Figure 4

Hierarchical clustering of replicates based on expression profiles using the R statistical package. Genes are organized vertically based on expression in W23 ES sample 1. (A) Clustering based on FGS gene expression FPKM except for genes with 0 FPKM in all 18 samples. (B) Same as in (A) except that genes having 0 FPKM in all 6 W23 ES and Ov samples but having reads above 0 in the B73 ES or Ov samples were also omitted to remove possible artifacts caused by read mapping difficulties.