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. 2019 Oct 30;10(11):862. doi: 10.3390/genes10110862

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© 2019 by the authors.

Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and conditions of the Creative Commons Attribution (CC BY) license (http://creativecommons.org/licenses/by/4.0/).

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The evaluation results on chromosome 18 in mES cells between experimental high-resolution Hi-C (5 kb resolution) from Bonev lab and each of the five predicted Hi-C data sets, namely, HiCPlus-enhanced, HiCNN-enhanced, HiCNN2-1-enhanced, HiCNN2-2-enhanced, and HiCNN2-3-enhanced: (a) mean squared error and Pearson’s correlations with three different down-sampling ratios (1/8, 1/16, and 1/25); (b) the effectiveness of recovering significant interactions (detected by Fit-Hi-C with q-value < 0.05 within the genomic distances from 50 kb to 4 Mb) with a down-sampling ratio of 1/8; and (c) the reproducibility scores with the three down-sampling ratios.