CGH-Plotter: MATLAB toolbox for CGH-data analysis

Reija Autio; Sampsa Hautaniemi; Päivikki Kauraniemi; Olli Yli-Harja; Jaakko Astola; Maija Wolf; Anne Kallioniemi

doi:10.1093/bioinformatics/btg230

CGH-Plotter: MATLAB toolbox for CGH-data analysis

Reija Autio (Corresponding Author), Sampsa Hautaniemi, Päivikki Kauraniemi, Olli Yli-Harja, Jaakko Astola, Maija Wolf, Anne Kallioniemi

VTT Technical Research Centre of Finland

Research output: Contribution to journal › Article › Scientific › peer-review

89 Citations (Scopus)

Abstract

Summary: CGH-Plotter is a MATLAB toolbox with a graphical user interface for the analysis of comparative genomic hybridization (CGH) microarray data. CGH-Plotter provides a tool for rapid visualization of CGH-data according to the locations of the genes along the genome. In addition, the CGH-Plotter identifies regions of amplifications and deletions, using k-means clustering and dynamic programming. The application offers a convenient way to analyze CGH-data and can also be applied for the analysis of cDNA microarray expression data. CGH-Plotter toolbox is platform independent and requires MATLAB 6.1 or higher to operate.

Original language	English
Pages (from-to)	1714-1715
Journal	Bioinformatics
Volume	19
Issue number	13
DOIs	https://doi.org/10.1093/bioinformatics/btg230
Publication status	Published - 2003
MoE publication type	A1 Journal article-refereed

Keywords

comparative genomic hybridization
CGH
cDNA microarrays
CGH microarray
microarray

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10.1093/bioinformatics/btg230

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title = "CGH-Plotter: MATLAB toolbox for CGH-data analysis",

abstract = "Summary: CGH-Plotter is a MATLAB toolbox with a graphical user interface for the analysis of comparative genomic hybridization (CGH) microarray data. CGH-Plotter provides a tool for rapid visualization of CGH-data according to the locations of the genes along the genome. In addition, the CGH-Plotter identifies regions of amplifications and deletions, using k-means clustering and dynamic programming. The application offers a convenient way to analyze CGH-data and can also be applied for the analysis of cDNA microarray expression data. CGH-Plotter toolbox is platform independent and requires MATLAB 6.1 or higher to operate.",

keywords = "comparative genomic hybridization, CGH, cDNA microarrays, CGH microarray, microarray",

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T1 - CGH-Plotter

T2 - MATLAB toolbox for CGH-data analysis

AU - Autio, Reija

AU - Hautaniemi, Sampsa

AU - Kauraniemi, Päivikki

AU - Yli-Harja, Olli

AU - Astola, Jaakko

AU - Wolf, Maija

AU - Kallioniemi, Anne

PY - 2003

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N2 - Summary: CGH-Plotter is a MATLAB toolbox with a graphical user interface for the analysis of comparative genomic hybridization (CGH) microarray data. CGH-Plotter provides a tool for rapid visualization of CGH-data according to the locations of the genes along the genome. In addition, the CGH-Plotter identifies regions of amplifications and deletions, using k-means clustering and dynamic programming. The application offers a convenient way to analyze CGH-data and can also be applied for the analysis of cDNA microarray expression data. CGH-Plotter toolbox is platform independent and requires MATLAB 6.1 or higher to operate.

AB - Summary: CGH-Plotter is a MATLAB toolbox with a graphical user interface for the analysis of comparative genomic hybridization (CGH) microarray data. CGH-Plotter provides a tool for rapid visualization of CGH-data according to the locations of the genes along the genome. In addition, the CGH-Plotter identifies regions of amplifications and deletions, using k-means clustering and dynamic programming. The application offers a convenient way to analyze CGH-data and can also be applied for the analysis of cDNA microarray expression data. CGH-Plotter toolbox is platform independent and requires MATLAB 6.1 or higher to operate.

KW - comparative genomic hybridization

KW - CGH

KW - cDNA microarrays

KW - CGH microarray

KW - microarray

U2 - 10.1093/bioinformatics/btg230

DO - 10.1093/bioinformatics/btg230

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SN - 1367-4803

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SP - 1714

EP - 1715

JO - Bioinformatics

JF - Bioinformatics

IS - 13

ER -

CGH-Plotter: MATLAB toolbox for CGH-data analysis

Abstract

Keywords

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