tRFtarget


37811890	tRFtarget 2.0: expanding the targetome landscape of transfer RNA-derived fragments. [PMID: 37811890] Ningshan Li, Siqiong Yao, Guangjun Yu, Lingeng Lu, Zuoheng Wang Abstract tRFtarget 1.0 (http://trftarget.net/) is a platform consolidating both computationally predicted and experimentally validated binding sites between transfer RNA-derived fragments (tRFs) and target genes (or transcripts) across multiple organisms. Here, we introduce a newly released version of tRFtarget 2.0, in which we integrated 6 additional tRF sources, resulting in a comprehensive collection of 2614 high-quality tRF sequences spanning across 9 species, including 1944 Homo sapiens tRFs and one newly incorporated species Rattus norvegicus. We also expanded target genes by including ribosomal RNAs, long non-coding RNAs, and coding genes >50 kb in length. The predicted binding sites have surged up to approximately 6 billion, a 20.5-fold increase than that in tRFtarget 1.0. The manually curated publications relevant to tRF targets have increased to 400 and the gene-level experimental evidence has risen to 232. tRFtarget 2.0 introduces several new features, including a web-based tool that identifies potential binding sites of tRFs in user's own datasets, integration of standardized tRF IDs, and inclusion of external links to contents within the database. Additionally, we enhanced website framework and user interface. With these improvements, tRFtarget 2.0 is more user-friendly, providing researchers a streamlined and comprehensive platform to accelerate their research progress. Nucleic Acids Res. 2024:52(D1) \| 2 Citations (from Europe PMC, 2025-03-22)
33035346	tRFtarget: a database for transfer RNA-derived fragment targets. [PMID: 33035346] Li N, Shan N, Lu L, Wang Z. Abstract 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® 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. Nucleic Acids Res. 2021:49(D1) \| 32 Citations (from Europe PMC, 2025-03-22)

tRFtarget 2.0: expanding the targetome landscape of transfer RNA-derived fragments. [PMID: 37811890]

Ningshan Li, Siqiong Yao, Guangjun Yu, Lingeng Lu, Zuoheng Wang

tRFtarget 1.0 (http://trftarget.net/) is a platform consolidating both computationally predicted and experimentally validated binding sites between transfer RNA-derived fragments (tRFs) and target genes (or transcripts) across multiple organisms. Here, we introduce a newly released version of tRFtarget 2.0, in which we integrated 6 additional tRF sources, resulting in a comprehensive collection of 2614 high-quality tRF sequences spanning across 9 species, including 1944 Homo sapiens tRFs and one newly incorporated species Rattus norvegicus. We also expanded target genes by including ribosomal RNAs, long non-coding RNAs, and coding genes >50 kb in length. The predicted binding sites have surged up to approximately 6 billion, a 20.5-fold increase than that in tRFtarget 1.0. The manually curated publications relevant to tRF targets have increased to 400 and the gene-level experimental evidence has risen to 232. tRFtarget 2.0 introduces several new features, including a web-based tool that identifies potential binding sites of tRFs in user's own datasets, integration of standardized tRF IDs, and inclusion of external links to contents within the database. Additionally, we enhanced website framework and user interface. With these improvements, tRFtarget 2.0 is more user-friendly, providing researchers a streamlined and comprehensive platform to accelerate their research progress.

Nucleic Acids Res. 2024:52(D1) | 2 Citations (from Europe PMC, 2025-03-22)

tRFtarget: a database for transfer RNA-derived fragment targets. [PMID: 33035346]

Li N, Shan N, Lu L, Wang Z.

Abstract

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® 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.

Nucleic Acids Res. 2021:49(D1) | 32 Citations (from Europe PMC, 2025-03-22)

URL:	http://trftarget.net
Full name:	Transfer RNA-derived Fragment Targets Database
Description:	tRFtarget is a relational database respect to the computational predicted binding interactions between tRFs and target transcripts for multiple organisms based on the state-of-the-art prediction tools RNAhybrid and IntaRNA.The database can provide detailed information about the binding interactions as well as an illustration of the interaction sequences. Furthermore, the database can be also searched by tRF ID, gene or transcript to get a comprehensive transcriptome-wide overview of tRF-target interactions.The database also provides experimental evidence of the predicted tRF-mRNA interactions and functional studies on tRFs based on manually curated publications. The experimental evidence are classed into 2 categories: gene level evidence and site level evidence.
Year founded:	2021
Last update:
Version:
Accessibility:	Accessible
Country/Region:	China

Data type:	RNA
Data object:	Animal
Database category:	Interaction
Major species:	Homo sapiens
Keywords:	Transfer RNA-derived fragments

University/Institution:	Shanghai Jiao Tong University
Address:	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.
City:	Shanghai
Province/State:	Shanghai
Country/Region:	China
Contact name (PI/Team):	Zuoheng Wang
Contact email (PI/Helpdesk):	zuoheng.wang@yale.edu

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Database Commons a catalog of worldwide biological databases