Fig. 4

Systematic application of JAMS. A Pie charts of the main TF families (left) and C2H2-ZF proteins subfamilies (right) for TFs with at least one high-quality JAMS model. B Pie chart of the methyl-binding preferences of TFs with at least one high-quality JAMS model. We obtained high-quality models for a total of 260 TFs. Note that no-effect means no statistically significant effect was found using the current data. C Dot plot representations of the sequence/methylation preference of ZBTB33, CEBPB, MAX, and NRF1, as inferred by JAMS (see Fig. 2A for a description of how these representations should be interpreted). D The table on the top shows the confusion matrix of TF classifications by JAMS (columns) and methyl/bisulfite-SELEX [5] (rows). The pie charts at the bottom illustrate how JAMS methyl-minus (left) and methyl-plus (right) predictions correspond to different SELEX-based classifications