COSMOS

COSMOS integrates phosphoproteomics, transcriptomics, and metabolomics with prior knowledge of signaling pathways, metabolic networks, and gene regulation to extract mechanistic hypotheses and estimate transcription factor and kinase activities.

Key Features:

• Integration of Multi-Omics Data: Combines phosphoproteomics, transcriptomics, and metabolomics to provide a holistic view of molecular interactions.
• Mechanistic Hypothesis Generation: Estimates transcription factor and kinase activities and performs network-level causal reasoning to produce mechanistic explanations.
• Prior Knowledge Utilization: Incorporates extensive databases on signaling pathways, metabolic networks, and gene regulation to inform inference.

Scientific Applications:

• Mechanistic insight generation: Derives mechanistic hypotheses from complex multi-omics datasets.
• Comparative tissue analysis: Applied to datasets from healthy and cancerous tissues, including renal cell carcinoma.
• Hypothesis example — Androgen Receptor: Identified potential impacts of the Androgen Receptor on nucleoside metabolism.
• Hypothesis example — JAK-STAT pathway: Identified potential influences of the JAK-STAT pathway on propionyl coenzyme A production.

Methodology:

Integrates multi-omics data with prior biological knowledge to estimate molecular activities (transcription factors and kinases) and applies network-level causal reasoning.