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 sho...

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Detalles Bibliográficos
Autores principales: Nilsson, Björn, Johansson, Mikael, Heyden, Anders, Nelander, Sven, Fioretos, Thoas
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2008
Materias:
Method
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395254/
https://www.ncbi.nlm.nih.gov/pubmed/18208590
http://dx.doi.org/10.1186/gb-2008-9-1-r13
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author Nilsson, Björn
Johansson, Mikael
Heyden, Anders
Nelander, Sven
Fioretos, Thoas
author_facet Nilsson, Björn
Johansson, Mikael
Heyden, Anders
Nelander, Sven
Fioretos, Thoas
author_sort Nilsson, Björn
collection PubMed
description 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.
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spelling pubmed-23952542008-05-29 An improved method for detecting and delineating genomic regions with altered gene expression in cancer Nilsson, Björn Johansson, Mikael Heyden, Anders Nelander, Sven Fioretos, Thoas Genome Biol Method 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. BioMed Central 2008-01-21 /pmc/articles/PMC2395254/ /pubmed/18208590 http://dx.doi.org/10.1186/gb-2008-9-1-r13 Text en Copyright © 2008 Nilsson et al.; licensee BioMed Central Ltd. https://creativecommons.org/licenses/by/2.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0 (https://creativecommons.org/licenses/by/2.0/) ), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Method
Nilsson, Björn
Johansson, Mikael
Heyden, Anders
Nelander, Sven
Fioretos, Thoas
An improved method for detecting and delineating genomic regions with altered gene expression in cancer
title An improved method for detecting and delineating genomic regions with altered gene expression in cancer
title_full An improved method for detecting and delineating genomic regions with altered gene expression in cancer
title_fullStr An improved method for detecting and delineating genomic regions with altered gene expression in cancer
title_full_unstemmed An improved method for detecting and delineating genomic regions with altered gene expression in cancer
title_short An improved method for detecting and delineating genomic regions with altered gene expression in cancer
title_sort improved method for detecting and delineating genomic regions with altered gene expression in cancer
topic Method
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2395254/
https://www.ncbi.nlm.nih.gov/pubmed/18208590
http://dx.doi.org/10.1186/gb-2008-9-1-r13
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