tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers.
tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers.
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tRF2Cancer：一个网络服务器，用于检测 tRNA 衍生的小 RNA 片段 (tRF) 及其在多种癌症中的表达
DOI：
10.1093/nar/gkw414
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发表时间：
2016-07-08
影响因子：
14.9
通讯作者：
Qu LH
中科院分区：
文献类型：
--
作者：
Zheng LL;Xu WL;Liu S;Sun WJ;Li JH;Wu J;Yang JH;Qu LH
tRNA衍生的小RNA片段（tRFs）是一类来源于转运RNA（transferRNA，tRNA）的非编码小RNA。tRF在细胞过程中发挥重要作用，并参与多种癌症。高通量小RNA（sRNA）测序实验可以检测所有细胞表达的sRNA，包括tRF。然而，区分真正的tRF和随机降解产生的RNA片段仍然是一个重大挑战。在这项研究中，我们开发了一个集成的基于网络的计算系统tRF 2Cancer，用于从sRNA深度测序数据中准确识别tRFs，并评估它们在多种癌症中的表达。引入二项式检验来评估来自小RNA-seq数据集的读数是否代表tRF或降解片段。然后使用分类方法基于它们在前tRNA或成熟tRNA中的起源位点来注释tRFs的类型。我们应用该管道分析了来自32种癌症的10991个数据集，并确定了数千个表达的tRF。开发了一种名为“tRFinCancer”的工具，以方便用户检查不同类型癌症中tRFs的表达。另一个名为“tRFBrowser”的工具显示了tRFs在其源tRNA上的起源位点和化学修饰位点的分布。tRF 2Cancer网络服务器可在http://rna.sysu.edu.cn/tRFfinder/上获得。
tRNA-derived small RNA fragments (tRFs) are one class of small non-coding RNAs derived from transfer RNAs (tRNAs). tRFs play important roles in cellular processes and are involved in multiple cancers. High-throughput small RNA (sRNA) sequencing experiments can detect all the cellular expressed sRNAs, including tRFs. However, distinguishing genuine tRFs from RNA fragments generated by random degradation remains a major challenge. In this study, we developed an integrated web-based computing system, tRF2Cancer, to accurately identify tRFs from sRNA deep-sequencing data and evaluate their expression in multiple cancers. The binomial test was introduced to evaluate whether reads from a small RNA-seq data set represent tRFs or degraded fragments. A classification method was then used to annotate the types of tRFs based on their sites of origin in pre-tRNA or mature tRNA. We applied the pipeline to analyze 10 991 data sets from 32 types of cancers and identified thousands of expressed tRFs. A tool called ‘tRFinCancer’ was developed to facilitate the users to inspect the expression of tRFs across different types of cancers. Another tool called ‘tRFBrowser’ shows both the sites of origin and the distribution of chemical modification sites in tRFs on their source tRNA. The tRF2Cancer web server is available at http://rna.sysu.edu.cn/tRFfinder/.