volcano plot
Definition
A volcano plot is a scatter plot visualization used in omics research to simultaneously display statistical significance and magnitude of change across thousands of features. The x-axis represents fold change (typically log2-transformed), while the y-axis shows statistical significance (typically -log10 p-value). Features in the upper corners represent both large magnitude changes and high statistical significance, making them priority candidates for further investigation. Volcano plots are essential in differential expression analysis, enabling researchers to quickly identify genes, proteins, or metabolites that are significantly altered between experimental conditions while filtering out changes that are statistically significant but biologically negligible, or vice versa.
Visualize volcano plot in Nodes Bio
Researchers can extend volcano plot insights by importing significantly altered features into Nodes Bio to map them onto biological networks. Differentially expressed genes or proteins identified in volcano plot corners can be visualized as network nodes, revealing functional clusters, pathway enrichment, and interaction patterns. This transforms static statistical results into dynamic network contexts, helping identify key regulatory hubs and downstream effects within biological systems.
Visualization Ideas:
- Protein-protein interaction networks of significantly differentially expressed genes
- Gene regulatory networks highlighting transcription factors from volcano plot hits
- Metabolic pathway networks showing enzyme-metabolite relationships for altered features
Example Use Case
A cancer researcher performs RNA-seq comparing tumor versus normal tissue, generating a volcano plot with 20,000 genes. While 500 genes show statistical significance, only 50 in the upper corners demonstrate both strong fold changes (>2-fold) and high significance (p<0.001). The researcher imports these 50 genes into Nodes Bio to visualize their protein-protein interactions, discovering that 15 genes cluster around the PI3K-AKT signaling pathway, suggesting this pathway as a potential therapeutic target for drug development.