Figure 3.

Principal component analysis and k-means clustering results of proteins of an S. aureus-infected murine kidney. (A) PCA was performed on protein LFQ intensity values acquired from 3 regions and 2 time points. This unsupervised approach separates the SAC and interface (left) from the cortex samples with no visible infection (right). (B) Samples also seem to cluster based on biological replicate within the PCA space. (C) There is a separation among the samples 4 and 10 days postinfection within samples acquired from region of infection; this separation is not seen from samples acquired from the cortex where there was no visible infection. (D) k-Means clustering was used to cluster the samples after PCA; k = 4 was determined using silhouette scores as a metric. To aid in interpretation, clusters are labeled by the regions and time points from which samples were collected.