title: CNAmet: an R package for integrating copy number, methylation and expression data.
abstract: CONCLUSIONS
  Gene copy number and DNA methylation alterations are key regulators of gene expression in cancer. Accordingly, genes that show simultaneous methylation, copy number and expression alterations are likely to have a key role in tumor progression. We have implemented a novel software package (CNAmet) for integrative analysis of high-throughput copy number, DNA methylation and gene expression data. To demonstrate the utility of CNAmet, we use copy number, DNA methylation and gene expression data from 50 glioblastoma multiforme and 188 ovarian cancer primary tumor samples. Our results reveal a synergistic effect of DNA methylation and copy number alterations on gene expression for several known oncogenes as well as novel candidate oncogenes.
  
  
  BACKGROUND
  CNAmet R-package and user guide are freely available under GNU General Public License at http://csbi.ltdk.helsinki.fi/CNAmet.
authors.affiliation: Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, Finland.
authors.forename: Riku
authors.initials: R
authors.lastname: Louhimo
authors.forename: Sampsa
authors.initials: S
authors.lastname: Hautaniemi
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods; D019175:DNA Methylation; D005260:Female; D018628:Gene Dosage; D020869:Gene Expression Profiling / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic; D042822:Genomic Instability; D005909:Glioblastoma / Q000235:genetics; D006801:Humans; D010051:Ovarian Neoplasms / Q000235:genetics; D012984:Software