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.