title: Gene-set analysis is severely biased when applied to genome-wide methylation data.
abstract: BACKGROUND
  DNA methylation is an epigenetic mark that can stably repress gene expression. Because of its biological and clinical significance, several methods have been developed to compare genome-wide patterns of methylation between groups of samples. The application of gene set analysis to identify relevant groups of genes that are enriched for differentially methylated genes is often a major component of the analysis of these data. This can be used, for example, to identify processes or pathways that are perturbed in disease development. We show that gene-set analysis, as it is typically applied to genome-wide methylation assays, is severely biased as a result of differences in the numbers of CpG sites associated with different classes of genes and gene promoters.
  
  
  RESULTS
  We demonstrate this bias using published data from a study of differential CpG island methylation in lung cancer and a dataset we generated to study methylation changes in patients with long-standing ulcerative colitis. We show that several of the gene sets that seem enriched would also be identified with randomized data. We suggest two existing approaches that can be adapted to correct the bias. Accounting for the bias in the lung cancer and ulcerative colitis datasets provides novel biological insights into the role of methylation in cancer development and chronic inflammation, respectively. Our results have significant implications for many previous genome-wide methylation studies that have drawn conclusions on the basis of such strongly biased analysis.
  
  
  BACKGROUND
  cathal.seoighe@nuigalway.ie
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Section of Hematology/Oncology, Department of Medicine, University of Chicago, Chicago, IL 60637 USA.
authors.forename: Paul
authors.initials: P
authors.lastname: Geeleher
authors.forename: Lori
authors.initials: L
authors.lastname: Hartnett
authors.forename: Laurance J
authors.initials: LJ
authors.lastname: Egan
authors.forename: Aaron
authors.initials: A
authors.lastname: Golden
authors.forename: Raja Affendi
authors.initials: RA
authors.lastname: Raja Ali
authors.forename: Cathal
authors.initials: C
authors.lastname: Seoighe
mesh_terms: D003093:Colitis, Ulcerative / Q000235:genetics; D018899:CpG Islands; D019175:DNA Methylation; D005796:Genes; D023281:Genomics / Q000379:methods*; D006801:Humans; D008175:Lung Neoplasms / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis