Epigenome Analysis: RRBS_TechDev_Human_protocolOptimization

Basic Results

• Input data as UCSC Genome Browser tracks (these links work only if the source data directory is accessible over the Internet)
  Meth_Jurkat_BS14h.RRBS: RRBS CpG Track, RRBS Fragment Track, RRBS Read Track
  Meth_Jurkat_BS5h.RRBS: RRBS CpG Track, RRBS Fragment Track, RRBS Read Track
  Meth_Jurkat_BS2x5h.RRBS: RRBS CpG Track, RRBS Fragment Track, RRBS Read Track
  Demeth_Jurkat_BS14h.RRBS: RRBS CpG Track, RRBS Fragment Track, RRBS Read Track
  Demeth_Jurkat_BS5h.RRBS: RRBS CpG Track, RRBS Fragment Track, RRBS Read Track
  Demeth_Jurkat_BS2x5h.RRBS: RRBS CpG Track, RRBS Fragment Track, RRBS Read Track
  Human_colon_tumor_BS14h.RRBS: RRBS CpG Track, RRBS Fragment Track, RRBS Read Track
  Human_colon_normal_BS14h.RRBS: RRBS CpG Track, RRBS Fragment Track, RRBS Read Track
  


• Epigenome data by region (tab-separated tables)
  hg18, Promoter_ensembl, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Promoter_centered, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Promoter_region, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, CpG_Island, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, BonaFide_CGI, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, CGI_Promoter, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, NonCGI_Promoter, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, NonGenic_CGI, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Middle_Exon, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, 3prim_UTR, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Conserved_Region, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Open_Chromatin, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Enhancer_H3K4me2, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, CpG_Island_Shore, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, BonaFide_CGI_Shore, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, BonaFide_CGI_Border, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Imprinted_DMR, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Imprinted_Promoter, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, CancerGene_Promoter, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, CellStateGene_Promoter, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Tandem_Repeat, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Repeat_DNA, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Repeat_LINE, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Repeat_LowComplex, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Repeat_LTR, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Repeat_Simple, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Repeat_SINE, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Tiling_regions_5kb, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Tiling_regions_5kb_nonRepetitive, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  hg18, Tiling_regions_5kb_repetitive, RRBS:
  simple table - main table - filtered main table - pairwise comparison - filtered pairwise comparison
  
  

Diagrams and Visualizations

• Coverage pie charts:
  coverage_pie_chart_1_Promoter_ensembl.pdf
  coverage_pie_chart_2_Promoter_centered.pdf
  coverage_pie_chart_3_Promoter_region.pdf
  coverage_pie_chart_4_CpG_Island.pdf
  coverage_pie_chart_5_BonaFide_CGI.pdf
  coverage_pie_chart_6_CGI_Promoter.pdf
  coverage_pie_chart_7_NonCGI_Promoter.pdf
  coverage_pie_chart_8_NonGenic_CGI.pdf
  coverage_pie_chart_9_Middle_Exon.pdf
  coverage_pie_chart_10_3prim_UTR.pdf
  coverage_pie_chart_11_Conserved_Region.pdf
  coverage_pie_chart_12_Open_Chromatin.pdf
  coverage_pie_chart_13_Enhancer_H3K4me2.pdf
  coverage_pie_chart_14_CpG_Island_Shore.pdf
  coverage_pie_chart_15_BonaFide_CGI_Shore.pdf
  coverage_pie_chart_16_BonaFide_CGI_Border.pdf
  coverage_pie_chart_17_Imprinted_DMR.pdf
  coverage_pie_chart_18_Imprinted_Promoter.pdf
  coverage_pie_chart_19_CancerGene_Promoter.pdf
  coverage_pie_chart_20_CellStateGene_Promoter.pdf
  coverage_pie_chart_21_Tandem_Repeat.pdf
  coverage_pie_chart_22_Repeat_DNA.pdf
  coverage_pie_chart_23_Repeat_LINE.pdf
  coverage_pie_chart_24_Repeat_LowComplex.pdf
  coverage_pie_chart_25_Repeat_LTR.pdf
  coverage_pie_chart_26_Repeat_Simple.pdf
  coverage_pie_chart_27_Repeat_SINE.pdf
  coverage_pie_chart_28_Tiling_regions_5kb.pdf
  coverage_pie_chart_29_Tiling_regions_5kb_nonRepetitive.pdf
  coverage_pie_chart_30_Tiling_regions_5kb_repetitive.pdf
  


