Figure 4

Approaches for visualizing histone modification data. A) The UCSC Genome browser provides area charts organized by cell lines. B) Comparison of H3K4me3 and H3ac histone signals in a normal (GM06990) and cancer (K562) cell lines, over chromosome 7. Data was retrieved from the UCSC DAS server using DASMiner API, and the plot can be easily prepared using plottools, a GUI tool to make graphics in Matlab (see file Fig4B_histonesPlots_CancervsNormal.fig in the examples folder of the distributed source code). C) Hierarchical clustering of histone profiles for DNA regions measured in chromosome 7, GM06990 cell line. The data set for clustering was built by fetching data from 3 DAS sources, namely ChIP-chip arrays from UCSC, gene annotation from Havana Database and cancer link from Genetic Association Disease. D) Group of 39 regions exhibiting strong enrichment of positive histone marks H3ac, H3K4me2 and H3K4me3. To reproduce the clustering, see file performHistoneClustering_Fig4CD.m in the examples folder of the source code.