Fig. 6: IQ-plots enable detailed architectural analysis of individual cis-regulatory elements.
From: IceQream: Quantitative chromosome accessibility analysis using physical TF models
A, B - IQ-plots (IQP) for the Fgf3 locus in the epiblast to mesoderm trajectory (A) and the Foxa1 locus in the epiblast to endoderm trajectory (B). Each IQ-plot consists of three main components: Top panels: Normalized ATAC signal for the respective trajectories at 200 kbp (upper) and 500 bp (lower) resolutions. Black dashed lines indicate transcription start sites (TSS) with gene names above. Colored lines above plots represent exons. Middle panel: 500 bp DNA sequence, focusing on central gray loci from the top panel, with letter size indicating binding affinity to any model. Letter colors represent predicted contributions of each TF motif (rows) to the dAP. Red letters indicate predicted positive dAP (chromatin opening) while blue letters indicate negative dAP (chromatin closing). Bottom panel: Conservation score for each base pair. Green indicates positive scores, and orange indicates negative scores. Vertical gray and black guide lines connect corresponding positions between the top panels and the DNA sequence panel. Source data are provided as a Source Data file.
