Cui Shidong, Yu Sicong, Huang Hsi-Yuan, Lin Yang-Chi-Dung, Huang Yixian, Zhang Bojian, Xiao Jihan, Zuo Huali, Wang Jiayi, Li Zhuoran, Li Guanghao, Ma Jiajun, Chen Baiming, Zhang Haoxuan, Fu Jiehui, Wang Liang, Huang Hsien-Da
School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P.R. China.
Warshel Institute for Computational Biology, School of Medicine, The Chinese University of Hong Kong, Shenzhen, Guangdong 518172, P.R. China.
Nucleic Acids Res. 2025 Jan 6;53(D1):D147-D156. doi: 10.1093/nar/gkae1072.
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.
微小RNA（miRNA）是一类小的非编码RNA（18 - 26个核苷酸），通过与靶mRNA相互作用来调控基因表达，影响各种生理和病理过程。miRTarBase是一个经过实验验证的miRNA - 靶标相互作用（MTI）数据库，目前拥有来自13690篇文章的超过3817550个经过验证的MTI，相比其先前版本有了显著扩展。更新后的数据库包括miRNA与治疗药物的相互作用，揭示了其在耐药性和治疗策略中的作用。它还强调了miRNA作为预测性、安全性和监测生物标志物在毒性评估、临床治疗指导和治疗优化中的作用。miRNA - mRNA和miRNA - miRNA网络的扩展使得能够识别关键调控基因和共调控miRNA，从而更深入地了解miRNA功能和关键靶基因。已添加了氧化miRNA序列的信息，有助于了解氧化修饰如何影响miRNA的靶向和调控。将LLAMA3模型集成到自然语言处理管道中，并结合提示工程，无需大量训练数据集就能高效识别MTI和miRNA - 疾病关联。更新的数据整合和重新设计的用户界面提高了可访问性，强化了miRTarBase作为分子肿瘤学、药物开发及相关领域重要资源的地位。更新后的miRTarBase可在https://mirtarbase.cuhk.edu.cn/∼miRTarBase/miRTarBase_2025获取。
