Jove
Visualize
Contact Us
JoVE
x logofacebook logolinkedin logoyoutube logo
ABOUT JoVE
OverviewLeadershipBlogJoVE Help Center
AUTHORS
Publishing ProcessEditorial BoardScope & PoliciesPeer ReviewFAQSubmit
LIBRARIANS
TestimonialsSubscriptionsAccessResourcesLibrary Advisory BoardFAQ
RESEARCH
JoVE JournalMethods CollectionsJoVE Encyclopedia of ExperimentsArchive
EDUCATION
JoVE CoreJoVE BusinessJoVE Science EducationJoVE Lab ManualFaculty Resource CenterFaculty Site
Terms & Conditions of Use
Privacy Policy
Policies

Related Experiment Videos

M-CGH: analysing microarray-based CGH experiments.

Junbai Wang1, Leonardo A Meza-Zepeda, Stine H Kresse

  • 1Department of Tumor Biology, The Norwegian Radium Hospital, Montebello, N-0310 Oslo, Norway. junbaiw@radium.uio.no

BMC Bioinformatics
|June 11, 2004
PubMed
Summary
This summary is machine-generated.

Related Concept Videos

You might also read

Related Articles

Articles linked to this work by shared authors, journal, and citation graph.

Sort by
Same author

Protocol for identifying functional regulatory mutation blocks by integrating genome sequencing and transcriptome data.

STAR protocols·2026
Same author

BayesPI-FLY: a Bayesian neural network approach for inferring feature weighted TF-DNA interaction.

Briefings in bioinformatics·2026
Same author

Validation of a Seven-Gene Predictive SIGNature for the Efficacy of Immuno-Oncology PD-1 Inhibitors in Patients with Sarcoma.

Clinical cancer research : an official journal of the American Association for Cancer Research·2026
Same author

Global mapping of RNA N<sup>6</sup>-methyladenosine (m<sup>6</sup>A) in human subcutaneous and visceral adipose tissue reveals novel targets that correlate with clinical variables of obesity.

Biomarker research·2025
Same author

DNA glycosylases Ogg1 and Mutyh influence gene expression of PRC2 targets associated with cognition.

Cellular and molecular life sciences : CMLS·2025
Same author

SMUG1 DNA glycosylase modulates reward behaviour through regulation of olfactory receptor gene expression.

Nucleic acids research·2025

This study introduces M-CGH, a MATLAB toolbox for analyzing microarray-based comparative genomic hybridization (array CGH) data. It provides tools for visualizing copy number variations and identifying amplicon boundaries in cancer research.

Area of Science:

  • Genomics
  • Bioinformatics
  • Cancer Research

Background:

  • Microarray-based comparative genomic hybridization (array CGH) analyzes relative copy number variations between genomes.
  • This technique is crucial for detecting chromosomal amplifications and deletions in cancer.
  • Specialized tools are required for analyzing array CGH data, including visualization and consideration of probe genomic relationships.

Purpose of the Study:

  • To develop and present M-CGH, a dedicated MATLAB toolbox for array CGH data analysis.
  • To provide essential tools for the visualization and interpretation of array CGH experimental results.
  • To facilitate the identification of DNA copy number alterations and amplicon boundaries.

Main Methods:

  • M-CGH utilizes a graphical user interface for array CGH analysis.

Related Experiment Videos

  • It incorporates multiple ratio normalization approaches.
  • Maximum likelihood estimation is used for DNA copy number distribution analysis (gains, normal, losses).
  • Amplicon boundaries are determined using fuzzy K-nearest neighbor or wavelet methods.
  • Integration with the Ensembl database for genomic information linking.

    • Main Results:

    • M-CGH offers a comprehensive suite of tools for array CGH data analysis.
    • The toolbox enables accurate estimation of DNA copy number states.
    • It effectively computes amplicon boundaries using advanced algorithms.
    • M-CGH facilitates the linkage of genomic clones to relevant genomic information.

    Conclusions:

    • M-CGH provides essential tools for analyzing array CGH experiments.
    • The software is freely available to academic users.
    • M-CGH does not require additional MATLAB toolboxes for operation.