An improved method for detecting and delineating genomic regions with altered gene expression in cancer

Genome Biol. 2008 Jan 21;9(1):R13. doi: 10.1186/gb-2008-9-1-r13.

Abstract

Genomic regions with altered gene expression are a characteristic feature of cancer cells. We present a novel method for identifying such regions in gene expression maps. This method is based on total variation minimization, a classical signal restoration technique. In systematic evaluations, we show that our method combines top-notch detection performance with an ability to delineate relevant regions without excessive over-segmentation, making it a significant advance over existing methods. Software (Rendersome) is provided.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Chromosome Mapping / methods
  • Computational Biology / methods*
  • Gene Expression Regulation, Neoplastic / genetics*
  • Humans
  • Methods
  • Neoplasms / genetics
  • Software