Fig. 1

Design of MethylSeqLogo. Proportional shading of C’s and G’s indicates the methylation level of TFBS cytosines on the forward and reverse strands respectively; while a dashed line indicates the expected level of methylation based on the background distribution. The methylation key at lower right of the logo shows background methylation probabilities of CG, CHG and CHH, respectively; and the four single nucleotide background probabilities. The top track shows the relative entropy contributed by methylation in each context/strand combination, with information associated with cytosines on the reverse strand displayed downward. In the bottom track positive height indicating the presence of under-represented dimers (typically CpG), and negative height (not seen in this example) indicating the presence of over-represented dimers. For reference, the theoretical maximum and minimum possible dimer relative entropy contribution achievable for the given background are also shown