Effect of epigenetic modifications on gene expression and replication timing.

1 Epigenetic modifications for chr4 genes were determined from the epigenetic modifications of overlapping probes. Genes with no or incomplete epigenetic data were omitted. K4 – H3K4me1/2, K9 – H3K9me2, K56 – H3K56ac and 5mC – DNA cytosine methylation.
2 Pattern numbers are provided for convenience and correspond to the rank of gene activity.
3 Mean expression levels were determined with gcRMA and are provided for comparison only.
4 Gene activity is derived from MAS5 presence/absence calls. The percentage of active genes with the specified epigenetic modifications was compared to the percentage of active genes regardless of modifications. Percentages signficantly different than the percentage for all genes are indicated. P values were calculated from the binomial distribution with significance codes as follows: * p<0.05, ** p<0.01, *** p<0.001.
5 The replication time for all genes was determined from the replication time of overlapping probes. Percentages reflect the number of genes within a group with the indicated replication time. Groups with a significantly higher or lower percentage than the percentage of all genes with that replication time are indicated. P values were calculated from the hypergeometric distribution with significance codes as follows: * p<0.05, ** p<0.01, *** p<0.001.