved role of intragenic DNA methylation in regulating alternative promoters. Nature, 466, 253-257.
14. Portela,A. and Esteller,M. (2010) Epigenetic modifications and human disease. Nat. Biotechnol., 28, 1057-1068.
15. Rocke,D.M. (1993) On the beta transformation family. Technometrics, 35, 72-81.
16. Siegmund,K.D. (2011) Statistical approaches for the analysis of DNA methylation microarray data. Hum. Genet., 129, 585-595.
17. Teschendorff,A.E. et al. (2009) An epigenetic signature in peripheral blood predicts active ovarian cancer. PLoS One, 4.