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Fig. 4 | Genome Biology

Fig. 4

From: FAN-C: a feature-rich framework for the analysis and visualisation of chromosome conformation capture data

Fig. 4

FAN-C comparison workflow for neuronal differentiation. ESC, embryonic stem cells; NPC, neuronal precursor cells; CN, cortical neurons. a Saddle plots showing contacts relative to expectation among regions with different compartment eigenvector values (binned by 2% percentiles). b Compartment strength barplot. c Heatmap of insulation scores at all boundaries in ESC, NPC, and CN, sorted by insulation score in CN. d Heatmap of insulation scores at differentially insulated regions between ESC and CN. e Aggregate matrices of 1mb windows centred at all boundaries in ESC, NPC, and CN. f Aggregate matrices of 1mb windows centred at ESC-specific boundaries. g Example of a differentially insulated region at the Pbx1 locus, showing Hi-C matrices for ESC and CN, a difference Hi-C matrix of CN- ESC, insulation scores of ESC and CN at various window sizes, insulation score difference between ESC and CN, and genes in the region, coloured by strand (orange = forward, cyan = reverse)

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