Figure 8
From: Promoter features related to tissue specificity as measured by Shannon entropy
The cumulative distribution of promoter classes as a function of entropy is similar in human and mouse. The cumulative fractions of genes with all possible combinations of CGI and TATA box features for (a) human and (b) mouse as a function of entropy H g as computed from GNF-GEA data is shown. For example, in human about 50% of the genes with H g ≤ 2.5 have a CGI-/TATA+ promoter. The gray bars indicate the entropy range that is not significantly different from uniform ubiquitous expression. Curves are compiled from genes that express above 200 AU in at least one tissue. As expected, CGI+/TATA- genes are most common in less specific genes and CGI-/TATA+ genes are most common in tissue-specific genes. CGI-/TATA- genes are very common and are found nearly uniformly at every level of specificity. Furthermore, CGI+/TATA- and CGI-/TATA+ genes are both common in mid-specificity (3 ≤ H g ≤ 4) genes showing that specificity is not determined by these features alone. The trends in human and mouse data are nearly identical despite the lower rate of CpG islands in mouse. The large variations in the graph at low entropy are due to the noise inherent in the small number of genes in this range.