Figure 5

Genome wide distribution of FOXM1 binding in HCT116 cells. (A) Venn diagram representing the shared FOXM1 peaks between HCT116 and DLD1 cells. (B) Graphs displaying statistics about the association of input genomic regions to the TSS of all the genes putatively regulated by the genomic regions. The ‘Number of associated genes per region’ graph shows how many genes each genomic region is assigned as putatively regulating based on the association rule used. (C) The distance to TSS graphs show the distance between input regions and their putatively regulated genes. The distances are divided into four separate bins: one from 0 to 5 kb, another from 5 kb to 50 kb, a third from 50 kb to 500 kb, and a final bin of all associations over 500 Kb. (D) Heat map showing FOXM1 binding events in HCT116 (right) and DLD1 (left) and HCT116 DLD1 shared reads. Heatmap was generated using ChAsE (Chromatin Analysis and Exploration) platform. Settings (peak extensions 5 kb upstream and 5 kb downstream of the peak summit and bin size 50 (bp). (E) The Integrative Genomics Viewer (IGV) browser was used to visualise the FOXM1 binding in down-stream targets. The input track has been subtracted from the data shown above. Blue peaks represent FOXM1 enrichment in 5-FU targets: TYMS, TYMP, and TK-1. (F) To confirm the IGV ChIP-seq data of FOXM1 binding, RT-PCR was carried out on HCT116 (A) and DLD1 (B) cells. The result shows FOXM1 binding on TK-1, TYMP, E2F1, E2F2, MMP2, and MLH1. P38, which is not a FOXM1 regulator, does not show any FOXM1 enrichment.