Figure 1.

Utilizing EpiExplorer for interactive analysis and hypothesis generation. After uploading a set of published 5-hydroxymethylcytosine (5hmC) hotspots [35] into EpiExplorer, various options for genome-wide analysis are available. All diagrams are generated dynamically in response to user interactions. (a) Bar chart summarizing the percent overlap (y-axis) between 5hmC hotspots and various genomic datasets (x-axis) in H1hESC cells. (b) Bar chart comparing the percent overlap of 5hmC hotspots (orange) and randomized control regions (grey) with histone H3K4me1 peaks, based on ENCODE data [60]. (c) Genomic neighborhood plot illustrating the percent overlap (y-axis) with H3K4me1 peaks in the vicinity of 5hmC hotspots (x-axis). Different line colors correspond to H3K4me1 data for different cell types. (d) Bar chart comparing the percent overlap of 5hmC hotspots (orange) and randomized control regions (grey) with a comprehensive catalog of epigenetic states derived by computational segmentation of ENCODE histone modification data [39]. (e) Histogram illustrating the distribution of DNA methylation levels among 5hmC hotspots (orange) and randomized control regions (grey), based on Roadmap Epigenomics data [52]. (f) Enrichment table (left) and word cloud (right) illustrating the most highly enriched Gene Ontology (GO) terms among genes whose transcribed region is within 10 kb of a 5hmC hotspot. The most general (more than 5,000 associated genes) and most specific GO terms (less than 50 associated genes) were suppressed in this analysis.

Halachev et al. Genome Biology 2012 13:R96   doi:10.1186/gb-2012-13-10-r96
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