tRFexplorer

tRFexplorer catalogs tRNA-derived non-coding RNAs (tRF-5s, tRF-3s, tsRNAs, and tRNA 5' leader RNAs) across the NCI-60 cell line panel and TCGA tumor types to support expression profiling, differential expression, and correlation analyses with gene/miRNA expression and CellMiner compound-activity data.

Key Features:

• Extensive dataset: Contains 322 distinct tRNA-derived ncRNAs identified in the NCI-60 cell line panel and 232 distinct tRNA-derived ncRNAs identified in TCGA, each classified as tRF-5s, tRF-3s, tsRNAs, or tRNA 5' leader RNAs.
• Expression profiling: Provides expression profiles of each tRNA-derived ncRNA across all NCI-60 cell lines and across TCGA tumor types.
• Differential expression analysis: Supports differential expression comparisons of tRNA-derived ncRNAs within the TCGA dataset.
• Correlation analyses: Enables correlation of tRNA-derived ncRNA expression with gene expression, miRNA expression, and compound activities, using TCGA, NCI-60, and CellMiner data.
• Integration with omics and compound-activity data: Integrates tRNA-derived ncRNA data with omics layers and CellMiner compound-activity data to investigate potential molecular associations.

Scientific Applications:

• Non-coding RNA characterization: Characterize and classify tRNA-derived ncRNAs across cell lines and tumor types.
• Cancer research: Investigate associations between tRNA-derived ncRNA expression and cancer-related molecular profiles in TCGA and NCI-60.
• Molecular association discovery: Explore relationships between tRNA-derived ncRNAs and gene/miRNA expression or compound activities (CellMiner) to generate hypotheses about biological roles.

Methodology:

tRNA-derived ncRNAs were identified and characterized using next-generation sequencing of NCI-60 cell lines and TCGA samples, and the resource supports differential expression and correlation analyses with gene, miRNA, and CellMiner compound-activity data.