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 Concept Videos

DNA Microarrays02:34

DNA Microarrays

Microarrays are high-throughput and relatively inexpensive assays that can be automated to analyze large quantities of data at a time. They are used in genome-wide studies to compare gene or protein expression under two varied conditions, such as healthy and diseased states. Microarrays consist of glass or silica slides on which probe molecules are covalently attached through surface functionalization. Most commonly, the slides are prepared through the chemisorption of silanes to silica...

You might also read

Related Articles

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

Sort by
Same author

Intra-Exon Motif Correlations as a Proxy Measure for Mean Per-Tile Sequence Quality Data in RNA-Seq.

Journal of computational biology : a journal of computational molecular cell biology·2023
Same author

Projected expansion of Trichodesmium's geographical distribution and increase in growth potential in response to climate change.

Global change biology·2020
Same author

The application of Hadoop in structural bioinformatics.

Briefings in bioinformatics·2018
Same author

A Novel Method to Detect Bias in Short Read NGS Data.

Journal of integrative bioinformatics·2017
Same author

Crowdsourced direct-to-consumer genomic analysis of a family quartet.

BMC genomics·2015
Same author

The roles of cross-talk epigenetic patterns in Arabidopsis thaliana.

Briefings in functional genomics·2015
Same journal

Correction to 'New origin firing is inhibited by APC/CCdh1 activation in S-phase after severe replication stress'.

Nucleic acids research·2026
Same journal

VeloRM: disentangling pre- and post-splicing RNA modification dynamics at single-cell resolution.

Nucleic acids research·2026
Same journal

Accessibility of telomeric overhangs to stabilizing small-molecule ligands.

Nucleic acids research·2026
Same journal

Multivalent interactions mediate SNAIL transcription factor stimulation of the nucleosome deacetylase activity of the CoREST complex.

Nucleic acids research·2026
Same journal

Genome-wide mapping of DNA G-quadruplexes in Trypanosoma brucei chromatin reveals enrichment in coding regions and transcription start sites.

Nucleic acids research·2026
Same journal

Correction to 'The Gene Ontology knowledgebase in 2026'.

Nucleic acids research·2026
See all related articles

Related Experiment Video

Updated: May 26, 2026

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

Normalized Affymetrix expression data are biased by G-quadruplex formation.

Hugh P Shanahan1, Farhat N Memon, Graham J G Upton

  • 1Department of Computer Science, Royal Holloway, University of London, Egham, Surrey, TW20 0EX, UK. Hugh.Shanahan@rhul.ac.uk

Nucleic Acids Research
|December 27, 2011
PubMed
Summary
This summary is machine-generated.

Microarray probes containing guanine-rich sequences (G-stacks) can form G-quadruplexes, leading to biased gene expression data. Removing these probes improves data accuracy, even with increased noise.

More Related Videos

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform
13:14

Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform

Published on: August 10, 2009

Related Experiment Videos

Last Updated: May 26, 2026

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes
05:37

Single-Molecule Fluorescence Visualization of DNA Polymerase Dynamics at G-Quadruplexes

Published on: April 4, 2025

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations
10:17

An Allele-specific Gene Expression Assay to Test the Functional Basis of Genetic Associations

Published on: November 3, 2010

Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform
13:14

Global Gene Expression Analysis Using a Zebrafish Oligonucleotide Microarray Platform

Published on: August 10, 2009

Area of Science:

  • Genomics
  • Bioinformatics
  • Molecular Biology

Background:

  • Microarray analysis relies on accurate gene expression measurement.
  • Probes with G-rich sequences (G-stacks) can form G-quadruplex structures.
  • G-quadruplex formation can interfere with probe hybridization and data interpretation.

Purpose of the Study:

  • To investigate the impact of G-stack probes on microarray data quality.
  • To quantify the bias introduced by G-quadruplex-forming probes.
  • To evaluate normalization methods for mitigating G-stack probe bias.

Main Methods:

  • Analysis of a Human HG_U133A Affymetrix GeneChip dataset.
  • Application of Robust Multi-array Average (RMA) normalization.
  • Comparison with FARMS and PLIER normalization pipelines.
  • Assessment of bias in expression levels, fold change, and gene correlations.

Main Results:

  • G-stack probes introduce significant bias in expression levels, fold change, and correlations.
  • Bias increases with the number of G-stack probes per probe set.
  • Approximately 14% of probe sets were directly affected in the analyzed dataset.
  • FARMS and PLIER normalization methods partially reduced the observed bias.
  • An estimated 15% of GEO database datasets may be susceptible to this bias.

Conclusions:

  • G-stack probes pose a significant challenge to the accuracy of microarray data analysis.
  • The presence of G-stack probes can lead to erroneous gene selection and clustering.
  • Eliminating G-stack probes is recommended for affected datasets, as benefits outweigh potential noise increase.