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

Research output: Contribution to journalArticleScientificpeer-review

87 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 languageEnglish
Pages (from-to)1714-1715
Number of pages2
JournalBioinformatics
Volume19
Issue number13
DOIs
Publication statusPublished - 2003
MoE publication typeA1 Journal article-refereed

Fingerprint

Comparative Genomics
Comparative Genomic Hybridization
Microarrays
MATLAB
Data analysis
Genes
Graphical user interfaces
Dynamic programming
Amplification
Visualization
Complementary DNA
CDNA Microarray
K-means Clustering
Graphical User Interface
Microarray Data
Oligonucleotide Array Sequence Analysis
Deletion
Dynamic Programming
Cluster Analysis
Genome

Keywords

  • comparative genomic hybridization
  • CGH
  • cDNA microarrays
  • CGH microarray
  • microarray

Cite this

Autio, R., Hautaniemi, S., Kauraniemi, P., Yli-Harja, O., Astola, J., Wolf, M., & Kallioniemi, A. (2003). CGH-Plotter: MATLAB toolbox for CGH-data analysis. Bioinformatics, 19(13), 1714-1715. https://doi.org/10.1093/bioinformatics/btg230
Autio, Reija ; Hautaniemi, Sampsa ; Kauraniemi, Päivikki ; Yli-Harja, Olli ; Astola, Jaakko ; Wolf, Maija ; Kallioniemi, Anne. / CGH-Plotter : MATLAB toolbox for CGH-data analysis. In: Bioinformatics. 2003 ; Vol. 19, No. 13. pp. 1714-1715.
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Autio, R, Hautaniemi, S, Kauraniemi, P, Yli-Harja, O, Astola, J, Wolf, M & Kallioniemi, A 2003, 'CGH-Plotter: MATLAB toolbox for CGH-data analysis', Bioinformatics, vol. 19, no. 13, pp. 1714-1715. https://doi.org/10.1093/bioinformatics/btg230

CGH-Plotter : MATLAB toolbox for CGH-data analysis. / Autio, Reija (Corresponding Author); Hautaniemi, Sampsa; Kauraniemi, Päivikki; Yli-Harja, Olli; Astola, Jaakko; Wolf, Maija; Kallioniemi, Anne.

In: Bioinformatics, Vol. 19, No. 13, 2003, p. 1714-1715.

Research output: Contribution to journalArticleScientificpeer-review

TY - JOUR

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

Y1 - 2003

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

M3 - Article

VL - 19

SP - 1714

EP - 1715

JO - Bioinformatics

JF - Bioinformatics

SN - 1367-4803

IS - 13

ER -

Autio R, Hautaniemi S, Kauraniemi P, Yli-Harja O, Astola J, Wolf M et al. CGH-Plotter: MATLAB toolbox for CGH-data analysis. Bioinformatics. 2003;19(13):1714-1715. https://doi.org/10.1093/bioinformatics/btg230