Detecting differentially methylated loci for Illumina Array methylation data based on human ovarian cancer data

BMC Medical Genomics

Volumn 6, Issue SUPPL.1, 2013, Pages

  Chen, Zhongxue ^a   Huang, Hanwen ^b   Liu, Jianzhong ^c   Tony Ng, Hon Keung ^d   Nadarajah, Saralees ^e   Huang, Xudong ^f   Deng, Youping ^g  

^a INDIANA UNIVERSITY   (United States)

^b UNIVERSITY OF TEXAS   (United States)

^c Chem21 Group Inc   (United States)

^d SOUTHERN METHODIST UNIVERSITY   (United States)

^e UNIVERSITY OF MANCHESTER   (United Kingdom)

^f MASSACHUSETTS GENERAL HOSPITAL   (United States)

^g RUSH UNIVERSITY MEDICAL CENTER   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

ARTICLE; CONTROLLED STUDY; DATA ANALYSIS; DNA METHYLATION; GENE LOCUS; INTERMETHOD COMPARISON; LINEAR REGRESSION ANALYSIS; NONPARAMETRIC TEST; OVARY CANCER; PRIORITY JOURNAL; STATISTICAL SIGNIFICANCE;

AGED; AGED, 80 AND OVER; ALGORITHMS; DNA METHYLATION; FEMALE; GENETIC LOCI; HUMANS; MIDDLE AGED; OLIGONUCLEOTIDE ARRAY SEQUENCE ANALYSIS; OVARIAN NEOPLASMS;

EID: 84872963418     PISSN: None     EISSN: 17558794     Source Type: Journal    
DOI: 10.1186/1755-8794-6-S1-S9     Document Type: Article

References (28)

