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

IF 16.6 2区生物学 Q1 BIOCHEMISTRY & MOLECULAR BIOLOGY

Nucleic Acids Research Pub Date : 2024-11-23 DOI:10.1093/nar/gkae1072

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

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引用次数: 0

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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miRTarBase 2025：更新经实验验证的 microRNA-目标相互作用集合。

微RNA（miRNA）是一种小型非编码RNA（18-26个核苷酸），通过与靶mRNA相互作用来调节基因表达，影响各种生理和病理过程。更新后的数据库包括 miRNA 与治疗药物的相互作用，揭示了 miRNA 在耐药性和治疗策略中的作用。它还强调了 miRNA 作为毒性评估、临床治疗指导和治疗优化的预测性、安全性和监测生物标志物的作用。通过扩展 miRNA-mRNA 和 miRNA-miRNA 网络，可以确定关键调控基因和共调控 miRNA，从而更深入地了解 miRNA 的功能和关键靶基因。新增的氧化 miRNA 序列信息，揭示了氧化修饰如何影响 miRNA 的靶向和调控。将 LLAMA3 模型集成到 NLP 管道中，再加上提示工程，无需大量训练数据集，就能高效识别 MTI 和 miRNA 与疾病的关联。更新的数据集成和重新设计的用户界面提高了可访问性，使 miRTarBase 成为分子肿瘤学、药物开发和相关领域的重要资源。更新后的 miRTarBase 可在 https://mirtarbase.cuhk.edu.cn/∼miRTarBase/miRTarBase_2025。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Nucleic Acids Research 生物-生化与分子生物学

CiteScore

27.10

自引率

4.70%

发文量

1057

审稿时长

2 months

期刊介绍： Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.