ExomiRHub: a comprehensive database platform to integrate and analyze human extracellular miRNA transcriptome for discovering non-invasive biomarkers

Abstract

Background Although studies reported that extracellular miRNAs have significant functions in regulating the development of human diseases, our understanding of their role in human diseases remains to be further addressed. Many extracellular miRNA expression data were deposited in public resources, which are heterogeneous and difficult to investigate due to the data generated from different high throughput platforms. To use these invaluable data for accelerating the discovery of non-invasive miRNA biomarkers, a comprehensive and user-friendly database platform is essential, especially for bench researchers who lack bioinformatics skills. Methods We integrated, standardized, and annotated human extracellular miRNA expression data and cancer-related miRNA transcriptome data from NCBI GEO and The Cancer Genome Atlas (TCGA), respectively. Moreover, we developed the ExomiRHub database platform that designed with comprehensive online analysis functions and tools to analyze these data or User's own data. These analysis functions and tools were designed to enable users to select samples, define groups and parameters for their own analysis. Results ExomiRHub includes 191 human extracellular miRNA expression datasets associated with 112 disease phenotypes, 62 treatments, and 24 genotypes, including 29,198 samples and 23 sample types. ExomiRHub further includes 16,012 miRNA transcriptome data of 156 cancer sub-types to enhance the usability of it in cancer research. To accelerate the identification of non-invasive miRNA biomarkers, ExomiRHub provides 25 online analytical and visualization functions to individually analyze these data. Moreover, ExomiRHub provides Web Service to enable users in conducting the analyses on their uploaded data. Furthermore, ExomiRHub provides four additional tools to evaluate the functions and targets of miRNAs and their variations. Finally, we used ExomiRHub and discovered non-invasive miRNA biomarkers associated with angiogenesis-related pathways for monitoring glioma progression. Conclusion The comprehensive data and functions of ExomiRHub can greatly accelerate the discovery of non-invasive miRNA biomarkers. It is freely accessible at the websites of http://hpcc.siat.ac.cn/exomirhub/ & http://www.biomedical-web.com/exomirhub/.