CONTOURv1

CONTOURv1 tracks dysregulated functional modules in cancer by comparing protein-protein interaction (PPI) complexes, pathways, gene-expression profiles, and mutation data to identify genes and module behaviors associated with cancer progression.

Key Features:

• Systematic identification and comparison: Tracks and contrasts core modules such as PPI complexes and pathways between normal and cancerous tissue conditions.
• Integration of multi-omics data: Integrates PPI networks, gene-expression profiles, and mutation data for combined analysis of module behavior.
• Pattern recognition in gene composition and expression correlations: Detects changes in gene membership and co-expression within modules that indicate impairment or strengthening of functions such as DNA damage repair.
• Identification of novel cancer genes linked to copy-number alterations: Reports genes implicated in cancer susceptibility to copy-number alterations, including USP15 (pancreatic cancer and glioblastoma) and YWHAE, DISC1, TRIM5, NCOA6 (BRCA1 and BRCA2 breast tumors).
• Insight into compensatory mechanisms: Reveals compensatory module-level mechanisms such as recruitment of tumor inducers (e.g., SOX2) and switches in transcriptional regulation.

Scientific Applications:

• Cancer genomics research: Elucidates module-level dysregulation and candidate genes for studies of cancer biology across tissues and subtypes.
• Therapeutic target identification: Highlights genes and module perturbations related to genome stability and DNA damage repair that may inform target selection.
• Cross-cancer and subtype comparisons: Enables comparative analysis of module dynamics across cancer types and within subtypes such as BRCA1 versus BRCA2 tumors.

Methodology:

Systematically tracks core modules across conditions by integrating PPI networks, gene-expression profiles, and mutation data and analyzing changes in gene composition and expression correlations.