ExomirHub：一个用于托管和分析与人类疾病相关的细胞外microRNA转录组学数据的综合数据库
ExomiRHub: A comprehensive database for hosting and analyzing human disease-related extracellular microRNA transcriptomics data
影响因子:4.10000
分区:生物学3区 / 生化与分子生物学3区
发表日期:2024 Dec
作者:
Yang Liu, Zhuochao Min, Jing Mo, Zhen Ju, Jianliang Chen, Weiling Liang, Lantian Zhang, Hanguang Li, Godfrey Chi-Fung Chan, Yanjie Wei, Wenliang Zhang
摘要
由不同实验室产生的细胞外微洋（miRNA）表达数据表现出异质性，这对没有生物信息专业知识的生物学家带来了挑战。为了解决这个问题，我们介绍了ExomirHub（http://www.biomedical-web.com/exomirhub/），这是一个为生物学家设计的用户友好数据库。该数据库结合了191个与112个疾病表型，62种处理和24种基因型相关的人类细胞外miRNA表达数据集，其中包括29,198和23种样本类型。 Exomirhub还整合了来自癌症基因组图集的156个癌症亚型的16,012个miRNA转录组。 Exomirhub中的所有数据均已进一步标准化并通过注释策划。该平台提供25个分析功能，包括差分表达，共表达，加权基因共表达网络分析（WGCNA），功能选择和功能丰富，使用户能够选择样本，定义组并自定义参数以进行分析。此外，ExomirHub提供了一项Web服务，该服务允许生物学家分析其上载的miRNA表达数据。开发了四个其他工具来评估miRNA和miRNA变化的功能和靶标。通过Exomirhub，我们确定了与血管生成有关的细胞外miRNA生物标志物，以监测胶质瘤进展，这表明其潜力显着加速了细胞外miRNA生物标志物的发现。
Abstract
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.