BRM

BRM integrates microRNA (miRNA) and multi-omics datasets across multiple species to enable identifier conversion, orthologous mapping, and cross-species data integration for comparative transcriptomic and regulatory analyses.

Key Features:

• Species support: Supports identifier conversion and data integration for Homo sapiens, Mus musculus, Rattus norvegicus, Danio rerio, and Macaca mulatta.
• Identifier conversion: Performs identifier conversion across common identifier types and retrieves background identifiers to enable dataset integration across platforms and species.
• Orthologous conversion: Performs orthologous conversions to enable seamless cross-species analysis.
• miRNA-target database integration: Integrates multiple miRNA-target databases to allow queries of target genes and reverse lookups using gene identifiers.
• Simultaneous target retrieval: Retrieves miRNA targets from multiple databases concurrently and consolidates results for downstream analysis.
• Integration with experimental data: Integrates retrieved miRNA-target information with experimental mRNA and RNA sequencing data.
• Workflows: Includes workflows such as a miRNA Target workflow to aid experimental determination and prediction of miRNA regulatory roles.
• Output compatibility: Produces outputs compatible with external visualization tools for downstream interpretation.

Scientific Applications:

• BAP exposure biomarker identification: Identification of biomarkers of exposure to benzo[a]pyrene (BAP) in human lung cells and zebrafish.
• Cross-species RNA-seq integration: Integration of RNA sequencing data across species to elucidate shared biomarkers and conserved responses.
• miRNA regulatory role analysis: Determination of miRNA roles as regulators of BAP toxicity using the miRNA Target workflow and predicted miRNA-target functional consequences.
• Functional process analysis: Elucidation of miRNA impacts on processes such as cell migration, cell communication, junction assembly, and regulation of cell death in the context of BAP exposure.

Methodology:

Computational methods explicitly include identifier conversion, orthologous conversions, background identifier retrievals, simultaneous retrieval from multiple miRNA-target databases, integration with experimental mRNA and RNA-seq data, and a miRNA Target workflow; development used Java and other open-source technologies.