Method
An improved method for detecting and delineating genomic regions with altered gene expression in cancer
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* Corresponding author: Björn Nilsson bjorn.nilsson@med.lu.se
1 Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden
2 Department of Transfusion Medicine, Lund University Hospital, SE-221 85 Lund, Sweden
3 Imaging Platform, Broad Institute of Harvard University and MIT, Cambridge, MA 02142, USA
4 Department of Automatic Control, Royal Institute of Technology, SE-100 44 Stockholm, Sweden
5 Department of Applied Mathematics, Malmö University, Malmö, SE-205 06 Malmö, Sweden
6 Computational Biology Center, Memorial Sloan-Kettering Cancer Center, New York, NY 10021, USA
Genome Biology 2008, 9:R13 doi:10.1186/gb-2008-9-1-r13
Published: 21 January 2008Abstract
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.