An improved method for detecting and delineating genomic regions with altered gene expression in cancer.
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.
Nilsson
Björn
B
Department of Clinical Genetics, Lund University Hospital, SE-221 85 Lund, Sweden. bjorn.nilsson@med.lu.se
Johansson
Mikael
M
Heyden
Anders
A
Nelander
Sven
S
Fioretos
Thoas
T
D002874:Chromosome Mapping / Q000379:methods; D019295:Computational Biology / Q000379:methods*; D015972:Gene Expression Regulation, Neoplastic / Q000235:genetics*; D006801:Humans; D008722:Methods; D009369:Neoplasms / Q000235:genetics; D012984:Software