Figure 6. The distribution of Spearman correlation coefficients for the domain-identical PWM and all other PWMs from the same homeodomain family for each TF from the test set in Figure 1 .

In each case, the correlation coefficient for the domain-identical PWM either clearly outperforms or is in the cluster of top performing PWMs, demonstrating that domain-identical PWMs capture the DNA sequence affinity and specificity of transcription factors better than considering the TF family alone.