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DNA Microarrays

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...

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Related Experiment Video

Updated: Jun 13, 2026

Performing Custom MicroRNA Microarray Experiments

Performing Custom MicroRNA Microarray Experiments

Published on: October 28, 2011

Shared probe design and existing microarray reanalysis using PICKY.

Hui-Hsien Chou¹

¹Department of Genetics, Development and Cell Biology, and Department of Computer Science, Iowa State University, Ames, IA, 50011-3223, USA. hhchou@iastate.edu

BMC Bioinformatics

|April 22, 2010

Summary

This summary is machine-generated.

PICKY 2.1 software designs shared probes for gene families and reanalyzes existing microarray probes against updated gene sets, improving gene detection and data interpretation.

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Performing Custom MicroRNA Microarray Experiments

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DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

DNA Microarrays: Sample Quality Control, Array Hybridization and Scanning

Published on: March 15, 2011

Area of Science:

Genomics
Bioinformatics
Molecular Biology

Background:

Microarray probe design faces limitations in identifying highly similar genes within large genomes due to thermodynamic constraints.
Gene annotations are frequently updated, necessitating reanalysis of existing microarrays to ensure probe validity.

Purpose of the Study:

To develop a computational method for designing shared probes to detect gene families.
To enable reanalysis of existing microarray probes against updated gene annotations.
To improve the precision and versatility of microarray analysis.

Main Methods:

Utilized novel algorithms in PICKY 2.0 to identify and design shared probes for gene families by tracking sharable regions.
Implemented thermodynamic comparisons to distinguish target regions from highly similar non-target regions.
Integrated a probe reanalysis function and enhanced nonlinear salt effect calculations in PICKY 2.1.

Main Results:

PICKY 2.0 successfully designed shared probes for gene sets that are difficult to identify with unique probes.
PICKY 2.1 can reanalyze existing microarray probes against updated gene sets, identifying valid probes.
Improved nonlinear salt effect estimates enhance probe precision at lower salt concentrations.

Conclusions:

Shared probes facilitate the detection of expressed gene family members and enable cross-genome microarray design for applications like environmental sample analysis.
The probe reanalysis function enhances the interpretation of existing microarray results.
PICKY 2.1 offers increased versatility and precision for microarray users.