• Boxplots of mean DNA methylation (RRBS) or read frequency (ChIP, MethylCap):
  boxplot_diagram_1_Promoter_ensembl.pdf
  boxplot_diagram_2_Promoter_centered.pdf
  boxplot_diagram_3_Promoter_region.pdf
  boxplot_diagram_4_CpG_Island.pdf
  boxplot_diagram_5_BonaFide_CGI.pdf
  boxplot_diagram_6_CGI_Promoter.pdf
  boxplot_diagram_7_NonCGI_Promoter.pdf
  boxplot_diagram_8_NonGenic_CGI.pdf
  boxplot_diagram_9_Middle_Exon.pdf
  boxplot_diagram_10_3prim_UTR.pdf
  boxplot_diagram_11_Conserved_Region.pdf
  boxplot_diagram_12_Open_Chromatin.pdf
  boxplot_diagram_13_Enhancer_H3K4me2.pdf
  boxplot_diagram_14_CpG_Island_Shore.pdf
  boxplot_diagram_15_BonaFide_CGI_Shore.pdf
  boxplot_diagram_16_BonaFide_CGI_Border.pdf
  boxplot_diagram_17_Imprinted_DMR.pdf
  boxplot_diagram_18_Imprinted_Promoter.pdf
  boxplot_diagram_19_CancerGene_Promoter.pdf
  boxplot_diagram_20_CellStateGene_Promoter.pdf
  boxplot_diagram_21_Tandem_Repeat.pdf
  boxplot_diagram_22_Repeat_DNA.pdf
  boxplot_diagram_23_Repeat_LINE.pdf
  boxplot_diagram_24_Repeat_LowComplex.pdf
  boxplot_diagram_25_Repeat_LTR.pdf
  boxplot_diagram_26_Repeat_Simple.pdf
  boxplot_diagram_27_Repeat_SINE.pdf
  boxplot_diagram_28_Tiling_regions_5kb.pdf
  boxplot_diagram_29_Tiling_regions_5kb_nonRepetitive.pdf
  boxplot_diagram_30_Tiling_regions_5kb_repetitive.pdf
  


• Significant regions frequency bar chart - methylated/unmethylated regions and enriched/depeleted regions - general summary
  frequency_barchart_overview_1_Promoter_ensembl.pdf
  frequency_barchart_overview_2_Promoter_centered.pdf
  frequency_barchart_overview_3_Promoter_region.pdf
  frequency_barchart_overview_4_CpG_Island.pdf
  frequency_barchart_overview_5_BonaFide_CGI.pdf
  frequency_barchart_overview_6_CGI_Promoter.pdf
  frequency_barchart_overview_7_NonCGI_Promoter.pdf
  frequency_barchart_overview_8_NonGenic_CGI.pdf
  frequency_barchart_overview_9_Middle_Exon.pdf
  frequency_barchart_overview_10_3prim_UTR.pdf
  frequency_barchart_overview_11_Conserved_Region.pdf
  frequency_barchart_overview_12_Open_Chromatin.pdf
  frequency_barchart_overview_13_Enhancer_H3K4me2.pdf
  frequency_barchart_overview_14_CpG_Island_Shore.pdf
  frequency_barchart_overview_15_BonaFide_CGI_Shore.pdf
  frequency_barchart_overview_16_BonaFide_CGI_Border.pdf
  frequency_barchart_overview_17_Imprinted_DMR.pdf
  frequency_barchart_overview_18_Imprinted_Promoter.pdf
  frequency_barchart_overview_19_CancerGene_Promoter.pdf
  frequency_barchart_overview_20_CellStateGene_Promoter.pdf
  frequency_barchart_overview_21_Tandem_Repeat.pdf
  frequency_barchart_overview_22_Repeat_DNA.pdf
  frequency_barchart_overview_23_Repeat_LINE.pdf
  frequency_barchart_overview_24_Repeat_LowComplex.pdf
  frequency_barchart_overview_25_Repeat_LTR.pdf
  frequency_barchart_overview_26_Repeat_Simple.pdf
  frequency_barchart_overview_27_Repeat_SINE.pdf
  frequency_barchart_overview_28_Tiling_regions_5kb.pdf
  frequency_barchart_overview_29_Tiling_regions_5kb_nonRepetitive.pdf
  frequency_barchart_overview_30_Tiling_regions_5kb_repetitive.pdf
  


