OncoDB

OncoDB integrates RNA sequencing (RNA-seq), DNA methylation, and clinical data from TCGA and GTEx to enable analysis of oncovirus associations with host gene expression and clinical outcomes in cancer.

Key Features:

• Comprehensive Data Integration: Consolidates RNA sequencing (RNA-seq), DNA methylation, and clinical information from over 10,000 cancer patients in TCGA together with normal tissue data from GTEx to support integrated multi-omics analyses.
• Focus on Oncoviruses: Identifies and correlates six major oncoviruses across various cancer types to link viral infections with alterations in host gene expression and clinical outcomes.
• Clinical Correlation: Correlates abnormal gene expression patterns and viral infection status with clinical features to support investigation of molecular mechanisms and potential therapeutic targets.

Scientific Applications:

• Multi-omics cancer characterization: Uses TCGA RNA-seq and DNA methylation data with GTEx normal tissue data to characterize tumor molecular profiles.
• Oncovirus–host interaction analysis: Analyzes associations between six major oncoviruses and host gene expression changes across cancer types using RNA-seq data.
• Biomarker discovery: Identifies gene expression and DNA methylation patterns associated with viral infection and clinical outcomes to support discovery of diagnostic, prognostic, and therapeutic biomarkers.
• Clinical association studies: Correlates molecular alterations and viral status with clinical features to investigate prognosis and therapeutic implications.

Methodology:

Mines TCGA RNA-seq data to identify oncoviruses and their impact on host gene expression and integrates those findings with DNA methylation and clinical datasets.