title: Detecting differentially methylated loci for multiple treatments based on high-throughput methylation data.
abstract: BACKGROUND
  Because of its important effects, as an epigenetic factor, on gene expression and disease development, DNA methylation has drawn much attention from researchers. Detecting differentially methylated loci is an important but challenging step in studying the regulatory roles of DNA methylation in a broad range of biological processes and diseases. Several statistical approaches have been proposed to detect significant methylated loci; however, most of them were designed specifically for case-control studies.
  
  
  RESULTS
  Noticing that the age is associated with methylation level and the methylation data are not normally distributed, in this paper, we propose a nonparametric method to detect differentially methylated loci under multiple conditions with trend for Illumina Array Methylation data. The nonparametric method, Cuzick test is used to detect the differences among treatment groups with trend for each age group; then an overall p-value is calculated based on the method of combining those independent p-values each from one age group.
  
  
  CONCLUSIONS
  We compare the new approach with other methods using simulated and real data. Our study shows that the proposed method outperforms other methods considered in this paper in term of power: it detected more biological meaningful differentially methylated loci than others.
authors.affiliation: Department of Epidemiology and Biostatistics, School of Public Health, Indiana University Bloomington, 1025 E, 7th street, PH C104, Bloomington, IN 47405, USA. zc3@indiana.edu.
authors.forename: Zhongxue
authors.initials: Z
authors.lastname: Chen
authors.forename: Hanwen
authors.initials: H
authors.lastname: Huang
authors.forename: Qingzhong
authors.initials: Q
authors.lastname: Liu
mesh_terms: D016022:Case-Control Studies; D019175:DNA Methylation; D005260:Female; D056426:Genetic Loci; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D010051:Ovarian Neoplasms / Q000235:genetics; D018709:Statistics, Nonparametric