Motifs associated with transcription factors and tissue-specific genes. (A) For transcription factors (TF), HLH-1, LIN-13, MEP-1, and PHA-4, we obtained TF-binding scores (ChIP-seq signals) from the modENCODE database (Gerstein et al. 2010), calculating the average TF-binding score around the representative TSSs. The TF-binding score is enriched 80–50 bp upstream of representative exon-TSSs as well as outron-TSSs, respectively. (B) Frequency distribution of motif occurrences around positions associated with locally maximum HLH-1 binding scores. The frequency distributions for LIN-13, MEP-1, and PHA-4 can be found in Supplemental Figure S7. Color shade represents conservation rates (see Fig. 4B; Methods). We checked the null hypothesis that two distributions of conservation rates of a motif in proximity to TF-binding sites and in the other nonpromoter genomic regions were equal, by using the Wilcoxon rank-sum test (see Methods). A lower P-value of a motif indicates a higher enrichment of the motif at the binding sites. (C) The rows present sequence motifs, and the columns show tissue types in the LongSAGE data, except for the last column that displays the number of genes associated with each sequence motif among 2342 genes. The table presents P-values of the Wilcoxon rank-sum test for assessing the null hypothesis that two distributions of expression levels of genes with the presence or the absence of the upstream motif were equal in each tissue. To highlight significantly low P-values according to the Bonferroni correction, we colored P-values ≤ 3.75 × 10−8 red, and P-values ranging from 3.75 × 10−8 to 10−3 orange.
