Protein–protein interaction (PPI) networks are widely used in molecular biology, systems biology, and bioinformatics research to visualize relationships among proteins. Each node represents a protein, while connecting edges indicate interaction evidence.
This tutorial provides a beginner-friendly workflow for building a protein–protein interaction (PPI) network using the STRING database and Cytoscape visualization software — a standard approach used in modern biological research and scientific publications.
Step 1: Prepare a Protein List
Organize proteins using official gene symbols, one per line:
TP53
AKT1
MYC
STAT3
EGFR
BRCA1
• Use standardized gene symbols.
• One protein per row.
• Save as TXT or copy directly for STRING input.
Step 2: Generate the Network Using STRING
Open the STRING database and choose Multiple proteins. Paste your protein list and select the correct organism (e.g., Human, Mouse, or Arabidopsis).
After clicking Search, STRING automatically constructs an interaction network displaying protein nodes and interaction edges.
Output Includes
• Protein nodes
• Interaction connections
• Automatically organized network layout
Step 3: Export Interaction Data
Export network data for advanced visualization:
Export → TSV / Network Data
Download the interaction file for Cytoscape analysis.
Step 4: Import Network into Cytoscape
Install Cytoscape and import the downloaded file:
File → Import → Network from File
The interaction network will be generated automatically.
Step 5: Create Publication-Quality Visualization
Automatic Layout
Layout → Prefuse Force Directed
This reorganizes the network into a clean structure commonly used in research publications.
Customize Nodes
• Node size → expression level or importance
• Node color → upregulated vs downregulated proteins
• Labels → protein names
Customize Edges
• Line thickness → interaction confidence
• Edge colors → different evidence sources
Conclusion
The STRING + Cytoscape workflow provides a fast and reliable way to construct professional protein–protein interaction networks suitable for publications, presentations, and bioinformatics analysis.
Frequently Asked Questions (FAQ)
What is a PPI network?
A protein–protein interaction network visualizes how proteins interact within biological systems, where nodes represent proteins and edges represent interaction relationships.
Why use Cytoscape?
Cytoscape enables advanced visualization, customization, and analysis of biological networks and is widely used in systems biology research.
Can STRING images be used directly in publications?
Yes, but many researchers further refine layouts and styling in Cytoscape to achieve publication-quality figures.
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