The two plots display pathways upregulated in two classes. The first plot shows pathways enriched in one class, while the second plot shows those enriched in the other. Pathways are ranked by Normalized Enrichment Score (NES), with p-values and adjusted p-values (padj) indicating statistical significance. Genes within each pathway are shown as ticks along the center line, sorted by the significance of their differential expression with direction; ticks above the line indicate positive correlation, and those below indicate negative correlation. The length of the ticks reflects the strength of correlation, while gaps indicate genes not included in the pathway.
Definitions and interpretations of table columns
At the bottom of the table, there is a "View" button that, when clicked, generates two visualizations. The first is a Pathway Inclusion and Overlap Heatmap, which visually displays the relationships between the selected pathways and their associated genes, highlighting both overlapping and unique gene-pathway associations. The second is a Gene Set Enrichment Analysis (GSEA) plot, showing the enrichment score curve for the selected pathways and indicating where the most significant gene contributions are along the ranked list. These graphs provide a detailed view of how the selected pathways interact with the gene expression data.
This plot depicts a ranked list of pathways based on their association with drug response. For each pathway, genes are represented as ticks along the center line, sorted according to their correlation with drug response; those above the line positively correlate, while those below indicate a negative correlation. The extent of the ticks reflects the magnitude of correlation. Areas without ticks indicate genes not included in the respective pathway. Pathways are ordered on the y-axis by their level of significance, with the most significant at the top.
This visualization displays the relationship between various biological pathways (rows) and individual genes (columns). Green bars indicate gene participation within the respective pathways, elucidating both overlapping and exclusive gene-pathway associations. Pathways are hierarchically clustered based on gene membership similarity. Note: Pathways with complete inclusion relationships may not cluster adjacently if other pathways with shared gene memberships influence the overall distance calculations. The clustering considers the presence or absence of all genes across the pathways, which may affect the proximity of even completely inclusive pathways within the dendrogram.
The GSEA plot demonstrates the enrichment of specific pathways based on a ranked list of genes and their differential expression between classes. The x-axis represents the rank of all genes in the dataset, while the y-axis shows the running enrichment score (ES) for the selected pathway. The green line indicates the cumulative ES, the peak of the ES curve indicates the point of maximum enrichment within the ranked gene list. The vertical black lines beneath the ES line represent genes that are part of the pathway, positioned according to the level and direction of differential expression. The red dashed line indicates the maximum positive ES for pathways upregulated in one class or the minimum negative ES for those upregulated in the other class, marking the points of strongest enrichment within the gene list.