Fig. 2.

Genes overlapped by CNDs can have differential gene expression. (A) An example of a gene overlapped by a CND in rhesus macaques as demonstrated by elevated aCGH log₂ ratios in these samples. Samples with higher copy number also have higher expression of this gene. (B) Samples with genes overlapped by gains tend to have higher expression of those genes whereas samples with genes overlapped by losses tend to have lower expression of those genes. Shown is the cumulative fraction plots of normalized read counts. The difference from samples with neutral copy number (no change relative to NA10851) is significant for gains and losses by a one-sided Kolmogorov–Smirnov test. (C) PANTHER enrichment analysis was performed to determine whether CND genes were enriched for specific molecular functions. The P values are the corrected probabilities that a given category of genes would be enriched by chance. The vertical dashed line indicates a P value of 0.01. Categories to the right of the line were considered significantly enriched among CND genes. Categories are listed starting with the most enriched. Details on the background set and P values are provided in SI Materials and Methods.