title: Towards understanding the breast cancer epigenome: a comparison of genome-wide DNA methylation and gene expression data.
abstract: Until recently, an elevated disease risk has been ascribed to a genetic predisposition, however, exciting progress over the past years has discovered alternate elements of inheritance that involve epigenetic regulation. Epigenetic changes are heritably stable alterations that include DNA methylation, histone modifications and RNA-mediated silencing. Aberrant DNA methylation is a common molecular basis for a number of important human diseases, including breast cancer. Changes in DNA methylation profoundly affect global gene expression patterns. What is emerging is a more dynamic and complex association between DNA methylation and gene expression than previously believed. Although many tools have already been developed for analyzing genome-wide gene expression data, tools for analyzing genome-wide DNA methylation have not yet reached the same level of refinement. Here we provide an in-depth analysis of DNA methylation in parallel with gene expression data characteristics and describe the particularities of low-level and high-level analyses of DNA methylation data. Low-level analysis refers to pre-processing of methylation data (i.e. normalization, transformation and filtering), whereas high-level analysis is focused on illustrating the application of the widely used class comparison, class prediction and class discovery methods to DNA methylation data. Furthermore, we investigate the influence of DNA methylation on gene expression by measuring the correlation between the degree of CpG methylation and the level of expression and to explore the pattern of methylation as a function of the promoter region.
authors.affiliation: Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Canada.
authors.forename: Sandeep K
authors.initials: SK
authors.lastname: Singhal
authors.affiliation: Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Canada.
authors.forename: Nawaid
authors.initials: N
authors.lastname: Usmani
authors.affiliation: Service de Biostatistique et d'Epidémiologie, Gustave Roussy, Villejuif, France.|INSERM U1018, CESP, Université Paris-Sud, Villejuif, France.
authors.forename: Stefan
authors.initials: S
authors.lastname: Michiels
authors.affiliation: Department of Medical Oncology, Dana-Farber Cancer Institute, Harvard Medical School, Boston, MA, USA.
authors.forename: Otto
authors.initials: O
authors.lastname: Metzger-Filho
authors.affiliation: Quantum Health Analytics SPRL, Liège, Belgium.
authors.forename: Kamal S
authors.initials: KS
authors.lastname: Saini
authors.affiliation: Department of Biological Sciences, University of Lethbridge, Lethbridge, Canada.|Canada Cancer and Aging Research Laboratories Ltd., Lethbridge, Canada.
authors.forename: Olga
authors.initials: O
authors.lastname: Kovalchuk
authors.affiliation: Department of Oncology, Cross Cancer Institute, University of Alberta, Edmonton, Canada.
authors.forename: Matthew
authors.initials: M
authors.lastname: Parliament
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics*; D002874:Chromosome Mapping; D018899:CpG Islands / Q000235:genetics; D004247:DNA / Q000378:metabolism*; D019175:DNA Methylation / Q000235:genetics*; D044127:Epigenesis, Genetic; D005260:Female; D015870:Gene Expression; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D020411:Oligonucleotide Array Sequence Analysis; D011401:Promoter Regions, Genetic / Q000235:genetics; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D004247:DNA
keywords: DNA methylation; breast cancer; epigenetics; expression; microarray