tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation

Antoine Chambaz; Pierre Neuvial

doi:10.1093/bioinformatics/btv320

tmle.npvi: targeted, integrative search of associations between DNA copy number and gene expression, accounting for DNA methylation

Bioinformatics. 2015 Sep 15;31(18):3054-6. doi: 10.1093/bioinformatics/btv320. Epub 2015 May 21.

Authors

Antoine Chambaz¹, Pierre Neuvial¹

Affiliation

¹ Modal'X, Université Paris Ouest Nanterre, Nanterre, France and Laboratoire de Mathématiques et Modélisation d'Évry, Université d'Évry val d'Essonne, UMR CNRS 8071, ENSIIE, USC INRA, Évry, France.

PMID: 26002884
DOI: 10.1093/bioinformatics/btv320

Abstract

We describe the implementation of the method introduced by Chambaz et al. in 2012. We also demonstrate its genome-wide application to the integrative search of new regions with strong association between DNA copy number and gene expression accounting for DNA methylation in breast cancers.

Availability and implementation: An open-source R package tmle.npvi is available from CRAN (http://cran.r-project.org/).

Contact: [email protected].

Publication types

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

MeSH terms

Algorithms
Breast Neoplasms / genetics*
Computational Biology / methods*
DNA Copy Number Variations*
DNA Methylation*
Female
Gene Expression Profiling
Gene Expression Regulation, Neoplastic*
Genome, Human*
Humans
Software*