CNA2Subpathway

CNA2Subpathway identifies subpathways dysregulated by copy number alterations (CNAs) in cancer by integrating multi-omics data and pathway topology in a network-based analysis.

Key Features:

• Integration of Multi-Omics Data: Utilizes high-throughput sequencing–derived multi-omics datasets to link CNAs with subpathway dysfunction.
• Pathway Topology Information: Incorporates pathway topology to evaluate the positional and interaction effects of altered genes within pathways.
• Subpathway Crosstalk Analysis: Accounts for interactions between subpathways to capture network-level crosstalk in dysregulation.
• Network-Based Approach: Applies a network-based computational framework to integrate topology, multi-omics signals, and subpathway crosstalk.
• Validation and Comparative Evaluation: Validated on breast cancer and head and neck cancer datasets and compared with five other pathway or subpathway analysis methods.
• Implementation: Implemented as an R package.

Scientific Applications:

• Subpathway discovery in cancer: Identification of dysfunctional subpathways associated with cancer development and progression.
• Immune-related pathway analysis: Detection of subpathways linked to cancer immune response.
• Prognostic association: Association of dysregulated subpathways with patient prognosis for potential prognostic assessment.
• Tumor-type validation: Application and validation in breast cancer and head and neck cancer datasets.

Methodology:

Uses a network-based method that integrates pathway topology, multi-omics data, and subpathway (SP) crosstalk to identify subpathways dysregulated by CNAs.