BMC Genomics 2009, 10:576 http://www.biomedcentral.com/1471-2164/10/576 FCiogrurreelat4ion of observed and expected dipeptides and statistical significance Correlation of observed and expected dipeptides and statistical significance. The mouse proteome was divided into olfactory genes (1,178) and all other genes (33,788) and the frequency of each dipeptide was tabulated. Of the possible 400 dipeptides, 49 can encode the core of the YY1 binding site. A) Observed vs. expected plot of 400 dipeptides (hollow dia- monds) as compared to the subset of 49 YY1 binding site core forming dipeptides (filled diamonds). The subset does not devi- ate from the overall pattern. Pro-Met is indicated as having a much larger observed than expected count. B) Z-score of the observed and expected counts of the subset of YY1 binding site core forming dipeptides. All but three fall within 1 standard deviation of their expected values. Only Ala-Ile, and Pro-Leu deviate significantly from their expected values. located within the protein-coding regions of the OLFR genes [22]. This is intriguing and consistent with the observation of the current study in that some critical cis- elements are located within the protein-coding regions of the OLFR genes. The genetic code is optimal for contain- ing multiple layers of encoded information within pro- tein-coding regions [33]. In sum, although further investigation is warranted, it is likely that the identified YY1 binding motifs are functionally important cis-regula- tory elements for the regulation of the OLFR genes. The YY1 binding motifs identified within the OLFR genes are unusual since they are localized within the protein- coding regions of these genes and are present at high den- sity. This is quite different from the typical pattern in which transcription factor binding sites (cis-regulatory ele- ments) are located in the genomic regions surrounding the protein-coding regions of genes. OLFR genes give a fit- ness advantage by duplication and divergence while remaining active, yet must also retain regulatory informa- tion. According to our statistical analyses (Figure 3&4), the identified YY1 binding motifs within the OLFR genes likely represent evolutionarily selected cis-regulatory ele- ments. Previous studies have shown high levels of YY1 binding affinity to the type of YY1 binding motifs found within OLFRs [1]. Though the functionality of the identi- Page 7 of 10 (page number not for citation purposes)