Fig. 4

Deregulation of pathways in obese and cancer patients. a Samples sorted by Pathway Deregulation scores (PDS) display strong clustering both for obesity data (batches 1–4), as well as cancer data (batch 9). b Projection of batches 1–4 samples, shown with red (obese) and green (lean) dots, onto the principal curve (black line) that is used to define PDS, see Methods. We show three pathways (nine in Supplementary Figure 4) from the 16 found to be significantly over-represented in the 38 genes of the obesity score. For the purposes of this visualization only, all data is further projected onto its first two principal components, PCA0 and PCA1. Axis labels display the ratio of explained variance. c Heatmap for PDS of all KEGG pathways. Each pixel represents the value of the PDS (from blue, low PDS, to red, high PDS) for a each sample (row) and pathway (column). Pathways are hierarchically clustered according to similarity of expression in obesity samples. Samples are sorted by their obesity score. Green/red labels in the right indicate lean/obese categories. Black labels in the bottom mark the nine KEGG pathways from the 16 selected using the obesity score. The panel shows that these pathways tend to cluster together and are among the most highly deregulated.