Figure 4

Different datasets of experimentally determined HDAC6 substrates show minor overlap and agreement. Comparison of substrate specificities of different experimental datasets, based on their sequence logos and correlation of substrate activities. (A) Plot of substrate activities for peptides shared between the D-13MER³ and D-SILAC¹⁴ datasets. (blue, red: predicted substrates and non-substrates by our protocol; triangles indicate peptides with H/L ratio > 3 in the SILAC experiment, or measured intensity > 2 in the peptide array, for which the values have been capped to fit into the plot; dashed lines indicate cutoffs for defining substrates and non-substrates; S, NS: substrates and non-substrates, respectively) (B–F) Sequence logos made with PSSMSearch⁸⁹ using its default background containing human sequences (B–D), and with Two Sample Logo⁹⁰ using the non-substrate peptides as background for each dataset (E–G). (B, E) D-13MER, (C, F) D-SILAC, and (D, G) D-3MER datasets.