pathway enrichment
Definition
Pathway enrichment is a computational method that identifies biological pathways, processes, or functions that are statistically overrepresented in a gene or protein list compared to what would be expected by chance. This technique helps researchers interpret large-scale omics data by determining which biological mechanisms are most relevant to their experimental conditions. The analysis uses statistical tests (typically hypergeometric or Fisher's exact test) to calculate enrichment scores and p-values, revealing whether specific pathways contain more genes from the input list than random expectation. Pathway enrichment transforms raw gene lists into biological insights by connecting molecular changes to known functional relationships, making it essential for understanding disease mechanisms, drug responses, and cellular processes.
Visualize pathway enrichment in Nodes Bio
Nodes Bio enables researchers to visualize enriched pathways as interactive network graphs, where nodes represent genes or proteins and edges show functional relationships. Users can overlay enrichment scores onto pathway networks, highlight significantly enriched terms, and explore cross-pathway connections. The platform facilitates identification of pathway crosstalk and hub genes by visualizing how enriched pathways interconnect within larger biological networks.
Visualization Ideas:
- Enriched pathway networks with color-coded significance levels
- Multi-pathway interaction maps showing crosstalk between enriched terms
- Gene-pathway bipartite networks displaying which genes contribute to multiple enriched pathways
Example Use Case
A cancer researcher performs RNA-seq on tumor samples and identifies 500 differentially expressed genes. Running pathway enrichment analysis reveals significant overrepresentation of cell cycle regulation, DNA repair, and immune response pathways. By visualizing these enriched pathways in a network context, the researcher discovers that TP53 and MYC act as central hubs connecting multiple enriched pathways, suggesting these genes coordinate the observed transcriptional changes. This insight guides follow-up experiments targeting these regulatory nodes for therapeutic intervention.