Figure 5

Characterization of sequence content and regulatory features of LUAT-associated promoters. Results in A-F and H-I are shown for the three set of genes described in Figure 2C. A) Average GC content (left panel) and percentage of CpG islands (right panel) around the TSS (bidirectional promoters are centered on the TSS from the genes that has been used to match the expression with the LUAT associated genes). B) Boxplot showing the distribution of sizes of the CpG islands overlapping the 2 kb region around the TSS (when several CpG islands were found, the sum was calculated). C) Boxplot showing the distribution of TATA box motif scores found in a 500 bp region around the TSS. D) Percentage of sequences with a conserved element at each position around the TSS. E) Average profiles of indicated ChIP-seq data in ES cells around the TSS. F) Percentage of genes having a bivalent domain in their promoter, as defined in [37]. Statistical significances were computed using the hypergeometric test. G) Percentage of genes associated with lymphoid-specific transcription factors. The histogram shows the overlap between indicated transcription factor peaks and regions around TSS (+/-5 kb) for the genes selected in DP thymocytes. Statistical significances were computed using the hypergeometric test (**p value < 0.01; *p value < 0.05). H) Average GC skew profiles, computed as (#G-#C)/(#G+#C). I) Boxplot showing the distribution of first exon length. J) The normalized number of cleavage sites in antisense orientation identified in two control and two U1 inhibition experiments in ES cells [43] was computed for a 5 kb region upstream the TSS of genes for which an associated LUAT was expressed in mouse ES cells (FPKM >1). In panels B, C, I and J, p values of the Wilcoxon rank sum test are shown.