How to Analyze Node Count, Degree, and Betweenness in PPI Networks-Cytoscape or Other Software?

Protein-Protein Interaction (PPI) network analysis can be performed using various software, including but not limited to Cytoscape.

 

Analyzing PPI Networks with Cytoscape

1. Import PPI Data

After installing and launching Cytoscape, import PPI data via the “File” menu. Supported formats include SIF or XGMML.

 

2. Node Count Analysis

The total number of nodes can be directly observed in the network visualization.

 

3. Node Degree Analysis

Node degree represents the number of edges connected to a node. Use the “NetworkAnalyzer” tool in Cytoscape to compute degree distribution.

 

4. Node Betweenness Analysis

Betweenness centrality reflects a node’s influence in the network. The “NetworkAnalyzer” tool also calculates this metric.

 

Alternative Software Options

1. Gephi

A tool for network visualization and analysis.

 

2. R and Python

Using packages such as igraph in R or NetworkX in Python, PPI networks can be analyzed with advanced statistical methods.

 

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Related Services

Protein Interaction Network Analysis Service