ExomiRHub: A comprehensive database for hosting and analyzing human disease-related extracellular microRNA transcriptomics data

doi:10.1016/j.csbj.2024.07.024

	ExomiRHub: A comprehensive database for hosting and analyzing human disease-related extracellular microRNA transcriptomics data
	Liu, Yang 1,2,3,4; Min, Zhuochao 5,6; Mo, Jing 4; Ju, Zhen 2; Chen, Jianliang 3; Liang, Weiling 3; Zhang, Lantian 1; Li, Hanguang 3; Chan, Godfrey Chi-Fung 3; Wei, Yanjie 2,7; Zhang, Wenliang 1,2,3,4
	2024-12-01
发表期刊	COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
ISSN	2001-0370
卷号	23 页码:3104-3116
摘要	Extracellular microRNA (miRNA) expression data generated by different laboratories exhibit heterogeneity, which poses challenges for biologists without bioinformatics expertise. To address this, we introduce ExomiRHub (http://www.biomedical-web.com/exomirhub/), a user-friendly database designed for biologists. This database incorporates 191 human extracellular miRNA expression datasets associated with 112 disease phenotypes, 62 treatments, and 24 genotypes, encompassing 29,198 and 23 sample types. ExomiRHub also integrates 16,012 miRNA transcriptomes of 156 cancer subtypes from The Cancer Genome Atlas. All the data in ExomiRHub were further standardized and curated with annotations. The platform offers 25 analytical functions, including differential expression, co-expression, Weighted Gene Co-Expression Network Analysis (WGCNA), feature selection, and functional enrichment, enabling users to select samples, define groups, and customize parameters for analyses. Moreover, ExomiRHub provides a web service that allows biologists to analyze their uploaded miRNA expression data. Four additional tools were developed to evaluate the functions and targets of miRNAs and miRNA variations. Through ExomiRHub, we identified extracellular miRNA biomarkers associated with angiogenesis for monitoring glioma progression, demonstrating its potential to significantly accelerate the discovery of extracellular miRNA biomarkers.
关键词	MiRNA Extracellular vesicle Exosome Cancer Liquid biopsy
DOI	10.1016/j.csbj.2024.07.024
收录类别	SCI
语种	英语
资助项目	National Natural Science Foundation of China[32100513] ; National Natural Science Foundation of China[62272449] ; Basic and Applied Basic Research Foundation of Guangdong Province, China[2020A1515110528] ; Basic and Applied Basic Research Foundation of Guangdong Province, China[2021B0101310002] ; Basic and Applied Basic Research Foundation of Guangzhou, China[SL2023A04J00291] ; Strategic Priority Project of Chinese Academy of Sciences, China[XDB38050100] ; Youth Innovation Pro-motion Association of Chinese Academy of Sciences, China[Y2021101] ; Shenzhen Basic Research Fund, China[RCYX20200714114734194] ; Shenzhen Science and Technology Program, China[KQTD20200820113106007] ; Science and Technology Program of Guangzhou, China[2024A04J3341]
WOS研究方向	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
WOS类目	Biochemistry & Molecular Biology ; Biotechnology & Applied Microbiology
WOS记录号	WOS:001292067900001
出版者	ELSEVIER
引用统计
文献类型	期刊论文
条目标识符	http://119.78.100.204/handle/2XEOYT63/39644
专题	中国科学院计算技术研究所期刊论文_英文
通讯作者	Chan, Godfrey Chi-Fung; Wei, Yanjie; Zhang, Wenliang
作者单位	1.Guangzhou Med Univ, Guangzhou Med Univ GIBH Joint Sch Life Sci, Affiliated Hosp 1,TheGuangdong-Hong Kong MacaoJoin, Key Lab Adv Interdisciplinary Studies, Hong Kong 510182, Peoples R China 2.Chinese Acad Sci, Ctr High Performance Comp, Shenzhen Inst Adv Technol, Shenzhen 518055, Peoples R China 3.Univ Hong Kong, Shenzhen Hosp, Dept Pediat, Shenzhen 518053, Peoples R China 4.Outstanding Biotechnol Co Ltd, Dept Bioinformat, Shenzhen 518026, Peoples R China 5.Tel Aviv Univ, George S Wise Fac Life Sci, Sch Zool, IL-6997801 Tel Aviv, Israel 6.Univ Elect Sci & Technol China, Sch Informat & Software Engn, Chengdu 610054, Peoples R China 7.Chinese Acad Sci, Shenzhen Inst Adv Technol, CAS Key Lab Hlth Informat, Shenzhen 518055, Peoples R China
推荐引用方式 GB/T 7714	Liu, Yang,Min, Zhuochao,Mo, Jing,et al. ExomiRHub: A comprehensive database for hosting and analyzing human disease-related extracellular microRNA transcriptomics data[J]. COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL,2024,23:3104-3116.
APA	Liu, Yang.,Min, Zhuochao.,Mo, Jing.,Ju, Zhen.,Chen, Jianliang.,...&Zhang, Wenliang.(2024).ExomiRHub: A comprehensive database for hosting and analyzing human disease-related extracellular microRNA transcriptomics data.COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL,23,3104-3116.
MLA	Liu, Yang,et al."ExomiRHub: A comprehensive database for hosting and analyzing human disease-related extracellular microRNA transcriptomics data".COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL 23(2024):3104-3116.