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

SNP Chart: an integrated platform for visualization and interpretation of microarray genotyping data.

Scott J Tebbutt1, Igor V Opushnyev, Ben W Tripp

  • 1James Hogg iCAPTURE Centre for Cardiovascular and Pulmonary Research, St Paul's Hospital, University of British Columbia Vancouver, Canada. stebbutt@mrl.ubc.ca

Bioinformatics (Oxford, England)
|August 17, 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

Newborns with sickle cell trait have distinct peripheral blood molecular signatures across the first week of life.

Blood. Red cells & iron·2026
Same author

Pilot longitudinal integrated transcriptomic-metabolomic study reveals immune and metabolic signatures in non-hospitalized healthcare workers with long COVID.

Frontiers in cellular and infection microbiology·2026
Same author

Using cell-specific late-phase asthma mRNA biomarkers to repurpose drugs that concurrently reverse disease signatures across multiple immune cell-types.

PLoS computational biology·2026
Same author

Donor-derived cell-free DNA associated with increased risk of chronic lung allograft dysfunction and mortality: Implications of immunosuppression and retransplantation.

The Journal of heart and lung transplantation : the official publication of the International Society for Heart Transplantation·2026
Same author

A randomized prospective study of neonatal hepatitis B vaccine immunogenicity in The Gambia and Papua New Guinea.

The journal of allergy and clinical immunology. Global·2026
Same author

2024-2025 Covid-19 Vaccine Outcomes in U.S. Veterans.

The New England journal of medicine·2026
Same journal

Biomedical Concept Recognition with Error-aware Negative-enhanced Ranking Framework.

Bioinformatics (Oxford, England)·2026
Same journal

TEDLH: Domain HMMs for sensitive detection of remote homologues.

Bioinformatics (Oxford, England)·2026
Same journal

PLNFGL: Joint Estimation of Multi-Condition Gene Networks from Single-cell RNA-seq Data.

Bioinformatics (Oxford, England)·2026
Same journal

MCFST: Spatial domain identification method based on multi-view graph convolutional network and graph fusion network.

Bioinformatics (Oxford, England)·2026
Same journal

SpaBiT: Enhancing Spatial Transcriptomics Resolution via Bidirectional Attention Transformers.

Bioinformatics (Oxford, England)·2026
Same journal

EDEL: Enhancing Dense Retrievers for Curation of Biomedical Knowledge Bases.

Bioinformatics (Oxford, England)·2026
See all related articles

SNP Chart is a Java application that visualizes and interprets microarray genotyping data. It aids in the quality control and interpretation of single nucleotide polymorphism (SNP) data for accurate genotype scoring.

Area of Science:

  • Bioinformatics
  • Genetics
  • Computational Biology

Background:

  • Microarray technology is crucial for genetic analysis.
  • Arrayed primer extension (APEX) chemistries generate genotyping data.
  • Effective visualization tools are needed for complex microarray data.

Purpose of the Study:

  • To introduce SNP Chart, a Java application for visualizing and interpreting microarray genotyping data.
  • To enable efficient quality control and genotype scoring from APEX-based microarray experiments.

Main Methods:

  • Importing spot intensity files and multi-channel TIFF images into SNP Chart.
  • Utilizing a list of single nucleotide polymorphisms (SNPs) being tested.
  • Reassembling scattered data from multiple probes interrogating the same SNP into a unified chart format.

Related Experiment Videos

Main Results:

  • SNP Chart facilitates the visualization of genotyping data for individual SNPs.
  • The application allows for the reassembly of data from scattered probes.
  • Enables quick and effective quality control and manual genotype scoring.

Conclusions:

  • SNP Chart provides an effective solution for visualizing and interpreting microarray genotyping data.
  • The tool enhances the quality control process for SNP data analysis.
  • Facilitates accurate manual genotype scoring from complex microarray experiments.