title: A test for comparing two groups of samples when analyzing multiple omics profiles.
abstract: BACKGROUND
  A number of statistical models has been proposed for studying the association between gene expression and copy number data in integrated analysis. The next step is to compare association patterns between different groups of samples.
  
  
  RESULTS
  We propose a method, named dSIM, to find differences in association between copy number and gene expression, when comparing two groups of samples. Firstly, we use ridge regression to correct for the baseline associations between copy number and gene expression. Secondly, the global test is applied to the corrected data in order to find differences in association patterns between two groups of samples. We show that dSIM detects differences even in small genomic regions in a simulation study. We also apply dSIM to two publicly available breast cancer datasets and identify chromosome arms where copy number led gene expression regulation differs between positive and negative estrogen receptor samples. In spite of differing genomic coverage, some selected arms are identified in both datasets.
  
  
  CONCLUSIONS
  We developed a flexible and robust method for studying association differences between two groups of samples while integrating genomic data from different platforms. dSIM can be used with most types of microarray/sequencing data, including methylation and microRNA expression. The method is implemented in R and will be made part of the BioConductor package SIM.
authors.affiliation: Epidemiology and Biostatistics, VU University Medical Center, Amsterdam, The Netherlands. n.chaturvedi@vumc.nl.
authors.forename: Nimisha
authors.initials: N
authors.lastname: Chaturvedi
authors.forename: Jelle J
authors.initials: JJ
authors.lastname: Goeman
authors.forename: Judith M
authors.initials: JM
authors.lastname: Boer
authors.forename: Wessel N
authors.initials: WN
authors.lastname: van Wieringen
authors.forename: Renée X
authors.initials: RX
authors.lastname: de Menezes
mesh_terms: D001943:Breast Neoplasms / Q000235:genetics / Q000378:metabolism; D019295:Computational Biology / Q000379:methods*; D005260:Female; D018628:Gene Dosage / Q000235:genetics; D020869:Gene Expression Profiling; D006801:Humans; D011960:Receptors, Estrogen / Q000378:metabolism
chemical_list: D011960:Receptors, Estrogen