CNAmet: an R package for integrating copy number, methylation and expression data

Riku Louhimo; Sampsa Hautaniemi

doi:10.1093/bioinformatics/btr019

CNAmet: an R package for integrating copy number, methylation and expression data

Bioinformatics. 2011 Mar 15;27(6):887-8. doi: 10.1093/bioinformatics/btr019. Epub 2011 Jan 12.

Authors

Riku Louhimo¹, Sampsa Hautaniemi

Affiliation

¹ Institute of Biomedicine and Genome-Scale Biology Research Program, University of Helsinki, Finland.

PMID: 21228048
DOI: 10.1093/bioinformatics/btr019

Abstract

Summary: 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.

Availability: CNAmet R-package and user guide are freely available under GNU General Public License at http://csbi.ltdk.helsinki.fi/CNAmet.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Algorithms
Computational Biology / methods
DNA Methylation*
Female
Gene Dosage*
Gene Expression Profiling / methods*
Gene Expression Regulation, Neoplastic
Genomic Instability
Glioblastoma / genetics
Humans
Ovarian Neoplasms / genetics
Software*