CancerEnD

CancerEnD annotates and analyzes expressed enhancers and their associated genes across 18 cancer types by integrating TCGA and COSMIC genomic datasets to assess somatic mutations, copy number variations, gene expression, and survival associations.

Key Features:

• Data scope: Coverage of 18 distinct cancer types encompassing 8063 samples from The Cancer Genome Atlas (TCGA).
• Expressed enhancer annotation: Annotation of expressed enhancers and mapping to their associated genes.
• Copy number variation analysis: Integration and analysis of enhancer-associated copy number variations.
• Somatic mutation integration (COSMIC): Incorporation of somatic mutation data from the COSMIC repository.
• Gene expression data: Inclusion of gene expression information linked to enhancers and associated genes.
• Survival analysis (R "survival" package): Use of the R "survival" package to assess prognostic significance of enhancer copy number variations.
• Survival-associated enhancers: Identification of 1762 enhancers associated with overall survival.
• Tissue-specific prognostication: Analysis enabling tissue-specific associations between enhancer alterations and patient outcomes.

Scientific Applications:

• Enhancer deregulation and tumorigenesis: Investigating the role of enhancer perturbations in cancer development (tumorigenesis).
• Prognostic biomarker discovery: Identifying enhancer-associated biomarkers linked to overall survival for prognosis.
• Therapy stratification: Informing potential therapy customization by linking enhancer alterations to clinical outcomes.
• Diagnostic marker research: Supporting discovery of enhancer-based markers relevant to cancer diagnosis.
• Genetic variation and progression studies: Exploring interactions between somatic mutations, CNVs, and cancer progression for personalized medicine and targeted therapeutic strategies.

Methodology:

Integration of TCGA data (18 cancer types, 8063 samples) and COSMIC somatic mutation data with compiled datasets of expressed enhancers, associated genes, somatic mutations, copy number variations, and gene expression; survival analyses were performed using the R "survival" package to identify enhancers associated with overall survival (1762 enhancers reported).