Workshop on Protein-Protein Interaction (PPI) Network Design and Structure

The workshop on Protein-Protein Interaction (PPI) Network Design and Structure is crafted for students, researchers, and professionals in the life sciences, biotechnology, and pharmaceutical industries. It emphasizes the significance of PPI networks in understanding cellular processes, signaling pathways, and disease mechanisms. Participants will gain a comprehensive understanding of bioinformatics tools used for PPI network construction, analysis, and functional annotation to drive innovations in therapeutic target identification and drug development.

To provide participants with the theoretical foundation and practical skills to construct, analyze, and interpret protein-protein interaction networks, fostering advancements in molecular biology, disease research, and systems biology.

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)