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NCBI GEO: archive for gene expression and epigenomics data sets: 23-year update
Emily Clough1, Tanya Barrett1, Stephen E Wilhite1
1National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, 20892, USA.
Nucleic Acids Research
|November 7, 2023
Summary
The Gene Expression Omnibus (GEO) is a public repository for gene expression and epigenomics data. Recent advancements enhance data analysis and visualization for researchers worldwide.
Area of Science:
- Bioinformatics
- Genomics
- Molecular Biology
Background:
- The Gene Expression Omnibus (GEO) serves as a crucial international public repository for archiving gene expression and epigenomics data.
- Data submission is driven by journal and funder mandates for public accessibility, ensuring widespread data sharing.
Purpose of the Study:
- To present the current status and recent advancements of the Gene Expression Omnibus (GEO) repository.
- To highlight improvements in data processing, analysis, and visualization tools available to researchers.
Main Methods:
- Archiving raw and processed data files, along with descriptive metadata for numerous studies and samples.
- Utilizing next-generation sequencing and microarray technologies for data generation.
- Developing web-based tools for differential gene expression analysis and visualization.
Main Results:
- GEO currently archives over 200,000 studies and 6.5 million samples, all indexed, searchable, and downloadable.
- Consistent gene expression count matrices are now generated for thousands of RNA-seq studies.
- New interactive graphical plots in GEO2R facilitate identification of differentially expressed genes and data set quality assessment.
Conclusions:
- The Gene Expression Omnibus (GEO) continues to evolve, offering enhanced capabilities for accessing and analyzing large-scale biological data.
- Advancements in GEO, including improved data processing and analysis tools, support the broader scientific community in genomic research.
- The repository, maintained by NCBI and NLM, remains a vital public resource for the scientific community.
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