Fig. 5

Correlation of cohesin binding and gene expression changes in mutant MEFs. a KS test indicating the degree of cohesin binding to genes changing expression in Nipbl+/− MEFs. X-axis represents all 13,587 genes from the microarray data [19] ranked by absolute fold expression changes from biggest on the left to the smallest on the right in the left panel. Fold changes are shown in different colors as indicated on the side. In the middle panel, gene expression changes were ranked from negative to positive with the color scale shown on the side. Both color scales apply to the rest of the figure. The Y-axis is the running enrichment score for cohesin binding (see the "Methods" section for details). Distribution of cohesin-bound genes among 13,587 genes examined is shown as a beanplot [62] at the top, and the number of cohesin-bound genes and p values are shown underneath. The schematic diagram showing the definition of the gene regions, promoter (2.5 kb upstream and 0.5 kb downstream of TSS), gene body, and downstream (2.5 kb downstream and 0.5 kb upstream of TTS) regions is shown on the right. b Similar KS test analysis as in a, in which cohesin binding to the promoter, gene body, and downstream regions are analyzed separately. c Genes are ranked by expression changes from positive on the left to negative on the right. Fold changes are shown by different colors as indicated on the right. CTCF binding to promoter regions (GSE22562) [40] was analyzed for a comparison. d Lack of correlation between the mutant expression changes and randomly chosen genes are shown on the right as a negative control