Epigenome data analysis for: DNA Methylation Technology Comparison - RRBS

Data

Each of the links below opens epigenome profile tracks in the UCSC Genome Browser and "CpG methylation" reports DNA methylation data per CpG, summarizing over all observed reads. "RRBS reads" shows DNA methylation data for each read separately. A more detailed explanation of these browser tracks is available in the RRBS track documentation sheet.

HUES6.RRBS CpG methylation RRBS reads
HUES8.RRBS CpG methylation RRBS reads
Colon_tumor.RRBS CpG methylation RRBS reads
Colon_normal.RRBS CpG methylation RRBS reads

Analysis

The following diagrams summarize the statistical analysis of all included epigenome data. A detailed description of each diagram type may be added in the future. For the time being, please contact us if any diagram is not self-explanatory.

Promoter_ensembl Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Promoter_centered Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Promoter_region Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
CpG_Island Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
BonaFide_CGI Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
CGI_Promoter Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
NonCGI_Promoter Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
NonGenic_CGI Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Middle_Exon Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
3prim_UTR Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Conserved_Region Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Open_Chromatin Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Enhancer_H3K4me2 Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
CpG_Island_Shore Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
BonaFide_CGI_Shore Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
BonaFide_CGI_Border Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Imprinted_DMR Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Imprinted_Promoter Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
CancerGene_Promoter Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
CellStateGene_Promoter Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Tandem_Repeat Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Repeat_DNA Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Repeat_LINE Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Repeat_LowComplex Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Repeat_LTR Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Repeat_Simple Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Repeat_SINE Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Tiling_regions_5kb Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Tiling_regions_5kb_nonRepetitive Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Tiling_regions_5kb_repetitive Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)
Tiling_regions_2kb Coverage pie chart Boxplot diagram Significance barchart Significance summary Scatterplot (shared CpGs weighted) Scatterplot (shared CpG unweighted) Scatterplot (entire region) Clustered heatmap (samples) Clustered heatmap (regions) Clustered heatmap (samples, regions)

Genomic Region Tracks

Each of the links below opens genomic region tracks in the UCSC Genome Browser. The first few tracks report the epigenetic state of each region in each sample, whereas the remaining tracks depict genomic regions that exhibit epigenetic differences between samples.

Promoter_ensembl Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Promoter_centered Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Promoter_region Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
CpG_Island Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
BonaFide_CGI Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
CGI_Promoter Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
NonCGI_Promoter Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
NonGenic_CGI Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Middle_Exon Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
3prim_UTR Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Conserved_Region Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Open_Chromatin Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Enhancer_H3K4me2 Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
CpG_Island_Shore Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
BonaFide_CGI_Shore Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
BonaFide_CGI_Border Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Imprinted_DMR Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Imprinted_Promoter Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
CancerGene_Promoter Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
CellStateGene_Promoter Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Tandem_Repeat Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Repeat_DNA Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Repeat_LINE Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Repeat_LowComplex Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Repeat_LTR Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Repeat_Simple Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Repeat_SINE Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Tiling_regions_5kb Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Tiling_regions_5kb_nonRepetitive Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Tiling_regions_5kb_repetitive Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)
Tiling_regions_2kb Region summary Region details Region vs. all (p-value) Region vs. all (q-value) Pairwise region-based (p-value) Pairwise region-based (q-value) Pairwise position-based (p-value) Pairwise position-based (q-value)

Supplementary Tables

The following tables contain the raw data behind all analyses reported above, and a wealth of candidate regions for biological interpretation and experimental follow-up. While the amount of information may be overwhelming, these tables can quite reasonably be analyzed with Excel. Once loaded into Excel, we recommend to hide or delete all columns that are not directly relevant to the comparison of interest, sort by the p-value or qvalClass column of interest and inspect the top hits using the UCSC Genome Browser (with all epigenome tracks from the Data section loaded).

Promoter_ensembl (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Promoter_centered (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Promoter_region (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
CpG_Island (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
BonaFide_CGI (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
CGI_Promoter (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
NonCGI_Promoter (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
NonGenic_CGI (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Middle_Exon (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
3prim_UTR (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Conserved_Region (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Open_Chromatin (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Enhancer_H3K4me2 (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
CpG_Island_Shore (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
BonaFide_CGI_Shore (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
BonaFide_CGI_Border (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Imprinted_DMR (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Imprinted_Promoter (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
CancerGene_Promoter (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
CellStateGene_Promoter (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Tandem_Repeat (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Repeat_DNA (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Repeat_LINE (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Repeat_LowComplex (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Repeat_LTR (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Repeat_Simple (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Repeat_SINE (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Tiling_regions_5kb (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Tiling_regions_5kb_nonRepetitive (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Tiling_regions_5kb_repetitive (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)
Tiling_regions_2kb (hg18) RRBS Basic table Comprehensive table Comprehensive table (filtered) Pairwise comparison (filtered)