THInCR

THInCR analyzes TCGA genomic, epigenomic, and transcriptomic data to investigate the molecular effects of human papillomaviruses (HPVs) in cervical squamous cell carcinoma (CESC) and head and neck squamous cell carcinoma (HNSC).

Key Features:

• Data Utilization: Uses TCGA genomic, epigenomic, and transcriptomic datasets from thousands of primary human cancer samples to compare HPV-positive cancers with HPV-negative counterparts and adjacent normal tissues.
• Gene Expression Analysis: Examines cellular mRNA and microRNA expression and correlates host gene expression with HPV gene activity.
• Epigenetic Insights: Analyzes altered gene DNA methylation patterns associated with HPV infection.
• Patient Survival Correlations: Correlates gene expression and epigenetic changes with patient survival data.
• Immune Landscape Analysis: Analyzes immune features including leukocyte infiltration, interferon gamma response, and T cell responses in HPV-associated cancers.

Scientific Applications:

• Validation of in vitro findings: Validate in vitro observations with large-scale TCGA clinical data for HPV-associated cancers.
• Hypothesis generation: Generate hypotheses about virus-mediated alterations in cell growth, behavior, and gene expression.
• Target identification: Identify candidate target genes that may be pivotal in HPV-dependent cancers.
• Host–virus interaction analysis: Analyze the interplay between HPV infection and host cellular mechanisms.

Methodology:

Performs analyses on TCGA genomic, epigenomic, and transcriptomic data including mRNA and microRNA expression profiling, DNA methylation analysis, correlation of molecular features with HPV gene activity, correlation with patient survival, and analysis of immune features such as leukocyte infiltration, interferon gamma response, and T cell responses, comparing HPV-positive versus HPV-negative and adjacent normal samples.