Additional file 11 of Reliable scaling of position weight matrices for binding strength comparisons between transcription factors

Figure S4. Comparison of Îť values calculated by using different pseudo-count values in PWMs. Subfigure A shows the comparison between the Îťvalues obtained by using PWMs with pseudocounts of 1 and 3 (the adjusted R 2 is 0.973), while subfigure B compares pseudocounts of 1 and 0.3 (the adjusted R 2 is 0.978). Each dot represents a TF from 100 randomly chosen vertebrate TFs in JASPAR database [5]. (PDF 31.2KB)