Fig. 5

HOCI interactions explain differential gene expression. a Scatter plot showing the RNA-seq expression of different types of genes in U266 vs RPMI-8226 cells. Blue, genes belonging to the same type in the two cell lines; green, genes whose type is hub in one cell line and dissociative in the other; orange, genes of other type changes; dashed lines, cutoff for expressed genes at RPKM > 0.5. b Top: barplots showing the number of genes in each category. “Promoter HOCI changed” are the genes whose promoters overlap with HOCIs in one cell line but do not overlap with HOCIs in the other cell line. Bottom: boxplots showing the change of transcription levels in the down-regulated (left) or up-regulated (right) gene groups. c The browser view of a 1-Mb genomic region showing the CIITA gene’s promoter has HOCI interactions in U266 cells but not in RPMI-8226 cells, which explains the gene’s differential transcription between these two cell lines