About NEXUS

Automated platform for network pharmacology and multi-method enrichment analysis in systems pharmacology research.

Cite NEXUS

Ping, T.B.; Alia, M.; Bagustari, B.A.; Alshehade, S.A. NeXus: An Automated Platform for Network Pharmacology and Multi-Method Enrichment Analysis. Int. J. Mol. Sci. 2025, 26, 11147.

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Overview

NEXUS is an automated platform for network pharmacology and multi-method enrichment analysis, designed to facilitate comprehensive drug-target-disease network construction and pathway enrichment studies.

The platform integrates advanced computational methods to analyze complex relationships between compounds, targets, and biological pathways, providing researchers with powerful tools for systems pharmacology research.

System Architecture

Data Processing Layer

Compound-target-disease data ingestion and validation

Network Construction Engine

Multi-layer graph building using NetworkX algorithms

Enrichment Analysis Module

KEGG, GO, Reactome, WikiPathways enrichment via gseapy

Visualization Framework

300 DPI publication-ready figures and interactive plots

Key Principles

Automation

Streamlined workflows minimize manual intervention

Multi-Method Approach

ORA + GSEA enrichment for robust pathway analysis

Reproducibility

Standardized protocols with full audit trail

User-Centric Design

Intuitive interface for researchers of all backgrounds

Analysis Workflow

Data Upload & Validation

Upload compound-target-disease relationships in CSV format. The system validates data integrity and checks for completeness.

Gene Selection & Network Construction

Automated gene ranking and multi-layer network construction with compound, plant, and gene nodes.

Pathway Enrichment Analysis

Multi-database enrichment (KEGG 2023, GO, Reactome, WikiPathways) with FDR correction.

Network Topology Analysis

Centrality measures, clustering coefficients, community detection, and network quality scoring.

Results & Publication Figures

Generation of 300 DPI figures, comprehensive tables, enrichment reports, and downloadable archives.

Key Features

Network Visualization

Interactive multi-layer network graphs with customizable layouts

Statistical Analysis

Network topology metrics and quality control measures

Multi-Database

KEGG, GO, Reactome, WikiPathways enrichment databases

Export Capabilities

Download results as CSV, PNG, GraphML, ZIP archives

Analysis History

Full audit trail with reproducible analysis records

Example Datasets

Pre-loaded examples for quick testing and learning

Ready to Get Started?

Go to Dashboard Start Analysis