Fig 3. SeqUnwinder analysis of Lhx3 binding classes during iMN programming. (A) Lhx3 binding sites labeled using their dynamic binding behavior and ES chromatin activity statuses. (B) Label-specific scores of de novo motifs identified at Lhx3 binding sites defined in “A” using MCC (left) and SeqUnwinder (right) models. For consistency across figures, we fix the color saturation values to -0.4 and 0.4. (C) Log-odds score distribution of de novo discovered Onecut-like motif at “ES-active”, “ES-inactive“, “Early”, “Shared”, and “Late” sites (left panel). Distribution of Onecut2 (48hr) ChIP-seq tag counts in log-scale at “ES-active”, “ES-inactive“, “Early”, “Shared”, and “Late” sites (right panel). (D) Log-odds score distribution of de novo discovered Oct4-like motif at “ES-active”, “ES-inactive“, “Early”, “Shared”, and “Late” sites (left panel). Distribution of Oct4 (0hr) ChIP-seq tag counts in log-scale at “ES-active”, “ES-inactive“, “Early”, “Shared”, and “Late” sites (right panel). Statistical significance calculated using Mann-Whitney-Wilcoxon test (*: P-value < 0.001).
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