Fig. 6.

PSYCHIC predictions are enriched for eQTLs and ultra-thin nuclear cryo-sectioning slices. a The majority of PSYCHIC’s promoter–enhancer interactions are supported by eQTL data from the Genotype-Tissue Expression (GTEx) Project⁶³. Shown is a comparison of the percentage of predicted interactions using various methods with eQTL data, including random promoter-proximal interactions (yellow), PSYCHIC predictions (blue, using FDR thresholds of 1e-2 and 1e-4. Results with FDR < 1e-10 are also shown for first 5 cell lines), HiCCUPS¹⁹ (green), or Fit-Hi-C⁶² (orange; q value thresholds of 1e-10, 1e-20, and for IMR90 also 1e-40), for various cell lines and tissues in human and mouse. Below each bar, we mark the number of predicted promoter–enhancer interactions. b Comparison of random (yellow), PSYCHIC (blue; FDR < 1e-2 and FDR < 1e-4) and Fit-Hi-C⁶² (orange; q value <1e-20) predictions, with regard to the sequencing of genomic DNA content in ultra-thin cryo-sectioning slices in mES cells⁶⁴. Y-axis marks the number of slices in which both the enhancer and the promoter regions were co-sequenced