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. 2019 Dec 6;10:5449. doi: 10.1038/s41467-019-13423-8

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© The Author(s) 2019

Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons license, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons license and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this license, visit http://creativecommons.org/licenses/by/4.0/.

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Fig. 8 — Examining HiC-Reg predictions at the HBA1 locus. a Shown are the features, true and predicted counts and q-value for $~$ 225 kb before and 1 MB after the 5 kb bins spanning the HBA1 gene promoter. Note, no features were measured for bins within 0 to 55 kb. The white-red heatmaps show the true counts for five cell lines and predicted counts, and the white-magenta heatmaps show q-value significance (0: q-value $\geq$ 0.05 or 1: q-value $<$ 0.05, q-values are assigned only to pairs that have a measured count in the original Hi-C data). Predicted counts are from five CV models, 20 cross-cell line models, and five Ensemble models. Test cell lines are mentioned above the red line, while the column names (vertical orientation) are for the training models. The white-blue heatmaps show the ChIP-seq and motif feature signals while the green column is for distance (colorscale: 0: 0 kb and 200:1 MB). The asterisks denote the 5 kb regions that interact with the 5 kb region spanning the HBA1 gene promoter from 5C. Only the bin with significant predicted interactions is shown. b Visualization of feature signals using WashU Epigenome Browser for significant interactions obtained from a model trained in K562 and tested in K562. Shown are also overlapping interactions with 5C pairs (magenta and green). Red vertical lines demarcate the 5 kb bin overlapping the HBA1 gene promoter and the distal region that interacts with it, as supported by 5C. The green arcs on both tracks depict the interactions predicted by HiC-Reg and supported by 5C. c Manhattan style plots of true and CV predicted counts around 1 MB radius of HBA1 promoter in K562. Interactions associated with both bins spanning HBA1 promoter are shown. The left part of each Manhattan plot is shortened because this region is towards the beginning of the chromosome. Blue diamonds are significant interactions, red stars are significant interactions that overlap a 5C interaction and purple diamonds are pairs overlapping a 5C interaction but not significant. Yellow dots are predictions for pairs that are not measured in K562. Gray dots denote pairs that are measured but are not significant. Source data for a and c are provided as a Source Data file.