ArticleDatabase : the journal of biological databases and curation2019
Identification of tRNA-derived ncRNAs in TCGA and NCI-60 panel cell lines and development of the public database tRFexplorer.
Article in Database : the journal of biological databases and curation, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Who cites it
42 citing papers in PubMed, 58 citations in OpenAlex.
- High-Throughput Sequencing Decodes tsRNA Landscapes: Insights into Cancer Biomarkers and Therapeutic Targets.International journal of molecular sciences · 2026Review
- Hidden in plain sight: illuminating the tRNA landscape by sequencing.Genome biology · 2026Review
- tsRNA's Biological Function and its Potential Application in Disease Diagnosis and Prognosis.Journal of Cancer · 2026Review
- Altered expression spectrum and target gene prediction of tRNA-derived small RNAs in clear cell renal cell carcinoma.BMC cancer · 2025Article
- Exploring the Potential of tsRNA as Biomarkers for Diagnosis and Treatment of Neurogenetic Disorders.Molecular neurobiology · 2025Review
- The role of tRNA-Derived small RNAs (tsRNAs) in pancreatic cancer and acute pancreatitis.Non-coding RNA research · 2025Review
- Research progress on the tsRNA biogenesis, function, and application in lung cancer.Non-coding RNA research · 2025Review
- ncRNA Editing: Functional Characterization and Computational Resources.Methods in molecular biology (Clifton, N.J.) · 2025Article
- Chemotherapeutic agents and leucine deprivation induce codon-biased aberrant protein production in cancer.Nucleic acids research · 2024Article
- tRNA modifications and tRNA-derived small RNAs: new insights of tRNA in human disease.Cell biology and toxicology · 2024Review
- Exploring the role of tRNA-derived small RNAs (tsRNAs) in disease: implications for HIF-1 pathway modulation.Journal of molecular medicine (Berlin, Germany) · 2024Review
- tRNA-derived small RNAs in human cancers: roles, mechanisms, and clinical application.Molecular cancer · 2024Review
- Effects of Eribulin on the RNA Content of Extracellular Vesicles Released by Metastatic Breast Cancer Cells.Cells · 2024Article
- Article
- tRFUniverse: A comprehensive resource for the interactive analyses of tRNA-derived ncRNAs in human cancer.iScience · 2024Article
- tRFtarget 2.0: expanding the targetome landscape of transfer RNA-derived fragments.Nucleic acids research · 2024Article
- The Emerging Function and Promise of tRNA-Derived Small RNAs in Cancer.Journal of Cancer · 2024Review
- Small Non-Coding RNAs in Soft-Tissue Sarcomas: State of the Art and Future Directions.Molecular cancer research : MCR · 2023Review
- An old friend with a new face: tRNA-derived small RNAs with big regulatory potential in cancer biology.British journal of cancer · 2023Review
- The role and mechanism of action of tRNA-derived fragments in the diagnosis and treatment of malignant tumors.Cell communication and signaling : CCS · 2023Review
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Authors and funding
8 authors at 3 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Next-generation sequencing is increasing our understanding and knowledge of non-coding RNAs (ncRNAs), elucidating their roles in molecular mechanisms and processes such as cell growth and development. Within such a class, tRNA-derived ncRNAs have been recently associated with gene expression regulation in cancer progression. In this paper, we characterize, for the first time, tRNA-derived ncRNAs in NCI-60. Furthermore, we assess their expression profile in The Cancer Genome Atlas (TCGA). Our comprehensive analysis allowed us to report 322 distinct tRNA-derived ncRNAs in NCI-60, categorized in tRNA-derived fragments (11 tRF-5s, 55 tRF-3s), tRNA-derived small RNAs (107 tsRNAs) and tRNA 5' leader RNAs (149 sequences identified). In TCGA, we were able to identify 232 distinct tRNA-derived ncRNAs categorized in 53 tRF-5s, 58 tRF-3s, 63 tsRNAs and 58 5' leader RNAs. This latter group represents an additional evidence of tRNA-derived ncRNAs originating from the 5' leader region of precursor tRNA. We developed a public database, tRFexplorer, which provides users with the expression profile of each tRNA-derived ncRNAs in every cell line in NCI-60 as well as for each TCGA tumor type. Moreover, the system allows us to perform differential expression analyses of such fragments in TCGA, as well as correlation analyses of tRNA-derived ncRNAs expression in TCGA and NCI-60 with gene and miRNA expression in TCGA samples, in association with all omics and compound activities data available on CellMiner. Hence, the tool provides an important opportunity to investigate their potential biological roles in absence of any direct experimental evidence. Database URL: https://trfexplorer.cloud/.
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