Help & User Guide

EV Barcode predicts the cellular source of extracellular vesicles (EVs) based on their cargo composition, enabling comparative analysis and visualization of EV-associated gene expression across biological conditions and cell types. This guide outlines input formats, data submission workflows, normalization steps, and output features.

Accepted Input Formats

EV Barcode supports multiple file formats to ensure compatibility with common bioinformatics workflows:

Plain text files (.txt)
Microsoft Excel files (.xls, .xlsx)
Comma-separated values (.csv)

The platform accepts the following gene identifier types:

Gene IDs
Ensembl IDs
Gene Symbols

All identifiers can be automatically mapped using the built-in gene mapping function to ensure consistent annotation.

Data Submission Methods

Real-Time Query (Query Tab)

The Query tab is optimized for smaller datasets and provides immediate analysis results. This mode is recommended for exploratory use and rapid data inspection.

Designed for small gene lists
Immediate result generation
No email notification required

Data Submission (Submit Data Tab)

The Submit Data tab supports large datasets and asynchronous processing. It is suitable for high-throughput analyses or delayed workflows.

Optimized for large gene lists
Asynchronous processing
Email notification upon completion

If a real-time query contains more than 4,000 genes, or if server utilization exceeds 75%, users will be automatically prompted to switch to data submission mode. In such cases, an email address is required, and a UUID will be issued for result tracking.

Group Comparison

EV Barcode enables comparative analysis across experimental groups to highlight biologically meaningful differences.

Comparison of two or more groups is supported
A maximum of four groups may be compared simultaneously
This limitation ensures clarity in visualization and interpretation

Expression Values and Replicates

Users may submit expression data in one of the following formats:

Fold values
Normalized expression values (e.g., NSPCC)
Raw or processed count data

For experiments containing multiple replicates:

Normalized replicate values may be submitted directly
Alternatively, average values per group may be provided

Upon submission, EV Barcode automatically normalizes data per gene and per condition, depending on the dataset structure and number of comparison groups.

Example Input Table Formats

Below are example table formats illustrating how gene-level data can be submitted for EV Barcode analysis.

Gene Symbol	Fold
Gene1	12
Gene2	14
Gene3	12
Gene4	18
Gene5	13
Gene6	18

Table 1: Example of input format.

Gene Symbol	Control	Group 1	Group 2
Gene1	11	20	20
Gene2	20	14	23
Gene3	11	5	23
Gene4	18	14	6
Gene5	19	9	13
Gene6	16	23	6

Table 2: Example of multi-group expression input format.

Output and Visualization

EV Barcode generates interactive, high-resolution visualizations combined with comprehensive data tables.

Interactive figures with selectable and deselectable cell types
Dynamic updates to facilitate exploration and interpretation
Publication-ready visual outputs

Users can export both figures and data tables and share results securely with collaborators using a unique access link.

Data Retention and Automated Maintenance

To ensure efficient storage management while maintaining accessibility:

Results from real-time queries are retained for 5 days
Results from data submissions are retained for 7 days

Each submission is assigned a Universally Unique Identifier (UUID), enabling secure access, traceability, and collaboration.

Due to the storage-intensive nature of EV Barcode, an automated maintenance routine runs daily at midnight. This process removes expired results, optimizes storage usage, and preserves overall system performance.