EVpedia: an integrated database of high-throughput data for systemic analyses of extracellular vesicles

Abstract

Secretion of extracellular vesicles is a general cellular activity that spans the range from simple unicellular organisms (e.g. archaea; Gram-positive and Gram-negative bacteria) to complex multicellular ones, suggesting that this extracellular vesicle-mediated communication is evolutionarily conserved. Extracellular vesicles are spherical bilayered proteolipids with a mean diameter of 20-1,000 nm, which are known to contain various bioactive molecules including proteins, lipids, and nucleic acids. Here, we present EVpedia, which is an integrated database of high-throughput datasets from prokaryotic and eukaryotic extracellular vesicles. EVpedia provides high-throughput datasets of vesicular components (proteins, mRNAs, miRNAs, and lipids) present on prokaryotic, non-mammalian eukaryotic, and mammalian extracellular vesicles. In addition, EVpedia also provides an array of tools, such as the search and browse of vesicular components, Gene Ontology enrichment analysis, network analysis of vesicular proteins and mRNAs, and a comparison of vesicular datasets by ortholog identification. Moreover, publications on extracellular vesicle studies are listed in the database. This free web-based database of EVpedia (http://evpedia.info) might serve as a fundamental repository to stimulate the advancement of extracellular vesicle studies and to elucidate the novel functions of these complex extracellular organelles.

Keywords: communicasomes; exosomes; membrane vesicles; microvesicles; nanocosmos; outer membrane vesicles; phylogenetic analyses; web portals.

Fig. 1

Snapshot of EVpedia homepage (http://evpedia.info). General introduction of EVs and statistics of EVpedia are provided in the “Home” menu.

Fig. 2

Browse function of EVpedia. With “Browse” menu, the protein list from the individual dataset or all the datasets can be browsed. In this figure, we browsed the vesicular proteins of the urine from normal donors (20).

Fig. 3

Gene Ontology enrichment and network analyses. All analyses in this figure involved mRNA transcriptome of EVs derived from Homo sapiens mast cell HMC-1 (21). In the “Analysis – Gene Ontology enrichment analysis” menu (a), by defining the species from which the analyzed list of proteins originates, the type of Gene Ontology terms (i.e. biological process, molecular function, and cellular component), and the cut-off of the enrichment p-value, the Gene Ontology enrichment analysis can be performed. In “Analysis – Network analysis” menu (b), by defining the species to which the functional interactome data belong, the number of additional nodes, and confidence of the interactome data, one can perform the network analysis of a protein list in EVpedia.

Fig. 4

Set analysis of EVpedia. In “Analysis – Set analysis” menu, the dataset of the “proteome+transcriptome (mRNA)”, “transcriptome (miRNA)”, and “lipidome” can be chosen for set analysis. Especially for the datasets of “proteome+transcriptome (mRNA)”, information from ortholog identification is used to build the Venn diagram (a). For example, the Venn diagram is drawn by comparing the ortholog clusters of vesicular proteomes from Homo sapiens SW480 and SW620 colorectal cancer cells (20). The functional network of SW480-specific vesicular proteins can be drawn (b).

Fig. 5

Publications in EVpedia. In “Publications” menu, one can browse papers related to prokaryotic (a) and eukaryotic (b) EVs. The bar graph shows the number of EV publications for each year. One can search the papers with a keyword in the type of “category”, “bibliography”, “title”, “author”, and “title+abstract”.