Fig. 2: Estimating the validity and performance of Si-C. | Nature Communications

Fig. 2: Estimating the validity and performance of Si-C.

From: Si-C is a method for inferring super-resolution intact genome structure from single-cell Hi-C data

Fig. 2

a The average percentages of experimental contact restraints violated in the Si-C ensembles at 100 kb (purple), 10 kb (red), and 1 kb (green) resolutions along with the average violation percentages of the published NucDynamics 100-kb structure ensembles of the same cells (blue) (structures downloaded from GEO with accession code GSE80280). The distance threshold to decide whether two beads are in contact set to 2 bead diameters. Data are presented as mean ± SD. For each structure ensemble generated by Si-C, 20 structure replicas are used in the statistical analysis. For structure ensemble downloaded from GEO, ten structure replicas are used. b Correlation between the median spatial distances measured by eight 3D-FISH probe pairs (from ref. 22) and the median distances of the corresponding pairs in the Si-C inferred structures of 10 kb resolution. Details for calculating the median spatial distances are shown in Supplement Note 4. c Comparison of Si-C (red) and NucDynamics (blue) in terms of computational cost for structure reconstruction for cell 1. Details are presented in Supplementary Note 3. d Boxplot of pairwise RMSDs within the Si-C ensembles at 100 kb (purple), 10 kb (red), and 1 kb (green) resolutions along with pairwise RMSDs within the published NucDynamics ensembles of the same cells (blue) (structures downloaded from GEO with accession code GSE80280). Median values are shown by black bars. Boxes represent the range from the 25th to the 75th percentile. The whiskers represent 1.5 times the inner quartile range. For each structure ensemble generated by Si-C, 20 structure replicas are used in the statistical analysis. For structure ensemble downloaded from GEO, ten structure replicas are used. e The 10 kb structures of two conformations of chromosome 1 of cell 6 with the RMSD between them of 0.29 nuclear radii. Chromosome regions are colored from blue to red (centromere to telomere). f The distance matrices derived from the two 3D structures shown in e. g Correlation between the two distance matrices in (f). The Pearson correlation coefficient (ρ) is 0.95. The red line is power-law fit with a scaling exponent (s) equal to 0.96. RMSD root-mean-square deviation.

Back to article page