OncotRF

OncotRF provides an integrated database and analysis resource for transfer RNA-derived fragments (tRFs) in human cancers, enabling identification, quantification, functional annotation, expression and correlation analyses, survival assessment, and functional enrichment to support biomarker and regulatory studies.

Key Features:

• Extensive Data Repository: Contains 11,211 small RNA sequencing samples and 8,776 RNA sequencing samples with clinicopathologic annotation data sourced from The Cancer Genome Atlas (TCGA).
• tRF Identification and Quantification: Identification and quantification of tRFs across 33 different cancer types.
• Expression Analysis: Analysis of abnormally expressed tRFs and associated gene expression across cancers.
• Correlation Networks: tRF–gene correlation analysis and construction of tRF–gene networks.
• Survival Analysis (Kaplan–Meier): Survival analyses including Kaplan–Meier plotting to assess clinical associations of tRF expression levels.
• Functional Enrichment: Functional enrichment analyses to predict biological roles and mechanisms of tRFs.
• Characterization and Functional Annotation: Integrated characterization and functional annotation of tRFs in cancer contexts.

Scientific Applications:

• Regulatory Function Analysis: Investigation of the regulatory roles of tRFs in cancer biology via expression and correlation studies.
• Biomarker Discovery: Identification of differentially expressed tRFs and evaluation of their diagnostic and prognostic potential.
• Integrative Clinical Research: Integration of tRF and gene expression data with TCGA clinicopathologic annotations for translational studies.

Methodology:

Implements an analysis pipeline using bioinformatics tools for tRF identification and quantification from small RNA-seq and RNA-seq data, expression analysis, tRF–gene correlation and network construction, Kaplan–Meier survival analysis, and functional enrichment.