ExomiRHub: a database to explore human extracellular and intracellular microRNA transcriptomics data

Abstract

Abstract Extracellular microRNA (miRNA) expression data, generated by different laboratories, exhibit heterogeneity, posing challenges for researchers lacking bioinformatics expertise to explore these valuable data. To expedite the discovery of clinically relevant miRNA biomarkers, a user-friendly database is mandatory. Therefore, we formulated ExomiRHub, a database that incorporates 191 human extracellular miRNA expression datasets associated with 112 disease phenotypes, 62 treatments, and 24 genotypes, including 29,198 samples and 23 sample types. To enhance usability, ExomiRHub integrates 16,012 miRNA transcriptomes of 156 cancer subtypes from The Cancer Genome Atlas. Instead of mere collection, ExomiRHub standardizes and annotates the datasets and samples with rich annotations. In addition, it offers 25 analytical and visualization functions to interpret these datasets for identification of non-invasive miRNA biomarkers. These 25 functions empower users to select samples, define groups, and set parameters for personalized analyses. Moreover, ExomiRHub offers a web service enabling users to conduct analyses on their uploaded data. To further assist users, four additional tools are designed for evaluating the functions and targets of miRNAs and their variations. In a notable application of ExomiRHub, we identified non-invasive miRNA biomarkers associated with angiogenesis for monitoring glioma progression. This exemplifies how ExomiRHub can significantly expedite the discovery of non-invasive miRNA biomarkers. ExomiRHub is available at http://www.biomedical-web.com/exomirhub/.