TCGAplot

TCGAplot provides integrative pan-cancer analysis and visualization of multi-omics data from The Cancer Genome Atlas (TCGA) to support comparative genomic, transcriptomic, epigenetic, and immune-related investigations across tumor types.

Key Features:

• Multi-Omics Data Integration: TCGAplot integrates TCGA gene expression, tumor mutational burden (TMB), microsatellite instability (MSI), tumor immune microenvironment (TIME), and methylation profiles for combined analyses.
• Pan-Cancer Analysis Capabilities: Supports analysis of commonality and heterogeneity across tumor types and performs paired and unpaired differential gene expression analyses.
• Correlation Analysis: Performs correlation analyses between gene expression and TMB, MSI, TIME, and promoter methylation.
• Visualization Tools: Generates paired and unpaired boxplots, survival plots, receiver operating characteristic (ROC) curves, heatmaps, scatter plots, radar charts, and forest plots.
• Gene Set Analysis: Conducts gene set-based pan-cancer and tumor-specific analyses using predefined gene sets.
• User-Defined Functions: Provides functions to extract built-in multi-omic data for custom computational analyses.

Scientific Applications:

• Molecular signature and biomarker identification: Identifies molecular signatures and candidate biomarkers across different cancers using multi-omic and differential expression analyses.
• Genetic and epigenetic driver investigation: Investigates genetic and epigenetic drivers of tumorigenesis via analysis of gene expression and methylation profiles.
• Immune–genomic relationship analysis: Explores relationships between genomic alterations and tumor immune responses using TMB, MSI, and TIME metrics.
• Tumor profiling for precision oncology: Enables detailed tumor profiling to inform personalized medicine approaches through integrated multi-omic characterization.

Methodology:

Implemented in R; applies statistical methods for differential expression and correlation analyses; and provides pre-built functions for common pan-cancer analyses.