Introduction
NeDRex is the first generically applicable integrated platform for network-based disease module discovery and drug repurposing. It is build of three main components: a knowledgebase (NeDRexDB), a Cytoscape app (NeDRexApp), and an API (NeDRexAPI).
This short video explains the NeDRex approach:
The NeDRex platform
The NeDRex platform provides a broad spectrum of systems medicine methods together with integrative networks of different biological entities. The platform is modular and new algorithms can be easily incorporated. In addition, the NeDRexDB knowledgebase serves as a useful resource for scientists to explore the relationships between different biological entities, such as drugs, disorders, genes, proteins, and pathways. Moreover, by using NeDRexApp, users can build customized networks from the NeDRexDB knowledgebase according to their needs and further explore them by the various functionalities available in NeDRexApp.
NeDRexDB
NeDRexDB integrates data from the following biomedical databases:
Integration of multiple databases enables us to construct heterogeneous networks representing distinct types of biomedical entities (diseases, genes, drugs, proteins, pathways) and the associations between them. These networks can be accessed and explored by three different means: the NeDRexApp, the NeDRexAPI, and a Neo4j endpoint.
NeDRexDB contains information from the Online Mendelian Inheritance in Man® (OMIM®) database, which has been obtained under a license from the Johns Hopkins University. NeDRexDB does not represent the entire, unmodified OMIM® database, which is available in its entirety https://omim.org/downloads.
NeDRexApp
NeDRexApp is a Cytoscape app that provides implementations of diverse network algorithms, such as Multi-Steiner Trees (MuST), TrustRank, Biclustering Constrained by Networks (BiCoN), and Disease Module Detection (DIAMOnD). All algorithms except for BiCoN (uses gene expression data) require a list of user-selected genes (referred to as seeds) as starting point. Seeds can be all or a subset of the genes associated with the disease, so-called disease genes, or genes contained in disease modules. Moreover, expert knowledge can be employed for seed selection. NeDRex hence allows researchers to leverage their expert knowledge for discovering drug repurposing candidates via network medicine methods. Moreover, our platform can also be used to identify disease modules and possibly repurposable drugs for any newly discovered disease such as COVID-19.
You can work through the use cases presented in this tutorial to get familiar with NeDRexApp.