Bioinformatics Tools for Extracellular Vesicles Research

Extracellular vesicles (EVs) are a class of membranous vesicles that are released by multiple cell types into the extracellular environment. This unique class of extracellular organelles which play pivotal role in intercellular communication are conserved across prokaryotes and eukaryotes. Depending upon the cell origin and the functional state, the molecular cargo including proteins, lipids, and RNA within the EVs are modulated. Owing to this, EVs are considered as a subrepertoire of the host cell and are rich reservoirs of disease biomarkers. In addition, the availability of EVs in multiple bodily fluids including blood has created significant interest in biomarker and signaling research. With the advancement in high-throughput techniques, multiple EV studies have embarked on profiling the molecular cargo. To benefit the scientific community, existing free Web-based resources including ExoCarta, EVpedia, and Vesiclepedia catalog multiple datasets. These resources aid in elucidating molecular mechanism and pathophysiology underlying different disease conditions from which EVs are isolated.

A flowchart to depict the integrated bioinformatics analysis that can be performed to identify key components in EV datasets. Isolated EVs can be analyzed to profile the genomic, transcriptomic, proteomic, and lipidomic contents. With the generated datasets, multiple integrated analyses can be performed including Gene Ontology (biological process and molecular function) enrichment, protein interaction network, pathway, domain enrichment, and subcellular localization analysis