1. A statistical framework for Illumina DNA methylation arrays. Kuan PF, Wang S, Zhou X, Chu H, Bioinformatics 2010 26 22 2849 10.1093/bioinformatics/ btq553 20880956
2. An integrated resource for genome-wide identification and analysis of human tissue-specific differentially methylated regions (tDMRs). Rakyan VK, Down TA, Thorne NP, Flicek P, Kulesha E, Gräf S, Tomazou EM, Bäckdahl L, Johnson N, Herberth M, Genome research 2008 18 9 1518 1529 10.1101/gr.077479.108 18577705
3. Epigenetic gene silencing in cancer-a mechanism for early oncogenic pathway addiction? Baylin SB, Ohm JE, Nature Reviews Cancer 2006 6 2 107 116 10.1038/nrc1799 16491070 (Pubitemid 43361543)
4. The history of cancer epigenetics. Feinberg AP, Tycko B, Nature Reviews Cancer 2004 4 2 143 153 10.1038/nrc1279 14732866 (Pubitemid 38198742)
5. Cytosine methylation and CpG, TpG (CpA) and TpA frequencies. Jabbari K, Bernardi G, Gene 2004 333 143 149 15177689 (Pubitemid 38737360)
6. The fundamental role of epigenetic events in cancer. Jones PA, Baylin SB, Nature Reviews Genetics 2002 3 6 415 428 12042769 (Pubitemid 34587077)
7. DNA methylation and cancer. Kulis M, Esteller M, Adv Genet 2010 70 27 56 20920744
8. Principles and challenges of genome-wide DNA methylation analysis. Laird PW, Nature Reviews Genetics 2010 11 3 191 203 20125086
9. Method to detect differentially methylated loci with case-control designs using Illumina arrays. Wang S, Genetic Epidemiology 2011 35 December 686 694 21818777
10. Chromosome instability and immunodeficiency syndrome caused by mutations in a DNA methyltransferase gene. Xu GL, Bestor TH, Bourc'his D, Hsieh CL, Tommerup N, Bugge M, Hulten M, Qu X, Russo JJ, Viegas-Péquignot E, Nature 1999 402 6758 187 191 10.1038/46052 10647011
11. Increased methylation variation in epigenetic domains across cancer types. Hansen KD, Timp W, Bravo HC, Sabunciyan S, Langmead B, McDonald OG, Wen B, Wu H, Liu Y, Diep D, Nature Genetics 2011 43 8 768 775 10.1038/ng.865 21706001
12. A new statistical approach to detecting differentially methylated loci for case control Illumina array methylation data. Chen Z, Liu Q, Nadarajah S, Bioinformatics 2012 28 8 1109 1113 10.1093/bioinformatics/bts093 22368244
13. Age adjusted nonparametric detection of differential DNA methylation with case-control designs. Huang H, Chen Z, Unpublished manuscript
14. Aging and environmental exposures alter tissue-specific DNA methylation dependent upon CpG island context. Christensen BC, Houseman EA, Marsit CJ, Zheng S, Wrensch MR, Wiemels JL, Nelson HH, Karagas MR, Padbury JF, Bueno R, PLoS genetics 2009 5 8 1000602 10.1371/journal.pgen.1000602 19680444
15. Age-dependent DNA methylation of genes that are suppressed in stem cells is a hallmark of cancer. Teschendorff AE, Menon U, Gentry-Maharaj A, Ramus SJ, Weisenberger DJ, Shen H, Campan M, Noushmehr H, Bell CG, Maxwell AP, Genome research 2010 20 4 440 446 10.1101/gr.103606.109 20219944
16. A robust method for testing association in genome-wide association studies. Chen Z, Ng HKT, Human Heredity 2012 73 1 26 34 10.1159/000334719 22212363
17. A new association test based on Chi-square partition for case-control GWA studies. Chen Z, Genetic Epidemiology 2011 35 658 658
18. Statistical methods for research workers. Fisher RA, Edinburgh: Oliver and Boyd 1932
19. On the comparison of several mean values: An alternative approach. Welch B, Biometrika 1951 38 3/4 330 336 10.2307/2332579
20. Problems arising in the analysis of a series of similar experiments. Cochran WG, Journal of Royal Statistical Society, Series C: Applied Statistics 1937 4 102 118
21. A note on Cochran test for homogeneity in one-way ANOVA and meta-analysis. Chen Z, Ng HKT, Nadarajah S, Statistical Papers 2012 1 10
22. Is the weighted z-test the best method for combining probabilities from independent tests? Chen Z, Journal of Evolutionary Biology 2011 24 4 926 930 10.1111/j.1420-9101.2010.02226.x 21401770
23. Comments on 'Choosing an optimal method to combine p-values' by Sungho Won, Nathan Morris, Qing Lu and Robert C. Elston, Statistics in Medicine 2009; 28: 1537-1553. Chen Z, Nadarajah S, Statistics in Medicine 2011 30 24 2959 2961 10.1002/sim.4222 21969252
24. Estimation of significance thresholds for genomewide association scans. Dudbridge F, Gusnanto A, Genet Epidemiol 2008 32 3 227 234 10.1002/gepi.20297 18300295 (Pubitemid 351550369)
25. A multiple testing correction method for genetic association studies using correlated single nucleotide polymorphisms. Gao X, Starmer J, Martin ER, Genet Epidemiol 2008 32 4 361 369 10.1002/gepi.20310 18271029 (Pubitemid 351656307)
26. On multiple-testing correction in genome-wide association studies. Moskvina V, Schmidt KM, Genet Epidemiol 2008 32 6 567 573 10.1002/gepi.20331 18425821
27. Estimation of the multiple testing burden for genomewide association studies of nearly all common variants. Pe'er I, Yelensky R, Altshuler D, Daly MJ, Genet Epidemiol 2008 32 4 381 385 10.1002/gepi.20303 18348202 (Pubitemid 351656309)
28. A new approach to account for the correlations among single nucleotide polymorphisms in genome-wide association studies. Chen Z, Liu Q, Human Heredity 2011 72 1 1 9 10.1159/000330135 21849789