Additional file 2 of Reliable scaling of position weight matrices for binding strength comparisons between transcription factors

Figure S5. Correlation of λ rank obtained by using different top score thresholds in Eq. 6. We compare the λ rank for different TFs in each group of organisms (subfigure A, B for S. cerevisiae, C and D for D. melanogaster, E and F for vertebrate PWM motifs) by adopting a different top score threshold of top 0.01 % or 0.001 % instead of the default value of 0.1 % in Eq. 6. The adjusted R 2 for the λ rank correlation between 0.1 % and 0.01 % thresholds for S. cerevisiae, D. melanogaster, and vertebrate motifs are 0.94, 0.89 and 0.80, respectively, with p-values all less than 10−8. As for the λrank correlation between 0.1 % and 0.001 % thresholds, the adjusted R 2 are 0.87, 0.92 and 0.74, respectively (p-values all less than 10−6). (PDF 33.2KB