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

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.

SUBMITTER: Nilsson B

PROVIDER: S-EPMC2395254 | biostudies-literature | 2008 Jan

REPOSITORIES: biostudies-literature

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

Nilsson Björn B Johansson Mikael M Heyden Anders A Nelander Sven S Fioretos Thoas T

Genome biology 20080121 1

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. Sof ...[more]

PMID: 18208590

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