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tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers.
Nucleic Acids Res 2016; 44(W1):W185-93NA

Abstract

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/.

Authors+Show Affiliations

Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China.Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China.Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China.Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China.Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China.Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China.Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China yangjh7@mail.sysu.edu.cn.Key Laboratory of Gene Engineering of the Ministry of Education, State Key Laboratory of Biocontrol, School of Life Sciences, Sun Yat-sen University, Guangzhou 510275, P. R. China lssqlh@mail.sysu.edu.cn.

Pub Type(s)

Journal Article
Research Support, Non-U.S. Gov't

Language

eng

PubMed ID

27179031

Citation

Zheng, Ling-Ling, et al. "TRF2Cancer: a Web Server to Detect tRNA-derived Small RNA Fragments (tRFs) and Their Expression in Multiple Cancers." Nucleic Acids Research, vol. 44, no. W1, 2016, pp. W185-93.
Zheng LL, Xu WL, Liu S, et al. TRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers. Nucleic Acids Res. 2016;44(W1):W185-93.
Zheng, L. L., Xu, W. L., Liu, S., Sun, W. J., Li, J. H., Wu, J., ... Qu, L. H. (2016). TRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers. Nucleic Acids Research, 44(W1), pp. W185-93. doi:10.1093/nar/gkw414.
Zheng LL, et al. TRF2Cancer: a Web Server to Detect tRNA-derived Small RNA Fragments (tRFs) and Their Expression in Multiple Cancers. Nucleic Acids Res. 2016 07 8;44(W1):W185-93. PubMed PMID: 27179031.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - tRF2Cancer: A web server to detect tRNA-derived small RNA fragments (tRFs) and their expression in multiple cancers. AU - Zheng,Ling-Ling, AU - Xu,Wei-Lin, AU - Liu,Shun, AU - Sun,Wen-Ju, AU - Li,Jun-Hao, AU - Wu,Jie, AU - Yang,Jian-Hua, AU - Qu,Liang-Hu, Y1 - 2016/05/13/ PY - 2016/05/04/accepted PY - 2016/02/28/received PY - 2016/5/15/entrez PY - 2016/5/15/pubmed PY - 2017/6/8/medline SP - W185 EP - 93 JF - Nucleic acids research JO - Nucleic Acids Res. VL - 44 IS - W1 N2 - 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/. SN - 1362-4962 UR - https://www.unboundmedicine.com/medline/citation/27179031/tRF2Cancer:_A_web_server_to_detect_tRNA_derived_small_RNA_fragments__tRFs__and_their_expression_in_multiple_cancers_ L2 - https://academic.oup.com/nar/article-lookup/doi/10.1093/nar/gkw414 DB - PRIME DP - Unbound Medicine ER -