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

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NCBI GEO: archive for functional genomics data sets--update.

Tanya Barrett¹, Stephen E Wilhite, Pierre Ledoux

¹National Center for Biotechnology Information, National Library of Medicine and Molecular Genetics Section, Genetics Branch, National Cancer Institute, National Institutes of Health, Bethesda, MD 20892, USA. barrett@ncbi.nlm.nih.gov

Nucleic Acids Research

|November 30, 2012

Summary

This summary is machine-generated.

The Gene Expression Omnibus (GEO) is a public data repository for functional genomics. Recent updates include GEO2R, a tool to help researchers analyze GEO data.

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Introductory Analysis and Validation of CUT&RUN Sequencing Data

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Area of Science:

Bioinformatics
Genomics
Data Science

Background:

The Gene Expression Omnibus (GEO) is a vital international public repository for functional genomic datasets.
It archives high-throughput microarray and next-generation sequencing data from the research community.
The resource ensures data is indexed, cross-linked, and searchable for broad accessibility.

Purpose of the Study:

To report the current status and recent developments of the Gene Expression Omnibus (GEO) database.
To highlight new tools and strategies for data querying, analysis, and visualization.
To introduce GEO2R, an R-based web application for analyzing GEO data.

Main Methods:

The study describes the infrastructure of the GEO repository, including data archiving and metadata management.
It outlines the web-based tools and strategies available for data access and analysis.
The development and functionality of GEO2R are detailed as a key recent advancement.

Main Results:

GEO continues to serve as a comprehensive public repository for functional genomic data.
New developments enhance data accessibility, analysis, and visualization capabilities for researchers.
The release of GEO2R provides a user-friendly, R-based solution for analyzing GEO datasets.

Conclusions:

The Gene Expression Omnibus (GEO) remains a critical resource for the genomics research community.
Ongoing developments, such as GEO2R, improve the utility and analytical power of the repository.
These advancements facilitate deeper insights from functional genomic data, supporting scientific discovery.