CoffeeProt

CoffeeProt integrates genomics, transcriptomics, proteomics, and phenotypic trait data to construct correlation networks annotated with protein-protein interactions, subcellular localization, drug associations, eQTLs/pQTLs and GWAS co-mapping to identify genetic regulators in systems genetics studies.

Key Features:

• Correlation Network Analysis: Constructs correlation networks from transcriptomics or proteomics datasets and annotates them with protein-protein interactions, subcellular localizations, and drug associations.
• Integration of Genetic Variants: Integrates genetic variants associated with gene expression (eQTLs) and protein abundance (pQTLs) and predicts potential consequences of these variants on gene function.
• Co-mapping to Traits: Co-maps genetic variants to molecular or phenotypic traits using user-supplied data or publicly available GWAS results to identify associations with clinical traits.
• Multi-omics Integration: Combines genomics, transcriptomics, proteomics, and phenotypic trait data for systems-level analysis.

Scientific Applications:

• Systems genetics: Identification of genetic regulators by integrating multi-omics and variant data to resolve network-level relationships.
• Drug target prioritization: Linking genetic variants to drug-associated proteins to support identification of druggable targets.
• Disease mechanism and trait mapping: Associating genetic variation with clinical traits through co-mapping with GWAS and phenotypic data.
• Comparative analysis: Enabling integration and interpretation of data across species, including mice and humans.

Methodology:

Integrates multi-omics and genetic variant data; constructs correlation networks from transcriptomic or proteomic datasets; annotates networks with protein-protein interactions, subcellular localizations and drug associations; incorporates eQTLs and pQTLs and performs co-mapping of variants to molecular and phenotypic traits.