The DisGeNET Cytoscape App
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 DisGeNET data (version 7.0). It assists the user in the interpretation and exploration of the genetic basis of human complex diseases by a variety of built-in functions. Using the DisGeNET Cytoscape App, gene-disease and variant-disease networks are easily generated. These networks can be restricted to:
- the original data source
- the association type
- a disease class of interest
- specific diseases, genes, or variants, and lists and combinations of them
- a range of score
- an Evidence Index range
- an Evidence Level category
Additionally, gene-gene, and disease-disease networks can be generated. In these type of graphs, two nodes are connected if they share a neighbor in the original gene-disease network. These networks can be filtered by source, disease class, or built around specific genes, or diseases.
The DisGeNET app includes an automation module with a set of REST endpoints which allows users to create workflows executed entirely within Cytoscape or by external tools (such as RStudio or Jupyter)
The DisGeNET Cytoscape App (version 7.0.0) is available at the Cytoscape App Store. See the tutorial for more information about how to install it and use it. The App is compatible with the Cytoscape 3.6.x versions, or later
Note: You need to have Java 1.8 or higher installed to use the app.
In case you encounter problems downloading the DisGeNET 7.0 SQLite database use this link to download the database and unpack it on the desired directory.
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In the image below, we represent the SQL schema of the DisGeNET sqlite database.
In this section you find some additional downloads that are related to the project but not compulsory to use the plugin.
DisGeNET Cytoscape App User guide
Download the DisGeNET Cytoscape App User Guide
In the App User Guide, you will find a tutorial addressing the following type of questions:
- How to create gene and variant-disease networks?
- What diseases are associated to a specific gene, or variant, or lists of genes or variants ?
- How to create networks by disease class?
- How can I filter the GDAs with a specific evidence level?
- How can I color the networks by disease class?
- How can I annotate my protein-protein network with DisGeNET data?
- How can I use the app in an automatic fashion from R or Python?
DisGeNET Cytoscape Style
Download the DisGeNET Cytoscape Style
If you use the DisGeNET Cytoscape App, please cite:
The DisGeNET cytoscape app: exploring and visualizing disease genomics data, Computational and Structural Biotechnology Journal (2021) Janet Piñero, Josep Saüch, Ferran Sanz, Laura I. Furlong. https://doi.org/10.1016/j.csbj.2021.05.015.