• Significant regions frequency bar chart - methylated/unmethylated regions and enriched/depeleted regions - detailed & stringent summary
  frequency_barchart_precise_1_Promoter_ensembl.pdf
  frequency_barchart_precise_2_Promoter_centered.pdf
  frequency_barchart_precise_3_Promoter_region.pdf
  frequency_barchart_precise_4_CpG_Island.pdf
  frequency_barchart_precise_5_BonaFide_CGI.pdf
  frequency_barchart_precise_6_CGI_Promoter.pdf
  frequency_barchart_precise_7_NonCGI_Promoter.pdf
  frequency_barchart_precise_8_NonGenic_CGI.pdf
  frequency_barchart_precise_9_Middle_Exon.pdf
  frequency_barchart_precise_10_3prim_UTR.pdf
  frequency_barchart_precise_11_Conserved_Region.pdf
  frequency_barchart_precise_12_Open_Chromatin.pdf
  frequency_barchart_precise_13_Enhancer_H3K4me2.pdf
  frequency_barchart_precise_14_CpG_Island_Shore.pdf
  frequency_barchart_precise_15_BonaFide_CGI_Shore.pdf
  frequency_barchart_precise_16_BonaFide_CGI_Border.pdf
  frequency_barchart_precise_17_Imprinted_DMR.pdf
  frequency_barchart_precise_18_Imprinted_Promoter.pdf
  frequency_barchart_precise_19_CancerGene_Promoter.pdf
  frequency_barchart_precise_20_CellStateGene_Promoter.pdf
  frequency_barchart_precise_21_Tandem_Repeat.pdf
  frequency_barchart_precise_22_Repeat_DNA.pdf
  frequency_barchart_precise_23_Repeat_LINE.pdf
  frequency_barchart_precise_24_Repeat_LowComplex.pdf
  frequency_barchart_precise_25_Repeat_LTR.pdf
  frequency_barchart_precise_26_Repeat_Simple.pdf
  frequency_barchart_precise_27_Repeat_SINE.pdf
  frequency_barchart_precise_28_Tiling_regions_5kb.pdf
  frequency_barchart_precise_29_Tiling_regions_5kb_nonRepetitive.pdf
  frequency_barchart_precise_30_Tiling_regions_5kb_repetitive.pdf
  


• Significant regions frequency bar chart - sample-specifically altered regions compared to all other samples (p-value based)
  frequency_barchart_pvalCompVsAll_1_Promoter_ensembl.pdf
  frequency_barchart_pvalCompVsAll_2_Promoter_centered.pdf
  frequency_barchart_pvalCompVsAll_3_Promoter_region.pdf
  frequency_barchart_pvalCompVsAll_4_CpG_Island.pdf
  frequency_barchart_pvalCompVsAll_5_BonaFide_CGI.pdf
  frequency_barchart_pvalCompVsAll_6_CGI_Promoter.pdf
  frequency_barchart_pvalCompVsAll_7_NonCGI_Promoter.pdf
  frequency_barchart_pvalCompVsAll_8_NonGenic_CGI.pdf
  frequency_barchart_pvalCompVsAll_9_Middle_Exon.pdf
  frequency_barchart_pvalCompVsAll_10_3prim_UTR.pdf
  frequency_barchart_pvalCompVsAll_11_Conserved_Region.pdf
  frequency_barchart_pvalCompVsAll_12_Open_Chromatin.pdf
  frequency_barchart_pvalCompVsAll_13_Enhancer_H3K4me2.pdf
  frequency_barchart_pvalCompVsAll_14_CpG_Island_Shore.pdf
  frequency_barchart_pvalCompVsAll_15_BonaFide_CGI_Shore.pdf
  frequency_barchart_pvalCompVsAll_16_BonaFide_CGI_Border.pdf
  frequency_barchart_pvalCompVsAll_17_Imprinted_DMR.pdf
  frequency_barchart_pvalCompVsAll_18_Imprinted_Promoter.pdf
  frequency_barchart_pvalCompVsAll_19_CancerGene_Promoter.pdf
  frequency_barchart_pvalCompVsAll_20_CellStateGene_Promoter.pdf
  frequency_barchart_pvalCompVsAll_21_Tandem_Repeat.pdf
  frequency_barchart_pvalCompVsAll_22_Repeat_DNA.pdf
  frequency_barchart_pvalCompVsAll_23_Repeat_LINE.pdf
  frequency_barchart_pvalCompVsAll_24_Repeat_LowComplex.pdf
  frequency_barchart_pvalCompVsAll_25_Repeat_LTR.pdf
  frequency_barchart_pvalCompVsAll_26_Repeat_Simple.pdf
  frequency_barchart_pvalCompVsAll_27_Repeat_SINE.pdf
  frequency_barchart_pvalCompVsAll_28_Tiling_regions_5kb.pdf
  frequency_barchart_pvalCompVsAll_29_Tiling_regions_5kb_nonRepetitive.pdf
  frequency_barchart_pvalCompVsAll_30_Tiling_regions_5kb_repetitive.pdf
  


