BEReX

BEReX integrates data from biomedical databases to construct an entity-relationship network for exploration of relationships among genes, proteins, drugs, diseases, and pathways.

Key Features:

• Integrated Network Construction: Synthesizes data from STRING, DrugBank, KEGG, PhamGKB, BioGRID, GO, HPRD, and MSigDB to create a unified biomedical entity-relationship network.
• Keyword-driven Subnetwork Generation: Processes keyword inputs to extract focused subnetworks that align with specified terms.
• Shortest-path Identification: Identifies shortest paths between two nodes to reveal potential indirect relationships and connections.
• Network Expansion and Modification: Supports addition and removal of specific nodes and relations to tailor network scope.
• Relevance Identification: Pinpoints the most relevant drugs, diseases, pathways, and other entities within a given network context.

Scientific Applications:

• Drug discovery: Integrates DrugBank and network connectivity to support identification of drug candidates and drug–target associations.
• Disease mechanism elucidation: Reveals putative disease mechanisms by connecting genes, proteins, and pathways across integrated databases.
• Pathway analysis: Maps and analyzes pathway-level interactions using KEGG and MSigDB within the integrated network.
• Identification of novel therapeutic targets: Identifies candidate targets through network connectivity and shortest-path relationships across databases.
• Hypothesis generation and validation: Extracts subnetworks and highlights relevant entities to support hypothesis formulation and testing.

Methodology:

Integrates data from STRING, DrugBank, KEGG, PhamGKB, BioGRID, GO, HPRD, and MSigDB to build an entity-relationship network; processes keyword queries to generate subnetworks; computes shortest paths between nodes; supports addition/removal of nodes and relations; and identifies relevant drugs, diseases, pathways, and other entities.