{"status":"ok","message-type":"work","message-version":"1.0.0","message":{"indexed":{"date-parts":[[2026,1,26]],"date-time":"2026-01-26T02:29:59Z","timestamp":1769394599778,"version":"3.49.0"},"reference-count":38,"publisher":"Oxford University Press (OUP)","issue":"D1","license":[{"start":{"date-parts":[[2020,10,9]],"date-time":"2020-10-09T00:00:00Z","timestamp":1602201600000},"content-version":"vor","delay-in-days":0,"URL":"http:\/\/creativecommons.org\/licenses\/by-nc\/4.0\/"}],"funder":[{"DOI":"10.13039\/100000002","name":"National Institutes of Health","doi-asserted-by":"publisher","award":["K01AA023321"],"award-info":[{"award-number":["K01AA023321"]}],"id":[{"id":"10.13039\/100000002","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/100000001","name":"National Science Foundation","doi-asserted-by":"publisher","award":["DMS1916246"],"award-info":[{"award-number":["DMS1916246"]}],"id":[{"id":"10.13039\/100000001","id-type":"DOI","asserted-by":"publisher"}]},{"DOI":"10.13039\/501100004543","name":"China Scholarship Council","doi-asserted-by":"publisher","id":[{"id":"10.13039\/501100004543","id-type":"DOI","asserted-by":"publisher"}]},{"name":"Neil Shen's SJTU Medical Research Fund"},{"name":"SJTU-Yale Collaborative Research Seed Fund"}],"content-domain":{"domain":[],"crossmark-restriction":false},"short-container-title":[],"published-print":{"date-parts":[[2021,1,8]]},"abstract":"<jats:title>Abstract<\/jats:title><jats:p>Transfer RNA-derived fragments (tRFs) are a new class of small non-coding RNAs and play important roles in biological and physiological processes. Prediction of tRF target genes and binding sites is crucial in understanding the biological functions of tRFs in the molecular mechanisms of human diseases. We developed a publicly accessible web-based database, tRFtarget (http:\/\/trftarget.net), for tRF target prediction. It contains the computationally predicted interactions between tRFs and mRNA transcripts using the two state-of-the-art prediction tools RNAhybrid and IntaRNA, including location of the binding sites on the target, the binding region, and free energy of the binding stability with graphic illustration. tRFtarget covers 936 tRFs and 135 thousand predicted targets in eight species. It allows researchers to search either target genes by tRF IDs or tRFs by gene symbols\/transcript names. We also integrated the manually curated experimental evidence of the predicted interactions into the database. Furthermore, we provided a convenient link to the DAVID\u00ae web server to perform downstream functional pathway analysis and gene ontology annotation on the predicted target genes. This database provides useful information for the scientific community to experimentally validate tRF target genes and facilitate the investigation of the molecular functions and mechanisms of tRFs.<\/jats:p>","DOI":"10.1093\/nar\/gkaa831","type":"journal-article","created":{"date-parts":[[2020,9,17]],"date-time":"2020-09-17T19:24:43Z","timestamp":1600370683000},"page":"D254-D260","source":"Crossref","is-referenced-by-count":51,"title":["tRFtarget: a database for transfer RNA-derived fragment targets"],"prefix":"10.1093","volume":"49","author":[{"given":"Ningshan","family":"Li","sequence":"first","affiliation":[{"name":"SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China"},{"name":"Department of Biostatistics, Yale School of\u00a0Public Health, New Haven, CT 06520, USA"}]},{"given":"Nayang","family":"Shan","sequence":"additional","affiliation":[{"name":"Department of Biostatistics, Yale School of\u00a0Public Health, New Haven, CT 06520, USA"},{"name":"Center for Statistical Science, Department of Industrial Engineering, Tsinghua University, Beijing 100084, China"}]},{"ORCID":"https:\/\/orcid.org\/0000-0001-9871-0809","authenticated-orcid":false,"given":"Lingeng","family":"Lu","sequence":"additional","affiliation":[{"name":"Department of Chronic Disease Epidemiology, Yale School of Public Health, New Haven, CT 06520, USA"}]},{"ORCID":"https:\/\/orcid.org\/0000-0002-7251-3687","authenticated-orcid":false,"given":"Zuoheng","family":"Wang","sequence":"additional","affiliation":[{"name":"SJTU-Yale Joint Center for Biostatistics and Data Science, Department of Bioinformatics and Biostatistics, School of Life Sciences and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China"}]}],"member":"286","published-online":{"date-parts":[[2020,10,9]]},"reference":[{"key":"2021010313132168600_B1","doi-asserted-by":"crossref","first-page":"2639","DOI":"10.1101\/gad.1837609","article-title":"A novel class of small RNAs: tRNA-derived RNA fragments (tRFs)","volume":"23","author":"Lee","year":"2009","journal-title":"Genes Dev."},{"key":"2021010313132168600_B2","doi-asserted-by":"crossref","first-page":"679","DOI":"10.1016\/j.tibs.2016.05.004","article-title":"Biogenesis and function of transfer RNA-related fragments (tRFs)","volume":"41","author":"Kumar","year":"2016","journal-title":"Trends Biochem. 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