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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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Updated: Oct 10, 2025

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization

Published on: October 3, 2025

Pathway Enrichment Analysis of Microarray Data.

Chiara Pastrello^1,2, Yun Niu^1,2, Igor Jurisica^3,4,5,6

¹Osteoarthritis Research Program, Division of Orthopedic Surgery, Schroeder Arthritis Institute, University Health Network, Toronto, ON, Canada.

Methods in Molecular Biology (Clifton, N.J.)

|December 13, 2021

Summary

This summary is machine-generated.

This study introduces a method for annotating differential genes from microarray analyses using pathway enrichment. It utilizes pathDIP, integrating 22 pathway databases, to enhance understanding of biological phenotypes and guide experiments.

Keywords:

Database coverage Database overlap Enrichment visualization Pathway consolidation Pathway enrichment analysis Pathway orphans

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Area of Science:

Genomics
Bioinformatics
Systems Biology

Background:

Microarray analyses yield lists of differentially expressed genes requiring annotation for biological interpretation.
Pathway enrichment analysis is a common method to link gene lists to biological functions and pathways.
Selecting an appropriate pathway database is crucial for accurate enrichment analysis.

Purpose of the Study:

To present a protocol for gene annotation and pathway enrichment analysis.
To demonstrate the utility of pathDIP for comprehensive pathway analysis by integrating multiple databases.
To describe pathway visualization using GSOAP.

Main Methods:

Focus on overrepresentation analysis, a frequent type of pathway enrichment.
Utilize pathDIP, a tool integrating 22 major pathway databases for comprehensive analysis.
Employ GSOAP for visualizing enriched pathways.

Main Results:

pathDIP facilitates a more thorough pathway enrichment by consolidating data from diverse sources.
The protocol provides a structured approach to interpret gene lists from microarray experiments.
Visualization of enriched pathways aids in understanding biological context.

Conclusions:

Integrating multiple pathway databases via pathDIP enhances the depth and reliability of enrichment analysis.
This protocol offers a practical framework for researchers to annotate and interpret gene expression data.
Effective pathway analysis and visualization are key to advancing biological discovery.