About SVAtlas
Extracellular vesicles (30–200 nm) shuttle diverse bioactive cargos to mediate intercellular signaling and immune regulation. Their disease‐relevant roles and retention of parent‐cell signatures render EVs attractive biomarkers and therapeutic targets. However, EV heterogeneity—spanning proteins, lipids, nucleic acids, and metabolites—limits the specificity of conventional bulk assays for biomarker discovery.
To address this, we established the first single vesicle database, the Single Vesicle Atlas (SVAtlas), which integrates and visualizes multi-category data of single EVs. The SVA delivers preliminary heterogeneity analyses, and incorporates a fully automated analytical toolkit.
Usage instructions are as follows:
The Atlas page provides a list of all datasets integrated into the Single Vesicle Atlas (SVA). Users can select datasets by choosing specific organs, body fluids, or tissues through an interactive human anatogram. Alternatively, the database can be filtered using broader parameters such as molecular category, sample origin or relative disease to refine the search.
(1) Click on “Atlas” to access the dataset overview page.
(2) Select a dataset of interest for in-depth exploration.
(3) Alternatively, navigate to the Disease page, view detailed annotations associated with relevant disease datasets.
Click on a dataset of interest to explore further. Each dataset is assigned a unique Project ID based on its source, and includes experimental parameters, protocols, EV isolation strategies, characterization metrics, marker annotations.
(1) The page includes sample origin, target organ, associated diseases, marker types, and PubMed ID. Click on the Project ID to access details.
(2) This Project: identified markers, gene information and detection methods. Select a marker for in-depth exploration.
(3) Detailed molecular metadata: including molecule name, source publication, sample details, experimental parameters, and functional annotations.
Multiple approaches enables more effective utilization of single vesicle data. Users can download raw data from the download page for import into the analysis pipeline, or upload their own data for fully automated analysis. Its integrated analytical environment and advanced visualization capabilities allow users to efficiently and conveniently obtain analytical results without the need for external software.
(1) This pipeline implements an automated single-EV analysis for clustering and subpopulation visualization from input expression matrices. It enforces a four-column upload format and automatically optimizes the number of principal components based on dimensionality-reduction results. Outputs comprise a t-SNE visualization of EV subclusters and clustering metadata exported in JSON format.
(2) EVisualizer, an interactive visualization platform, explores selected EV subgroups or markers across samples using clustering results. Users can load the JSON file from the first tool or upload their own JSON file. The tool supports arbitrary combination and comparison of clusters and markers across multiple views and enables users to delineate custom subpopulations.
(3) a customizable differential analysis tool that outputs volcano plots and tabulated results based on user-defined thresholds.
Heterogeneity analysis constitutes a core component of extracellular vesicle (EV) research. On this page, we provide a selection of generalized heterogeneity analyses. Users may directly download the complete dataset or utilize our analytical tools for further exploration.
The visualizations on the Analysis page, as well as the exploratory plots on the Heterogeneity page, can both be generated via this module. The upload procedure has already been detailed; the available functionalities are as follows:
Download：
1. SVA offers high-throughput single EV proteomics and transcriptomics data, with JSON files clustered by FlowSOM for further analysis.
2. Detailed project information—including samples and protocols—is downloadable, enabling comprehensive user insight.
Upload：
We continuously update and expand our data by following the latest research and encourage researchers to upload their study information. Users can submit trial details and raw data on the "share-your-study" page.
Fields marked with "*" are mandatory; others aid accurate classification. We look forward to your participation!
We have compiled single extracellular vesicle research techniques from 2015 to 2025 and conducted a preliminary classification. For more methods and detailed descriptions, please refer to the “Technical diagram.”
