BMC Genomics 2009, 10:576 http://www.biomedcentral.com/1471-2164/10/576 FHiigstuorgera2m of genes with increasing YY1 density Histogram of genes with increasing YY1 density. Each olfactory receptor gene was scanned for the number of YY1 binding sites found within its transcript. The combined score was divided by the gene length, resulting in the YY1 density for the given olfactory receptor gene. Note that the quality of the YY1 scores varies based on the match generated by the Position Weight Matrix, and thus the calculation of YY1 binding sites per 1 kb is approximate. Genes were ordered based on increasing YY1 density and the histograms were derived by the relative position of a gene within the group of all genes. A) The mouse non-olfactory genes binned by relative order of increasing YY1 density (x-axis). The y-axis indicates the number of genes in each bin. B) Mouse olfactory genes binned in the same fashion, also from their position within the group of all genes. The high- est group of bins corresponds to a density of 4-11 YY1 binding sites per 1 kb transcript for mouse though only 6 genes show a YY1 density corresponding to more than 8 YY1 sites per kb. For human and mouse (panels B&C), there is a large group of olfactory receptor genes with high YY1 density, whereas fish (D) does not show this pattern. 400 dipeptides. In parallel, we also separately calculated the frequencies of the 400 dipeptides, including the 49 dipeptides that can encode the YY1 core motif, using only the protein sequences of the mouse OLFR genes. The fre- quencies derived from the OLFR genes (Observed Values) were compared with the reference set (Expected Values) via the Z-score to identify any over-represented dipeptides within the OLFR genes (Figure 4a) (Table 1). This global comparison did not immediately identify any dipeptides that are unusually enriched within the protein sequences of the OLFR genes. However, according to the detailed analyses using the Z-score values, two dipeptides (PL and AI) among the 49 dipeptides for the YY1 core motif showed significant enrichment (P < 0.01, Figure 4b). Even so, this enrichment is limited to the 4 bp YY1 core binding site and not the complete 10 bp motif which we used to calculate YY1 density in OLFR genes. Furthermore, the reverse-translated sequences of these two peptides (PL and AI) have 24 and 12 fold degeneracy, respectively. This means that only one out of 24 PL or 12 AI dipeptides may Page 4 of 10 (page number not for citation purposes)