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

Evaluation of the gene-specific dye bias in cDNA microarray experiments.

Marie-Laure Martin-Magniette1, Julie Aubert, Eric Cabannes

  • 1URGV UMR INRA 1165--CNRS 8114--UEVE, Evry, France. mlmartin@inapg.fr

Bioinformatics (Oxford, England)
|February 5, 2005
PubMed
Summary

Gene-specific dye bias in cDNA microarray experiments significantly impacts results, leading to false positives. A new index quantifies this bias, crucial for accurate gene expression analysis.

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

16S rRNA gene sequencing dataset describing the diversity and structure of soil bacterial communities across four pesticide-free agroecological cropping systems of arable crops from the CA-SYS experiment between 2018 and 2021.

Data in brief·2026
Same author

Integration of proxy intermediate omics traits into a nonlinear two-step model for accurate phenotypic prediction.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·2026
Same author

A new scenario of pathogen-microbiota interactions involving the oomycete Plasmopara viticola.

FEMS microbiology ecology·2025
Same author

Interlaboratory evaluation of high molecular weight DNA extraction methods for long-read sequencing and structural variant analysis.

BMC genomics·2025
Same author

Medicago truncatula genotype drives the plant nutritional strategy and its associated rhizosphere bacterial communities.

The New phytologist·2024
Same author

Global genotype by environment prediction competition reveals that diverse modeling strategies can deliver satisfactory maize yield estimates.

Genetics·2024

Area of Science:

  • Molecular Biology
  • Genomics
  • Bioinformatics

Background:

  • Dual-color cDNA microarray experiments utilize Cy3 and Cy5 labels.
  • Observed systematic and gene-specific dye biases can affect experimental conclusions.
  • Gene-specific dye bias persists after normalization, unlike systematic effects.

Purpose of the Study:

  • To address the impact of gene-specific dye bias in cDNA microarray analysis.
  • To introduce a quantitative measure for gene-specific dye bias.
  • To evaluate the consequences of dye bias on gene expression data.

Main Methods:

  • Utilized an analysis of variance (ANOVA) model to account for gene-specific dye bias.
  • Developed a 'label bias index' to quantify this bias.

Related Experiment Videos

  • Required at least two self-self hybridization cDNA microarrays for analysis.

    • Main Results:

    • Gene-specific dye bias identified as a primary source of variability between replicates post-normalization.
    • Observed R/G ratios exceeding 2, indicating substantial bias.
    • Demonstrated that dye bias can lead to false positives in direct comparisons without dye-swaps.

    Conclusions:

    • Gene-specific dye bias is a critical artifact in cDNA microarray experiments.
    • The proposed label bias index aids in identifying and quantifying this bias.
    • Accurate gene expression analysis necessitates accounting for dye bias to avoid erroneous conclusions.