DSGeo: software tools for cross-platform analysis of gene expression data in GEO

Area of Science:

• Bioinformatics
• Genomics
• Data Science

Background:

• The Gene Expression Omnibus (GEO) is a vast public repository for gene expression data.
• Existing GEO tools offer browsing and retrieval but lack comprehensive cross-study aggregation and analysis capabilities.

Purpose of the Study:

• To introduce DSGeo, a suite of tools designed to overcome limitations in analyzing public gene expression data.
• To enable annotation, aggregation, integration, and analysis of data from the Gene Expression Omnibus.

Main Methods:

• DSGeo comprises a Relational Database, Data Loader, Data Browser, and Expression Combiner and Analyzer.
• The system allows querying samples by characteristics and identifying relevant studies.
• Data normalization, aggregation, and filtering are performed by the Expression Combiner.

Main Results:

• DSGeo provides a unified platform for accessing and analyzing annotated, cross-platform gene expression data.
• The Expression Analyzer enables straightforward statistical comparisons between data groups.
• Users can efficiently query, combine, and analyze data based on specific criteria.

Conclusions:

• DSGeo significantly enhances the utility of the Gene Expression Omnibus for researchers.
• The integrated toolset streamlines the process of cross-study gene expression data analysis.
• DSGeo facilitates deeper insights from public gene expression datasets.