Fig. 2: External validation of SCI-predicted sub-compartments using orthogonal ChIA-PET chromatin interaction data. | Nature Communications

Fig. 2: External validation of SCI-predicted sub-compartments using orthogonal ChIA-PET chromatin interaction data.

From: Graph embedding and unsupervised learning predict genomic sub-compartments from HiC chromatin interaction data

Fig. 2

Validation using CTCF ChIA-PET (a–c) and RNAPII ChIA-PET (d–f). a, d Heatmaps of ChIA-PET loop counts per predicted sub-compartment, based on the mapping of loop anchors to genomic bins. Loop counts normalized genome-wide using sub-compartments determined by SCI. b, e Plots visualizing the abundance of ChIA-PET loops across SCI-predicted sub-compartments. c, f Bar plots comparing the ratios of ChIA-PET loops connecting genomic bins within the same sub-compartments to the loops connecting genomic bins from different sub-compartments, based on the sub-compartment predictions by SCI and HMM. g Example regions of SCI sub-compartment predictions that have more intra-sub-compartment loops (intra-loops) than inter-sub-compartment loops (inter-loops) supported by CTCF and RNAPII ChIA-PET. Asterisks (***) represent p-value < 2.2 × 10−16 using Fisher’s exact test.

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