node
Definition
In network visualization, a node (also called a vertex) is a fundamental unit representing a discrete entity within a biological system. Nodes can represent genes, proteins, metabolites, diseases, drugs, or any biological component of interest. Each node serves as a connection point in the network, linked to other nodes through edges that represent relationships such as interactions, regulations, or correlations. The properties of nodes—including their position, connectivity (degree), and centrality—provide crucial insights into their biological importance. Highly connected nodes (hubs) often represent key regulatory elements or essential proteins, while peripheral nodes may indicate specialized functions. Understanding node characteristics is essential for identifying drug targets, biomarkers, and critical control points in biological pathways.
Visualize node in Nodes Bio
In Nodes Bio, researchers can visualize biological entities as nodes within interactive network graphs. Each node can be customized with attributes like expression levels, fold changes, or statistical significance, represented through size, color, or shape. Users can identify hub nodes with high connectivity, filter nodes by properties, and trace pathways between nodes of interest to understand molecular mechanisms and disease relationships.
Visualization Ideas:
- Protein-protein interaction networks with nodes sized by degree centrality
- Gene regulatory networks with nodes colored by expression levels
- Drug-target networks showing compounds and proteins as distinct node types
Example Use Case
A cancer researcher investigating resistance mechanisms to targeted therapy maps differentially expressed genes as nodes in a protein-protein interaction network. By analyzing node centrality metrics, they identify three hub proteins with significantly increased connectivity in resistant cell lines. These hub nodes connect multiple signaling pathways and represent potential combination therapy targets. The researcher then filters nodes by expression fold-change and validates that targeting these central nodes in combination with the original therapy restores drug sensitivity in resistant cancer models.