cmirC

cmirC provides insights into clustered miRNAs and their relationship with copy number variations and DNA methylation in cancer.

Key Features:

• Copy Number Variation Analysis: Identifies CNV-driven clustered miRNAs in cancer.
• DNA Methylation Analysis: Determines the impact of changes in DNA methylation status at clustered miRNAs using TCGA cancer datasets.
• Differential Expression Analysis: Identifies significantly upregulated clustered miRNAs across multiple cancer types.
• Integrated Multi-omics Data: Examines methylation datasets from 9,639 samples, pinpointing 215,435 methylation sites and 27,949 CpG islands with miRNA cluster information.
• Promoter Region Analysis: Identifies CpG islands in promoter regions of miRNA clusters with potential regulatory roles.
• Clustered miRNA Target Information: Provides information on regulation of clustered miRNA expression and their targeted oncogenes and tumor suppressors.

Scientific Applications:

• Cancer Progression Research: Explores miRNA expression patterns and identifies regulatory mechanisms associated with cancer progression.
• Epigenetic Regulation Studies: Investigates crosstalk between genetic and epigenetic mechanisms controlling differential expression of clustered miRNAs.
• Multi-cancer Analysis: Analyzes 17 cancer types for significantly upregulated clustered miRNAs including mir-96, mir-183, and mir-21.
• Differential Methylation Profiling: Identifies clusters exhibiting differentially methylated CpG sites across 14 cancer types.

Methodology:

cmirC utilizes The Cancer Genomic Atlas (TCGA) cancer datasets to analyze DNA methylation status at clustered miRNAs and identifies copy number variation-driven clustered miRNAs.