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. 2018 Jan 27;46(8):e44. doi: 10.1093/nar/gky027

Figure 7.

Figure 7.

Modularity analysis of the binding motifs of FOXC1. (A) The monomer model (λ1 = 0.071) and the COB table in units of integer multiples of 0.001. Also shown is the correlation analysis using only the monomer model. (B) Correlation analysis of the model learned for FOXC1 by MODER: the monomeric model and five dimeric PPMs τ1, 1, HH, −2, τ1, 1, HH, −3, τ1, 1, HT, −3, τ1, 1, TT, 10, τ1, 1, TT, 9 were included in the analysis by the 85% rule. Deviation matrices are depicted below the logos of the dimeric PPMs. The mixture of the PPMs uses weights λ = 0.071, 0.080, 0.033, 0.029, 0.012, 0.011. (C) Correlation analysis as in B but for the PPMs E1, 1, HH, −2, E1, 1, HH, −3, E1, 1, HT, −3, E1, 1, TT, 10, E1, 1, TT, 9 that are expected under the independence assumption. The R2-values for the learned and expected PPMs differ quite clearly, for HT –3 and HH –3 in particular, as also suggested by their large deviation matrices, while the difference is small for HH –2, the heaviest component of the mixture. It is obvious that the purely modular model is not able to fully capture the binding affinity of FOXC1. Note that expected palindromic PPM HH –3 becomes directed while expected PPM HH –2 stays palindromic in the learned model.