Fig. 1

Chromosomal compartments and gene expression. a A/B partition of chromosome 1 for different cell lines based on Hi–C data in 100-kb resolution. Dark-blue and white indicate A and B compartments, respectively. Light blue indicates areas which Hi–C could not measure interactions for, e.g., centromeres. b Comparison of gene expression levels in A and B compartments for each cell line. p values (in log10) for the significance of the difference are indicated below each comparison (Wilcoxon’s test). For all cell lines, genes in A compartment are significantly more highly expressed than genes in B compartment. C. Correlation between the magnitude of the first principal component (PC1) and gene expression level in GM12878 cell line. Genes were divided into ten bins according to the magnitude of PC1, and distribution of expression levels was calculated for each bin