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LncACTdb 3.0：一个经过实验验证的 ceRNA 相互作用和有助于精准医学的个性化网络的更新数据库。

LncACTdb 3.0: an updated database of experimentally supported ceRNA interactions and personalized networks contributing to precision medicine.

机构信息

College of Bioinformatics Science and Technology, Harbin Medical University, Harbin 150081, China.

Department of Gynecology, the First Affiliated Hospital of Harbin Medical University, Harbin 150081, China.

出版信息

Nucleic Acids Res. 2022 Jan 7;50(D1):D183-D189. doi: 10.1093/nar/gkab1092.

DOI:10.1093/nar/gkab1092
PMID:34850125
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC8728196/
Abstract

LncACTdb 3.0 is a comprehensive database of experimentally supported interactions among competing endogenous RNA (ceRNA) and the corresponding personalized networks contributing to precision medicine. LncACTdb 3.0 is freely available at http://bio-bigdata.hrbmu.edu.cn/LncACTdb or http://www.bio-bigdata.net/LncACTdb. We have updated the LncACTdb 3.0 database with several new features, including (i) 5669 experimentally validated ceRNA interactions across 25 species and 537 diseases/phenotypes through manual curation of published literature, (ii) personalized ceRNA interactions and networks for 16 228 patients from 62 datasets in TCGA and GEO, (iii) sub-cellular and extracellular vesicle locations of ceRNA manually curated from literature and data sources, (iv) more than 10 000 experimentally supported long noncoding RNA (lncRNA) biomarkers associated with tumor diagnosis and therapy, and (v) lncRNA/mRNA/miRNA expression profiles with clinical and pathological information of thousands of cancer patients. A panel of improved tools has been developed to explore the effects of ceRNA on individuals with specific pathological backgrounds. For example, a network tool provides a comprehensive view of lncRNA-related, patient-specific, and custom-designed ceRNA networks. LncACTdb 3.0 will provide novel insights for further studies of complex diseases at the individual level and will facilitate the development of precision medicine to treat such diseases.

摘要

LncACTdb 3.0 是一个综合性数据库，包含经过实验验证的竞争性内源 RNA (ceRNA) 相互作用以及相应的个性化网络，有助于精准医学。LncACTdb 3.0 可免费在 http://bio-bigdata.hrbmu.edu.cn/LncACTdb 或 http://www.bio-bigdata.net/LncACTdb 上获取。我们对 LncACTdb 3.0 数据库进行了多项更新，包括 (i) 通过对已发表文献的人工整理，涵盖 25 个物种和 537 种疾病/表型的 5669 个经过实验验证的 ceRNA 相互作用，(ii) TCGA 和 GEO 中 62 个数据集的 16228 名患者的个性化 ceRNA 相互作用和网络，(iii) 从文献和数据源中人工整理的 ceRNA 的亚细胞和细胞外囊泡位置，(iv) 超过 10000 个与肿瘤诊断和治疗相关的经过实验验证的长非编码 RNA (lncRNA) 生物标志物，以及 (v) 具有数千名癌症患者临床和病理信息的 lncRNA/mRNA/miRNA 表达谱。我们开发了一组改进的工具来探索 ceRNA 对具有特定病理背景的个体的影响。例如，网络工具提供了一个全面的视图，包括与 lncRNA 相关的、患者特异性的和定制设计的 ceRNA 网络。LncACTdb 3.0 将为在个体水平上进一步研究复杂疾病提供新的见解，并有助于开发治疗此类疾病的精准医学。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/df15/8728196/2cdf028fdf15/gkab1092fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/df15/8728196/144bd1501aac/gkab1092fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/df15/8728196/2cdf028fdf15/gkab1092fig2.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/df15/8728196/144bd1501aac/gkab1092fig1.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/df15/8728196/2cdf028fdf15/gkab1092fig2.jpg

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