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. 2025 Jan 6;53(D1):D147-D156.
doi: 10.1093/nar/gkae1072.

miRTarBase 2025: updates to the collection of experimentally validated microRNA-target interactions

Shidong Cui  1   2 , Sicong Yu  1   2 , Hsi-Yuan Huang  1   2 , Yang-Chi-Dung Lin  1   2 , Yixian Huang  1   2 , Bojian Zhang  1   2 , Jihan Xiao  1   2 , Huali Zuo  1   2 , Jiayi Wang  3 , Zhuoran Li  1   2 , Guanghao Li  2 , Jiajun Ma  1   2 , Baiming Chen  1   2 , Haoxuan Zhang  1   2 , Jiehui Fu  1   2 , Liang Wang  3 , Hsien-Da Huang  1   2   4   5
Affiliations

miRTarBase 2025: updates to the collection of experimentally validated microRNA-target interactions

Shidong Cui et al. Nucleic Acids Res. .

Abstract

MicroRNAs (miRNAs) are small non-coding RNAs (18-26 nucleotides) that regulate gene expression by interacting with target mRNAs, affecting various physiological and pathological processes. miRTarBase, a database of experimentally validated miRNA-target interactions (MTIs), now features over 3 817 550 validated MTIs from 13 690 articles, significantly expanding its previous version. The updated database includes miRNA interactions with therapeutic agents, revealing roles in drug resistance and therapeutic strategies. It also highlights miRNAs as predictive, safety and monitoring biomarkers for toxicity assessment, clinical treatment guidance and therapeutic optimization. The expansion of miRNA-mRNA and miRNA-miRNA networks allows the identification of key regulatory genes and co-regulatory miRNAs, providing deeper insights into miRNA functions and critical target genes. Information on oxidized miRNA sequences has been added, shedding light on how oxidative modifications influence miRNA targeting and regulation. The integration of the LLAMA3 model into the NLP pipeline, alongside prompt engineering, enables the efficient identification of MTIs and miRNA-disease associations without large training datasets. An updated data integration and a redesigned user interface enhance accessibility, reinforcing miRTarBase as an essential resource for molecular oncology, drug development and related fields. The updated miRTarBase is available at https://mirtarbase.cuhk.edu.cn/∼miRTarBase/miRTarBase_2025.

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Figures

Graphical Abstract
Graphical Abstract
Figure 1.
Figure 1.
Highlighted improvements of miRTarBase. As the most comprehensive resource on MTIs, this update accumulates >3 817 550 manually confirmed MTIs supported with experimental evidence.
Figure 2.
Figure 2.
The complete workflow of the NLP pipeline using LLAMA3 LLM for annotating miRNA articles and aiding in manual curation.
Figure 3.
Figure 3.
The enhanced web interface of miRTarBase. More comprehensive information related to miRNA–Drug associations, drug resistance, biomarker, and oxidation modification data is now accessible with improved visualization and network analysis features.
See this image and copyright information in PMC

References

    1. Bartel D.P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell. 2004; 116:281–297. - PubMed
    1. Engels B.M., Hutvagner G.. Principles and effects of microRNA-mediated post-transcriptional gene regulation. Oncogene. 2006; 25:6163–6169. - PubMed
    1. Stroynowska-Czerwinska A., Fiszer A., Krzyzosiak W.J.. The panorama of miRNA-mediated mechanisms in mammalian cells. Cell. Mol. Life Sci. 2014; 71:2253–2270. - PMC - PubMed
    1. Bartel D.P. MicroRNAs: target recognition and regulatory functions. Cell. 2009; 136:215–233. - PMC - PubMed
    1. Shukla G.C., Singh J., Barik S.. MicroRNAs: processing, maturation, target recognition and regulatory functions. Mol. Cell Pharmacol. 2011; 3:83–92. - PMC - PubMed

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