pathway
Definition
A pathway is a series of interconnected molecular interactions and biochemical reactions that lead to a specific cellular outcome. In biological systems, pathways represent chains of causality where upstream events trigger downstream effects through defined molecular mechanisms. These include signaling pathways (transmitting information from cell surface to nucleus), metabolic pathways (converting substrates through enzymatic reactions), and regulatory pathways (controlling gene expression). Pathways are fundamental frameworks for understanding how cells respond to stimuli, maintain homeostasis, and execute complex functions. They matter because disruptions in pathway components often underlie disease states, making them critical targets for therapeutic intervention and biomarker discovery.
Visualize pathway in Nodes Bio
Researchers can map pathways as directed network graphs where nodes represent proteins, genes, or metabolites, and edges show causal relationships or interactions. Nodes Bio enables visualization of pathway crosstalk, identification of key regulatory nodes, and integration of experimental data onto pathway structures. Users can overlay expression data, mutation status, or drug targets to identify dysregulated pathway segments and predict intervention points for therapeutic strategies.
Visualization Ideas:
- Directed graphs showing signal flow from receptors through kinase cascades to transcription factors
- Multi-pathway networks highlighting crosstalk points and shared regulatory nodes
- Metabolic pathway maps with flux analysis overlays showing reaction rates and bottlenecks
Example Use Case
A cancer researcher investigating resistance to EGFR inhibitors discovers that resistant tumors activate alternative survival pathways. By mapping the PI3K/AKT and MAPK/ERK signaling cascades in Nodes Bio, they visualize how mutations in downstream pathway components bypass EGFR blockade. The network reveals that mTOR activation provides a compensatory survival signal, suggesting combination therapy targeting both EGFR and mTOR. This pathway-level analysis identifies rational drug combinations that wouldn't be apparent from studying individual proteins in isolation.