• Introduce the concept and biological significance of protein-protein interaction networks.
• Equip participants with hands-on experience in constructing PPI networks using cutting-edge tools.
• Teach participants to analyze PPI networks to identify key hub proteins and their biological roles.
• Facilitate the understanding of functional enrichment and its integration with PPI networks.

Day 1: Basics of PPI and Target Data Retrieval
Introduction to PPI Networks

• Overview of protein-protein interactions and their importance in biological systems
• Insights into the applications of PPI networks in disease research and drug discovery

Target Data Retrieval for PPI Networks

• Accessing databases like STRING
• Techniques for filtering and preprocessing PPI data

Hands-On Session

• Practical demonstration of target data retrieval
• Organizing and preparing data for PPI network construction

Day 2: Network Construction and Centrality Analysis
Building PPI Networks

• Using Cytoscape and STRING for network construction
• Importing and visualizing PPI data

Network Analysis Using CytoNCA

• Introduction to centrality metrics: degree centrality, closeness centrality, betweenness centrality
• Identifying hub proteins and key network nodes

Hands-On Session

• Step-by-step network construction with Cytoscape
• Practical exercises on network analysis and interpretation

Day 3: Functional Enrichment and Advanced Visualization
Gene Ontology (GO) and Pathway Analysis

• Introduction to GO terms and KEGG pathways
• Understanding functional enrichment analysis

Functional Enrichment with ClueGO

• Setting up the ClueGO plugin in Cytoscape
• Configuring and interpreting enrichment results

Advanced Visualization Techniques

• Improving PPI network visualization for publication
• Integrating enriched biological functions into the network

Hands-On Session

• Practical implementation of GO and pathway enrichment analysis
• Finalizing a PPI network for research or presentation purposes

Requirements

• Hardware: Windows PC or laptop with stable internet connection
• Software:
  • Cytoscape (latest version)
  • Plugins: ClueGO, CytoNCA
  • Access to PPI databases (e.g., STRING)

• Undergraduate or graduate degree in Biotechnology, Bioinformatics, Life Sciences, or related fields.
• Professionals from the pharmaceutical, healthcare, and biotechnology industries.
• Researchers with an interest in molecular biology, disease research, and systems biology.