Figure 6
From: Promoter features related to tissue specificity as measured by Shannon entropy
YY1 motifs are found downstream of the transcription start site, depending on their orientation. (a) The top image shows a logo [69] representation of the YY1 motif in the (+10, +20) region of human CGI+ promoters identified using AlignACE. It is based on 102 sequences. The other two logos are for weight matrices contained in TRANSFAC v7.3 that represent activating and repressing YY1 binding sites. (b) Plot of the positional distribution of predicted YY1 sites and the fraction of genes with a predicted YY1 sites in the (+1, +60) region. YY1 sites were predicted using a weight matrix generated using AlignACE. YY1 sites are more than almost three times (P ≤ 2 × 10-7) as common in genes with nonspecific CGI+ genes (11%; N = 2,072) than in CGI- genes (4%; N = 607) and occur at more than 10 times the expected rate. Similar trends are observed in genes with 3 ≤ H ≤ 4 though with lower absolute and relative rates. The difference between CGI+ and CGI- genes is not statistically significant for genes in the 3 ≤ H ≤ 4 bin. Essentially no YY1 sites where observed in specific genes with H ≤ 3 bits whether or not they had a CpG island.