Table 2.
Exosome-related databases.
| Database | Introduction | Characteristics | Website | Ref. |
|---|---|---|---|---|
| ExoCarta | The first comprehensive database of exosomal markers, containing 286 research results on several species, e.g., humans, rats, mice, sheep, guinea pigs, fruit flies, horses, rabbits, and cattle; data on various tissue-derived exosomal proteins, mRNA, miRNAs, and lipids and other information from organ sources are available. | ExoCarta covers the protein–protein interaction network and biological pathways with exosomal protein dynamics. Users can download the most commonly used protein data from a large number of studies. The downloaded file can be directly imported into the FunRich tool for other function enrichment analysis and correlation network analysis. | http://www.exocarta.org/ | (83) |
| ExoRBase | A long-chain RNA-seq database of human blood exosomes. Currently, the database includes 92 blood samples, 58,330 circRNAs, 15,501 lncRNAs and 18,333 mRNAs, with annotations, expression levels and possible source tissues. | ExoRBase integrates and visualizes the RNA expression profiles based on normalized RNA-seq data spanning both normal individuals and patients with various diseases. | http://www.exorbase.org/ | (84) |
| EVmiRNA | A miRNA database of EVs, curating and analyzing 462 miRNA expression profile datasets on EVs in 17 tissues/diseases. EVmiRNA provides several functional modules—miRNA expression profiles and the sample information about EVs from different sources; specifically expressed miRNAs in different EVs that would be helpful for biomarker identification; miRNA annotations, including miRNA expression in EVs and TCGA cancer types, miRNA pathway regulation mechanisms, and miRNA functions and literary references. | EVmiRNA provides detailed miRNA expression profiles in EVs as well as valuable and comprehensive resources, including EV samples classification (source/cancer and exosome/MV), miRNA expression profile for each sample, the most expressed miRNAs, specifically expressed miRNAs for each EV type, and miRNA functions and regulation mechanisms. | http://bioinfo.life.hust.edu.cn/EVmiRNA | (85) |
| EV-TRACK | A crowdsourcing knowledge base that centralizes data on EV biology and methodology and comprises methodological specifications on 3,383 EV experiments in 1,699 documents. EV-TRACK evaluates EV separation and identification-related parameters based on Minimum Experimental Requirements for EV Research. | EV-TRACK collects the original data on EV separation and characterization and increases the authenticity and repeatability of the data. For each experiment, the website explains and sort out general and specific method information to help reproduce the experiment and evaluate it. | http://www.evtrack.org/ | (86) |
| EVpedia | A high-throughput comprehensive database of prokaryotic and eukaryotic EVs. EVpedia provides databases of prokaryotes, nonmammalian eukaryotes and mammalian vesicular mRNAs, miRNAs, and lipids. | EVpedia is an integrated and comprehensive proteome, transcriptome, and lipidome database of EVs derived from archaea, bacteria, and eukaryotes, including humans. EVpedia may serve as a useful community resource to trigger the advancement of systematic and comprehensive studies on EVs and for unveiling the fundamental roles of EVs | http://evpedia.info | (87) |
| Vesiclepedia | A manually curated compendium of molecular data on lipids, RNAs, and proteins identified in various classes of EVs. Currently, Vesiclepedia comprises 35,264 protein, 18,718 mRNA, 1,772 miRNA, and 342 lipid entries encompassing 341 independent studies published in the past several years. | Users can query and download EV cargo data, EV separation details, characterization methods, biophysical and molecular characteristics, and EV-METRIC according to various search criteria. This information helps biomedical scientists evaluate the quality of EV preparations and obtain the corresponding data. FunRich can help users directly analyze data. | http://www.microvesicles.org/ | (88) |
| EMBL-EBI | A comprehensive annotation database for the functional analysis of human exosomal proteins according to Gene Ontology information. | EMBL-EBI can identify the target protein used for focus annotation and annotation of exosomal experimental methodology. | http://www.ebi.ac.uk/GOA/exosome | (89) |
| ExRNA Atlas | A data repository of the Extracellular RNA Communication Consortium (ERCC). This database includes small RNA sequencing and RT-qPCR-derived extracellular-RNA profiles from human and mouse biofluids. | All RNA-seq datasets are processed using version 4 of the exceRpt small RNA-seq pipeline, and ERCC-developed quality metrics are uniformly applied to these datasets. | http://exrnaatlas.org/ | (90) |