Figure 5. Dynamic Ranges of Expression within Co-Expression Classes.

(A) Chromatin-associated transcript levels (RPKMs) in unstimulated macrophages are shown for all genes in each class. Genes containing CpG-island promoters (diamonds) and LCG promoters (stars) are shown separately. The median transcript level for each group is indicated by a black bar.

(B) Chromatin-associated transcript levels (RPKMs) at their peak time point are shown for all genes in each class, with CpG-island and LCG promoters shown separately.

(C) The maximum fold-induction of chromatin transcripts for each gene is shown, by dividing the peak RPKM by the RPKM in unstimulated cells. Representative genes with LCG promoters that exhibit strong activation are indicated.

(D) The numbers of genes in each class activated by more than 100-fold and by only 5–10-fold are shown.

(E) Over-represented transcription factor binding sites are shown for each class. Data are presented after hierarchical clustering. CpG-island and LCG promoters were analyzed separately. Transcription factor families are shown at the right (see Figure S6A for details). Color intensity is proportional to the negative log(p-value). Single and double stars indicate p-values < 0.01 and < 0.001, respectively. See also Figure S6.