Figure 4

Cluster analysis reveals distinct patterns of gene expression. All 1557 genes showing > four-fold change in ribosome footprint edgeR-normalized read counts (with FDR < 0.01 and excluding pseudogenes) between PCF and slBF or cBF were analyzed using MeV (see Methods). The ribosome footprint and mRNA read counts in each of the nine samples were converted to log₂ fold-change values compared to the corresponding median of the three PCF samples and segregated into four clusters (A-D) by K-means (KMC Support), each of which was then separated into 2 or 3 sub-sets by hierarchical clustering. Genes up-regulated in PCF are shown in aqua, while those up-regulated in slBF or cBF are shown in pink. The position of genes encoding transporters (olive), metabolic enzymes (blue), translation machinery (blue), VSGs/VRs (red) or ESAGs (black) are indicated by the colored bars to the right.