The DisGeNET Cytoscape App

This version of the app is still a beta version. If you find any problems, please contact us at support(at)disgenet(dot)org

The DisGeNET Cytoscape App is designed to visualize, query and analyse a network representation of the gene-disease associations in DisGeNET. The DisGeNET Cytoscape App uses the current version (4.0) of the DisGeNET database. In the App, gene-disease networks are represented as bipartite graphs. A bipartite graph has two types of vertices (genes, and diseases) and the edges run only between vertices of un-like types (Newman, et al., 2003). The bipartite graphs are multigraphs in which two vertices can be connected by more than one edge. In our networks, the multiple edges represent the multiple data sources reporting the gene-disease association. We generated two projections, one for the diseases and one for the genes using the igraph library in R (Gabor et al, 2006). The projected graphs contain only vertices of the same kind (monopartite) and two nodes are connected if they share a neighbor in the original bipartite graph. Before projecting the networks, we simplified the graphs and removed multiple edges. Hence, nodes that are connected by multiple edges are only connected by one edge in the simplified graph. This simplification is needed in order to correctly run the projection as implemented in the igraph library. Moreover, the node degree in the simplified graphs represents the number of first neighbors.

The App assists the user in the interpretation and exploration of human complex diseases with respect to their genetic origin by a variety of built-in functions. Using the DisGeNET Cytoscape App you can perform queries restricted to

    (i) the original data source
    (ii) the association type
    (iii) the disorder class of interest
    (iv) specific diseases or genes
    (v) a score range

1. Download the App


I have read and accepted the Terms and Conditions

Note: You need to have Java 1.8 or higher installed to use the app.

Download the current version (4.0) of the DisGeNET Cytoscape app

The database


1. Current version of the DisGeNET SQLite Database


I have read and accepted the Terms and Conditions

Download the current version (4.0) of the database

The DisGeNET sqlite database for version 4.0 has changed. Notice that we have now internal identifiers for the genes (geneNID) and the diseases (diseaseNID). In the image below, we represent the SQL schema of the database.

2. Previous versions of the DisGeNET SQLite Database


I have read and accepted the Terms and Conditions

Download the version (3.0) of the database

Download the version (2.1) of the database



Additional Files

In this section you find some additional downloads that are related to the project but not compulsory to use the plugin.

1. DisGeNET Cytoscape App User guide

Download the DisGeNET Cytoscape App User Guide

2. DisGeNET Cytoscape Style

Download the DisGeNET Cytoscape Style