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

Three microarray platforms: an analysis of their concordance in profiling gene expression.

David Petersen1, G V R Chandramouli, Joel Geoghegan

  • 1Advanced Technology Center, Center for Cancer Research, National Cancer Institute, Gaithersburg, MD 20877, USA. petersed@mail.nih.gov

BMC Genomics
|May 7, 2005
PubMed
Summary

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

Male Hypogonadism and Lower Urinary Tract Symptoms: Testicular Volume as an Independent Predictor.

International neurourology journal·2026
Same author

Human Epidermal Growth Factor Receptor 2 Quantification Using Computational Pathology to Identify Novel Biomarkers for Trastuzumab Deruxtecan-Treated Human Epidermal Growth Factor Receptor 2-Positive Gastric Cancer.

JCO precision oncology·2026
Same author

A randomized, double-blind, controlled, parallel group study with amustaline/glutathione pathogen reduced red blood cells in regions at potential risk for Zika virus transfusion-transmitted infections (RedeS Study)-protocol for a phase 3 clinical trial.

Trials·2026
Same author

Impact of Androgen Deprivation Therapy on Lower Urinary Tract Symptoms in Patients with Prostate Cancer.

Medicina (Kaunas, Lithuania)·2026
Same author

H&E-based MSI/MMR testing with AI in colorectal cancer: a multi-centred blinded evaluation.

NPJ digital medicine·2025
Same author

Where are all the job candidates?: geographic considerations for early career librarian recruitment in health sciences libraries.

Medical reference services quarterly·2025

Long oligonucleotide arrays offer reliable gene expression analysis, comparable to short oligonucleotide and cDNA platforms. These methods provide reproducible results, especially when focusing on the direction of gene expression changes.

Area of Science:

  • Genomics
  • Molecular Biology
  • Bioinformatics

Background:

  • Gene expression analysis utilizes short oligonucleotide, long oligonucleotide, and cDNA microarrays.
  • Long oligonucleotide platforms are increasingly adopted, potentially supplanting cDNA arrays.
  • A validation study compared expression profiles across these three microarray formats.

Purpose of the Study:

  • To compare and contrast gene expression profiles generated by short oligonucleotide, long oligonucleotide, and cDNA microarray platforms.
  • To validate the performance of long oligonucleotide arrays for gene expression analysis.
  • To assess the reproducibility and comparability of results across different microarray formats.

Main Methods:

  • Testing RNA from six distinct cell lines against a universal reference standard.

Related Experiment Videos

  • Utilizing three microarray formats: short oligonucleotide, long oligonucleotide, and cDNA.
  • Analyzing gene expression data through scatter plot analysis, principal component analysis, and quantitative RT-PCR.

    • Main Results:

    • A common set of 6430 genes was identified across all three platforms.
    • High correlation (r values 0.7-0.8) was observed in gene expression levels between platforms.
    • Agreement was very high (93%-100%) for significant expression changes (p<0.05, 1.5-2 fold change).

    Conclusions:

    • The long oligonucleotide platform is highly suitable and performs favorably compared to cDNA and short oligonucleotide arrays.
    • All three platforms yield similar and reproducible gene expression results.
    • Reproducibility is high when focusing on the direction of gene expression change rather than the magnitude.