Network Biology and Hub-Gene Discovery Using STRING and Cytoscape

Internship Details

About the Internship

The Network Biology and Hub-Gene Discovery Using STRING and Cytoscape Internship is a project-based programme designed to introduce participants to the construction, visualisation, and analysis of biological interaction networks.

Participants will collect disease-associated genes, construct protein–protein interaction networks, calculate network-centrality measures, identify hub genes, detect densely connected modules, and interpret module-specific biological pathways.

The internship also introduces regulatory-network integration using miRNAs and transcription factors, allowing participants to prioritise candidate biomarkers and therapeutic targets using both biological evidence and network topology.

Network Types Covered

• Protein–protein interaction and co-expression networks
• Gene-regulatory and transcription factor–gene networks
• miRNA–gene regulatory networks
• Gene–disease and pathway-interaction networks
• Drug–target and therapeutic-interaction networks
• Integrated multi-layer biological networks

Hands-on Activities

• Collect, clean, and standardise disease-associated gene lists.
• Construct and export protein-interaction networks using STRING.
• Import networks into Cytoscape and calculate centrality measures.
• Identify hub genes and densely connected functional modules.
• Develop miRNA–gene or transcription factor–gene networks.
• Prepare publication-quality network figures and biological interpretations.

Core Cytoscape Skills

• Import and organise node, edge, and attribute tables.
• Apply suitable layouts and customise network visualisation.
• Map node size, colour, and shape to biological attributes.
• Calculate degree, betweenness, and closeness centrality.
• Identify hub genes using cytoHubba and modules using MCODE.
• Group pathways with ClueGO and export high-quality figures.

Internship Curriculum

Final Deliverables

• Curated disease-gene database and standardised gene list
• STRING interaction network and exported interaction tables
• Cytoscape project file and centrality-analysis table
• Hub-gene ranking and MCODE module analysis
• Integrated miRNA or transcription factor regulatory network
• Publication-quality figures, GitHub repository, and final technical report

Suggested Project Titles

Real-World Applications

• Identification of disease-associated hub genes and biomarkers
• Discovery of functional modules and pathway interactions
• Prioritisation of potential therapeutic targets
• Analysis of miRNA and transcription-factor regulation
• Investigation of drug resistance and disease progression
• Preparation of network figures for research reports and publications

Who Should Attend & Prerequisites

• Biotechnology, bioinformatics, and computational biology students
• Genetics, molecular biology, and biomedical science learners
• Undergraduate and postgraduate students
• PhD scholars and early-career researchers
• Faculty members and research professionals
• Learners interested in network biology and disease-gene analysis

Prerequisites: Basic knowledge of molecular biology, genetics, gene expression, or bioinformatics is recommended. Previous Cytoscape or programming experience is helpful but not mandatory.

Frequently Asked Questions

The Network Biology and Hub-Gene Discovery Using STRING and Cytoscape Internship provides practical experience in disease-gene collection, protein-interaction analysis, network visualisation, centrality calculation, hub-gene discovery, module detection, and regulatory-network integration. Participants will complete a structured network-biology project suitable for academic research, thesis development, and publication-oriented analysis.