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RummaGEO: Automatic Mining of Human and Mouse Gene Sets from GEO
Giacomo B Marino1, Daniel J B Clarke1, Eden Z Deng1
1Mount Sinai Center for Bioinformatics, Department of Pharmacological Sciences, Department of Artificial Intelligence and Human Health, Icahn School of Medicine at Mount Sinai, New York 10029, NY USA.
RummaGEO enables global data-level search of the Gene Expression Omnibus (GEO) repository. This new tool facilitates gene expression signature searches across numerous human and mouse RNA-seq studies, aiding biomedical research and hypothesis generation.
Area of Science:
- Bioinformatics
- Genomics
- Computational Biology
Background:
- The Gene Expression Omnibus (GEO) is a vast repository for transcriptomics data, but lacks data-level search capabilities.
- Existing search methods for GEO focus on metadata, limiting direct data exploration and analysis.
Conclusions:
- RummaGEO addresses the need for data-level search in the GEO repository.
- This tool enhances biomedical research by enabling efficient exploration of gene expression data.
- RummaGEO offers a valuable resource for generating new hypotheses from existing transcriptomic data.
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