geo-database

GEO Database

Overview

The Gene Expression Omnibus (GEO) is NCBI's public repository for high-throughput gene expression and functional genomics data. GEO contains over 264,000 studies with more than 8 million samples from both array-based and sequence-based experiments.

When to Use This Skill

This skill should be used when searching for gene expression datasets, retrieving experimental data, downloading raw and processed files, querying expression profiles, or integrating GEO data into computational analysis workflows.

Core Capabilities

1. Understanding GEO Data Organization

GEO organizes data hierarchically using different accession types:

Series (GSE): A complete experiment with a set of related samples

• Example: GSE123456
• Contains experimental design, samples, and overall study information
• Largest organizational unit in GEO
• Current count: 264,928+ series

Sample (GSM): A single experimental sample or biological replicate

• Example: GSM987654
• Contains individual sample data, protocols, and metadata
• Linked to platforms and series
• Current count: 8,068,632+ samples

Platform (GPL): The microarray or sequencing platform used

• Example: GPL570 (Affymetrix Human Genome U133 Plus 2.0 Array)
• Describes the technology and probe/feature annotations
• Shared across multiple experiments
• Current count: 27,739+ platforms

DataSet (GDS): Curated collections with consistent formatting

• Example: GDS5678
• Experimentally-comparable samples organized by study design
• Processed for differential analysis
• Subset of GEO data (4,348 curated datasets)
• Ideal for quick comparative analyses

Profiles: Gene-specific expression data linked to sequence features

• Queryable by gene name or annotation
• Cross-references to Entrez Gene
• Enables gene-centric searches across all studies

2. Searching GEO Data

GEO DataSets Search:

Search for studies by keywords, organism, or experimental conditions:

from Bio import Entrez

# Configure Entrez (required)
Entrez.email = "[email protected]"

# Search for datasets
def search_geo_datasets(query, retmax=20):
    """Search GEO DataSets database"""
    handle = Entrez.esearch(
        db="gds",
        term=query,
        retmax=retmax,
        usehistory="y"
    )
    results = Entrez.read(handle)
    handle.close()
    return results

# Example searches
results = search_geo_datasets("breast cancer[MeSH] AND Homo sapiens[Organism]")
print(f"Found {results['Count']} datasets")

# Search by specific platform
results = search_geo_datasets("GPL570[Accession]")

# Search by study type
results = search_geo_datasets("expression profiling by array[DataSet Type]")