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Table 1 Accuracy measurement of SuperRec, ShRec3D and HSA based on real Hi-C data using Spearman’s rank/Pearson’s coefficient between distances calculated from reconstructions and all-pair shortest-path distances computed from contact information

From: Large-scale 3D chromatin reconstruction from chromosomal contacts

Correlation Method Chromosome
   1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 X All
Spearman SuperRec 0.981 0.986 0.973 0.942 0.971 0.964 0.989 0.993 0.997 0.981 0.987 0.979 0.991 0.992 0.976 0.976 0.973 0.980 0.979 0.974 0.974 0.970 0.982 0.880
  ShRec3D 0.981 0.983 0.984 0.988 0.985 0.989 0.990 0.987 0.998 0.991 0.977 0.981 0.985 0.991 0.986 0.986 0.974 0.983 0.986 0.982 0.992 0.979 0.990 0.851
  HSA 0.799 0.916 0.916 0.740 0.857 0.884 0.866 0.952 0.904 0.904 0.892 0.801 0.733 0.891 0.880 0.873 0.759 0.808 0.747 0.841 0.934 0.828 0.892 -
Pearson SuperRec 0.982 0.985 0.974 0.947 0.974 0.960 0.987 0.993 0.998 0.982 0.989 0.983 0.989 0.992 0.980 0.980 0.978 0.985 0.982 0.972 0.970 0.978 0.981 0.896
  ShRec3D 0.981 0.978 0.983 0.976 0.977 0.985 0.986 0.988 0.998 0.983 0.983 0.980 0.984 0.990 0.984 0.984 0.974 0.984 0.985 0.980 0.991 0.977 0.979 0.857
  HSA 0.820 0.915 0.904 0.719 0.812 0.831 0.835 0.935 0.909 0.897 0.879 0.813 0.757 0.893 0.851 0.890 0.790 0.813 0.752 0.786 0.914 0.763 0.836 -