Figure 1. Example TFBSshape analysis of DNA shape preferences for an Hnf4a TF dataset from UniPROBE. (A) Heat map showing predicted MGW profiles for individual.

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Figure 1. Example TFBSshape analysis of DNA shape preferences for an Hnf4a TF dataset from UniPROBE. (A) Heat map showing predicted MGW profiles for individual sequences, clustered based on EDs of MGW profiles, and (B) average heat map for all sequences. The colour code for both heat maps uses red for narrow MGW, blue for wide MGW and white for intermediate values. (C) PWM calculated using all analysed TFBS sequences, aligned with DNA shape heat maps as nucleotide sequence reference. From: TFBSshape: a motif database for DNA shape features of transcription factor binding sites Nucleic Acids Res. 2013;42(D1):D148-D155. doi:10.1093/nar/gkt1087 Nucleic Acids Res | © The Author(s) 2013. Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Figure 2. Example TFBSshape comparison of DNA shape preferences of two TF datasets from UniPROBE for the homologous TFs Max from mouse and Cbf1 from yeast. (A) PWMs calculated for Max and Cbf1 using all analysed TFBS sequences, with nucleotide positions numbered according to the user-determined alignment. (B) Using the chosen alignment, average heat maps for the four DNA shape features MGW, Roll, ProT and HelT are shown for Max (TF1) and Cbf1 (TF2). These shape profiles were quantitatively compared using PCC and ED. From: TFBSshape: a motif database for DNA shape features of transcription factor binding sites Nucleic Acids Res. 2013;42(D1):D148-D155. doi:10.1093/nar/gkt1087 Nucleic Acids Res | © The Author(s) 2013. Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Figure 3. DNA shape preferences of human bHLH TFs Figure 3. DNA shape preferences of human bHLH TFs. Heat maps illustrate MGW selections of (A) the Mad2-Max heterodimer (‘Mad’), the Max homodimer (‘Max’) and the c-Myc-Max heterodimer (‘Myc’). Sequence data were derived from gcPBM experiments (27) using 25% of the probes with highest signal intensities after removing probes with multiple TFBSs. (B) MGW preferences of the three TFs were compared, and nucleotide positions with significant MGW differences based on a K-S test were indicated for comparisons of Mad versus Max, Mad versus Myc and Max versus Myc (positions with different MGW distributions are shown in orange for P < 0.001 and yellow for P < 0.05; positions without significant differences are shown as green background). A replicate experiment for Myc verified that the gcPBM experiment and shape analysis did not detect any significant differences for Myc1 versus Myc2. The DNA shape features were symmetrized based on the palindromic E-box, which is located at the central positions –3 to +3 (frame). Detailed data for this analysis are provided in Supplementary Data (box plots in Supplementary Figure S2; P-values in Supplementary Table S1). (C) L2-regularized MLR and 10-fold cross-validation were used to test the accuracy of binding specificity predictions, showing that shape-augmented models (purple) outperformed specificity models using nucleotide sequence alone (brown) for all three human bHLH TFs. Adding randomly shuffled DNA shape features did not lead to the observed improvement (magenta). From: TFBSshape: a motif database for DNA shape features of transcription factor binding sites Nucleic Acids Res. 2013;42(D1):D148-D155. doi:10.1093/nar/gkt1087 Nucleic Acids Res | © The Author(s) 2013. Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.

Figure 4. DNA shape features distinguish TFBSs of anterior and posterior Hox proteins in mouse. (A) Heat map illustrating average MGW profiles of binding sites preferred by mouse Hox TFs determined by universal PBM (28). (B) A dendrogram based on EDs between average MGW profiles of preferred TFBSs demonstrates the different DNA shape preferences of anterior and posterior Hox TFs in mouse. From: TFBSshape: a motif database for DNA shape features of transcription factor binding sites Nucleic Acids Res. 2013;42(D1):D148-D155. doi:10.1093/nar/gkt1087 Nucleic Acids Res | © The Author(s) 2013. Published by Oxford University Press.This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/3.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited.