pathway view
Definition
Pathway view is a visualization approach that represents biological pathways as structured diagrams showing the sequential and interconnected relationships between genes, proteins, metabolites, and other molecular entities involved in specific cellular processes. Unlike static pathway diagrams, modern pathway views integrate experimental data overlays, allowing researchers to map expression levels, mutations, or activity states onto pathway components. This methodology enables systematic analysis of how perturbations propagate through biological systems, identification of regulatory bottlenecks, and discovery of therapeutic intervention points. Pathway views bridge reductionist molecular data with systems-level understanding of cellular function.
Visualize pathway view in Nodes Bio
Researchers can transform traditional pathway representations into interactive network graphs in Nodes Bio, where nodes represent pathway components (genes, proteins, metabolites) and edges show regulatory relationships, catalytic reactions, or physical interactions. Users can overlay multi-omics data, highlight dysregulated subnetworks, trace signal propagation paths, and identify crosstalk between pathways. Network centrality metrics reveal key regulatory hubs within pathways.
Visualization Ideas:
- KEGG or Reactome pathway networks with gene expression heatmap overlays on nodes
- Signal transduction cascades showing directional information flow from receptors to transcription factors
- Metabolic pathway networks with flux data and enzyme-substrate relationships
Example Use Case
A cancer researcher investigating resistance to EGFR inhibitors uses pathway view to map RNA-seq data from resistant cell lines onto the EGFR signaling pathway network. By visualizing expression changes across pathway components, they identify unexpected upregulation of alternative receptor tyrosine kinases and downstream PI3K/AKT pathway activation. The pathway view reveals compensatory signaling routes bypassing EGFR blockade, suggesting combination therapy targets. Network analysis highlights MET and HER3 as central nodes in the resistance mechanism.