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PPI Network Topology Explorer

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About This MicroSim

This MicroSim provides a topology explorer for a PPI network. The left panel shows the network with nodes colored by a selectable topological metric, while the right panel displays a histogram of that metric's distribution across all nodes.

Available Metrics

  • Degree — Number of direct interaction partners. High-degree nodes are hubs.
  • Betweenness Centrality — How often a node lies on shortest paths between other nodes. High betweenness indicates bridge proteins.
  • Clustering Coefficient — How densely a node's neighbors are interconnected. High clustering indicates membership in a tight protein complex.

Visual Encoding

  • Node color — Gradient from cool (low value) to warm (high value) for the selected metric
  • Histogram — Distribution of the selected metric across all nodes, showing whether the network has a few extreme values or is uniformly distributed

How to Use

  1. Metric dropdown — Switch between degree, betweenness centrality, and clustering coefficient
  2. Compare colorings — See how the same network looks different depending on which metric you visualize
  3. Hover over nodes to see their name and metric value
  4. Read the histogram — Understand the overall distribution of the metric

Suggested Experiments

  • Color by degree: identify the hub proteins (warmest colors)
  • Switch to betweenness: are the same proteins highlighted, or are there bridge proteins with moderate degree but high betweenness?
  • Switch to clustering coefficient: proteins in tight complexes will have high values, while connector proteins will have low values

Iframe Embed Code

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<iframe src="https://dmccreary.github.io/bioinformatics/sims/ppi-topology-explorer/main.html"
        height="542"
        width="100%"
        scrolling="no"></iframe>

Lesson Plan

Grade Level

College introductory bioinformatics

Duration

15-20 minutes

Prerequisites

  • Understanding of PPI networks
  • Basic graph theory metrics (degree, path length)
  • Concept of network centrality

Activities

  1. Exploration (5 min): Switch between all three metrics. For each, identify the top 3 proteins and note whether they overlap.
  2. Hub vs. Bridge (5 min): Find a protein that is a hub (high degree) but NOT a bridge (low betweenness). Find a bridge protein (high betweenness) with moderate degree. What biological roles might these different network positions reflect?
  3. Discussion (5 min): Which metric would be most useful for identifying essential genes? Drug targets? Members of protein complexes?
  4. Assessment (5 min): Answer the reflection questions below.

Assessment

  1. What does degree centrality measure, and why are high-degree proteins often essential?
  2. How does betweenness centrality differ from degree, and what biological role do high-betweenness proteins play?
  3. What does a high clustering coefficient indicate about a protein's network neighborhood?
  4. Why is it important to analyze multiple topological metrics rather than relying on degree alone?

References

  1. Centrality — Wikipedia
  2. Betweenness centrality — Wikipedia
  3. Clustering coefficient — Wikipedia
  4. Network biology — Wikipedia