Fig. 2

A case study in a head and neck squamous cell carcinoma (HNSCC) cell line Cal27, which belong to the HPV(−) subgroup of HNSCC but harbor no endogenous mutations affecting H3K36me. a Scatterplots and genome-browser tracks demonstrating how clusters of 10-kb bins identified using ChIPbinner correspond to specific genomic regions. A comparison of the wildtype cell line (WT) (dark red) and an NSD1 knockout cell line (NSD1-KO) (green) reveals depletion of intergenic H3K36me2 in Cluster B (highlighted in blue), where high levels of H3K36me2 are present in WT and low levels are found in NSD1-KO. In clusters A (highlighted in pink) and C (highlighted in brown), there is low and high levels of H3K36me2 in both conditions respectively. ChIP-seq signals were normalized using genome-wide modification percentage values obtained from mass spectrometry (MS). b Genome-browser tracks showing an example locus where ChIPbinner (blue boxes) detected more regions of H3K36me2 loss compared to csaw (purple boxes). c Genome-wide overlap analysis revealed that out of the 10 kb bins with loss of H3K36me2, ChIPbinner detected 51,607 out of 59,848 (86%) bins identified by csaw, while csaw only detected 51,607 out of 93,613 (55%) bins identified by ChIPbinner. d ChIPbinner allows users to perform differential enrichment and depletion analysis for a specified cluster. In this case, cluster B bins were tested for overlap with a specific class of annotated regions from Ensembl. **** represents p value < 0.0001 based on Fisher’s exact test. The results show that cluster B bins are enriched in intergenic regions, particularly at enhancers and open chromatin regions, and depleted in promoter flanking regions, exons and introns