ARGEOS

ARGEOS performs systematic searches and retrieval of microarray, RNA-seq, methylation, and CHIP-seq datasets from Gene Expression Omnibus (GEO) and ArrayExpress to support secondary transcriptome and genomic analyses.

Key Features:

• Systematic search across GEO and ArrayExpress: Queries Gene Expression Omnibus (GEO) and ArrayExpress to collect unique datasets relevant to specific research queries.
• Concurrent request handling: Supports submission and simultaneous processing of multiple search requests.
• Modifiable search requests: Allows modification of submitted search requests to refine dataset retrieval.
• Dataset metadata extraction: Retrieves detailed dataset information including experimental protocols, dataset counts, and raw data availability.
• Support for multiple data types: Targets microarray, RNA-seq, methylation profiles, and CHIP-seq datasets.
• Structured output format: Produces output formatted to minimize additional information processing for downstream analysis.

Scientific Applications:

• Secondary transcriptome and genomic analyses: Enables reanalysis and validation of existing microarray and RNA-seq datasets to generate new insights or corroborate findings.
• Studies of cell polarization and intracellular signaling: Facilitates systematic retrieval of transcriptome datasets related to activated/polarized cells triggered by immune stimuli.

Methodology:

Performs systematic searches across GEO and ArrayExpress, supports concurrent submission and modification of multiple search requests, retrieves dataset metadata (experimental protocols, dataset/sample counts, raw data availability), and outputs structured results for microarray, RNA-seq, methylation, and CHIP-seq datasets.