ABSTRACT

Transfer RNA-derived fragments (tRFs) are a new class of small non-coding RNAs whose biological roles in cancers are not well understood. Emerging evidence suggests that tRFs are involved in gene regulation at multiple levels. In this study, we constructed an integrative database, OncotRF (http://bioinformatics.zju.edu.cn/OncotRF), for in silico exploration of tRF functions, and identification of diagnostic and prognostic biomarkers in cancers. The database contains an analysis pipeline for tRF identification and characterization, analysis results of 11,211 small RNA sequencing samples and 8,776 RNA sequencing samples, and clinicopathologic annotation data from The Cancer Genome Atlas (TCGA). The results include: tRF identification and quantification across 33 cancers, abnormally expressed tRFs and genes, tRF-gene correlations, tRF-gene networks, survival analyses, and tRF-related functional enrichment analyses. Users are also able to identify differentially expressed tRFs, predict their functions, and assess the relevance of the tRF expression levels to the clinical outcome according to user-defined groups. Additionally, an online Kaplan-Meier plotter is available in OncotRF for plotting survival curves according to user-defined groups. OncotRF will be a valuable online database and functional annotation tool for researchers studying the roles, functions, and mechanisms of tRFs in human cancers.

摘要

转移RNA衍生片段（tRF）是一类新的小型非编码RNA，其在癌症中的生物学作用尚未得到很好的了解。新兴证据表明，tRFs在多个水平上参与基因调控。在这项研究中，我们构建了一个完整的数据库OncotRF（http://bioinformatics.zju.edu.cn/OncotRF），用于tRF功能的计算机分析以及鉴定癌症的诊断和预后生物标记。该数据库包含用于tRF鉴定和表征的分析管道，11,211个小RNA测序样品和8,776个RNA测序样品的分析结果，以及来自癌症基因组图谱（TCGA）的临床病理注释数据。结果包括：跨越33个区域的tRF鉴定和定量癌症，异常表达的tRF和基因，tRF基因相关性，tRF基因网络，生存率分析以及与tRF相关的功能性富集分析。用户还能够根据用户定义的组识别差异表达的tRF，预测其功能并评估tRF表达水平与临床结果的相关性。此外，OncotRF中提供了在线Kaplan-Meier绘图仪，可根据用户定义的组绘制生存曲线。OncotRF将成为研究人员研究tRF在人类癌症中的作用，功能和机制的重要在线数据库和功能注释工具。