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Updated: Jun 6, 2026
03:08
Using Human Differentially Expressed Gene Lists to Perform Downstream Pathway Enrichment Analysis and Target Prioritization
Published on: October 3, 2025
NCBI GEO: archive for functional genomics data sets--10 years on.
Tanya Barrett1, Dennis B Troup, Stephen E Wilhite
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, 45 Center Drive, Bethesda, MD 20892, USA. barrett@ncbi.nlm.nih.gov
Nucleic Acids Research
|November 25, 2010
Summary
The Gene Expression Omnibus (GEO) database, a public repository for functional genomics data, has adapted to store diverse data types, including next-generation sequencing. It offers tools for easy data access and visualization, supporting over 20,000 studies.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- The Gene Expression Omnibus (GEO) database was established at NCBI a decade ago.
- Initially designed for microarray gene expression data, GEO's flexible structure allowed adaptation for other data types.
Purpose of the Study:
- To describe recent enhancements to the GEO database.
- To review how the research community utilizes GEO data.
- To highlight GEO's role as a public repository for functional genomics studies.
Main Methods:
- Adaptation of the GEO database to accommodate diverse functional genomics data, including microarray and next-generation sequencing.
- Development of enhanced search, browse, download, and visualization tools for users.
- Hosting over 20,000 functional genomics studies.
Main Results:
- GEO successfully adapted to store non-gene-expression microarray data (e.g., copy number variation, DNA-binding proteins).
- GEO now hosts next-generation sequencing data, reflecting the shift in research technologies.
- The database provides multiple mechanisms for effective data retrieval and analysis.
Conclusions:
- GEO has evolved into a comprehensive repository for diverse functional genomics data.
- Ongoing enhancements ensure GEO remains a valuable resource for the research community.
- GEO continues to be a primary platform for direct high-throughput data submissions.
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