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

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.

• Authors: Peng Wang, Qiuyan Guo, Yue Qi, Yangyang Hao, Yue Gao, Hui Zhi, Yuanfu Zhang, Yue Sun, Yakun Zhang, Mengyu Xin, Yunpeng Zhang, Shangwei Ning, Xia Li
• Journal: Nucleic acids research (Nucleic Acids Res) Vol. 50 Issue D1 Pg. D183-D189 (01 07 2022) ISSN: 1362-4962 [Electronic] England
• PMID: 34850125 (Publication Type: Journal Article, Research Support, Non-U.S. Gov't)
• Copyright: © The Author(s) 2021. Published by Oxford University Press on behalf of Nucleic Acids Research.

Chemical References

• RNA

Topics

• Computational Biology
• Databases, Genetic
• Gene Expression Regulation, Neoplastic (genetics)
• Gene Regulatory Networks (genetics)
• Humans
• Precision Medicine
• RNA (classification, genetics)
• Software