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

Björn Nilsson¹^,2^,3 , Mikael Johansson⁴ , Anders Heyden⁵ , Sven Nelander⁶ and Thoas Fioretos¹

¹Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden

²Department of Transfusion Medicine, Lund University Hospital, SE-221 85 Lund, Sweden

³Imaging Platform, Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA

⁴Department of Automatic Control, Royal Institute of Technology, SE-100 44 Stockholm, Sweden

⁵Department of Applied Mathematics, Malmö University, Malmö, SE-205 06 Malmö, Sweden

⁶Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA

author email corresponding author email

Genome Biology 2008, 9:R13doi:10.1186/gb-2008-9-1-r13


Published:	21 January 2008

Subject areas: Bioinformatics, Cancer, Genome studies

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.