Fig. 4

SMAD5 is differentially regulating cell cycle pathway genes. a Spearman correlation between the log₂ fold change in gene expression (LCL-blood difference) of KEGG cell cycle pathway genes and the differential targeting they receive by the TF SMAD5. Red: evidence of SMAD5 ChIP-Seq binding in the promoter of the gene, black: no evidence of SMAD5 binding. The negative correlation observed indicates the cell cycle genes are more highly expressed but less targeted by SMAD5 in LCL compared to blood. b Boxplot of Spearman correlation coefficients between SMAD5 expression levels and expression levels of all genes, and between SMAD5 expression levels and the expression levels of cell cycle genes with SMAD5 ChIP-Seq binding evidence for LCL and blood samples. Difference in magnitude was tested using a Wilcoxon rank-sum test LCL-vs- blood comparison. c Visualization of the correlation between TF and cell cycle gene expression for interactions that have ChIP-Seq binding evidence. More positively-correlated associations are shown in red, more negatively correlated are blue, and correlations near zero are gray