• Significant regions frequency bar chart - sample-specifically altered regions compared to all other samples (q-value based)
  frequency_barchart_qvalCompVsAll_1_Promoter_ensembl.pdf
  frequency_barchart_qvalCompVsAll_2_Promoter_centered.pdf
  frequency_barchart_qvalCompVsAll_3_Promoter_region.pdf
  frequency_barchart_qvalCompVsAll_4_CpG_Island.pdf
  frequency_barchart_qvalCompVsAll_5_BonaFide_CGI.pdf
  frequency_barchart_qvalCompVsAll_6_CGI_Promoter.pdf
  frequency_barchart_qvalCompVsAll_7_NonCGI_Promoter.pdf
  frequency_barchart_qvalCompVsAll_8_NonGenic_CGI.pdf
  frequency_barchart_qvalCompVsAll_9_Middle_Exon.pdf
  frequency_barchart_qvalCompVsAll_10_3prim_UTR.pdf
  frequency_barchart_qvalCompVsAll_11_Conserved_Region.pdf
  frequency_barchart_qvalCompVsAll_12_Open_Chromatin.pdf
  frequency_barchart_qvalCompVsAll_13_Enhancer_H3K4me2.pdf
  frequency_barchart_qvalCompVsAll_14_CpG_Island_Shore.pdf
  frequency_barchart_qvalCompVsAll_15_BonaFide_CGI_Shore.pdf
  frequency_barchart_qvalCompVsAll_16_BonaFide_CGI_Border.pdf
  frequency_barchart_qvalCompVsAll_17_Imprinted_DMR.pdf
  frequency_barchart_qvalCompVsAll_18_Imprinted_Promoter.pdf
  frequency_barchart_qvalCompVsAll_19_CancerGene_Promoter.pdf
  frequency_barchart_qvalCompVsAll_20_CellStateGene_Promoter.pdf
  frequency_barchart_qvalCompVsAll_21_Tandem_Repeat.pdf
  frequency_barchart_qvalCompVsAll_22_Repeat_DNA.pdf
  frequency_barchart_qvalCompVsAll_23_Repeat_LINE.pdf
  frequency_barchart_qvalCompVsAll_24_Repeat_LowComplex.pdf
  frequency_barchart_qvalCompVsAll_25_Repeat_LTR.pdf
  frequency_barchart_qvalCompVsAll_26_Repeat_Simple.pdf
  frequency_barchart_qvalCompVsAll_27_Repeat_SINE.pdf
  frequency_barchart_qvalCompVsAll_28_Tiling_regions_5kb.pdf
  frequency_barchart_qvalCompVsAll_29_Tiling_regions_5kb_nonRepetitive.pdf
  frequency_barchart_qvalCompVsAll_30_Tiling_regions_5kb_repetitive.pdf
  


• Significant regions frequency bar chart - signficant differences between all pairs of samples (p-value based)
  frequency_barchart_pvalPairwiseComp_1_Promoter_ensembl.pdf
  frequency_barchart_pvalPairwiseComp_2_Promoter_centered.pdf
  frequency_barchart_pvalPairwiseComp_3_Promoter_region.pdf
  frequency_barchart_pvalPairwiseComp_4_CpG_Island.pdf
  frequency_barchart_pvalPairwiseComp_5_BonaFide_CGI.pdf
  frequency_barchart_pvalPairwiseComp_6_CGI_Promoter.pdf
  frequency_barchart_pvalPairwiseComp_7_NonCGI_Promoter.pdf
  frequency_barchart_pvalPairwiseComp_8_NonGenic_CGI.pdf
  frequency_barchart_pvalPairwiseComp_9_Middle_Exon.pdf
  frequency_barchart_pvalPairwiseComp_10_3prim_UTR.pdf
  frequency_barchart_pvalPairwiseComp_11_Conserved_Region.pdf
  frequency_barchart_pvalPairwiseComp_12_Open_Chromatin.pdf
  frequency_barchart_pvalPairwiseComp_13_Enhancer_H3K4me2.pdf
  frequency_barchart_pvalPairwiseComp_14_CpG_Island_Shore.pdf
  frequency_barchart_pvalPairwiseComp_15_BonaFide_CGI_Shore.pdf
  frequency_barchart_pvalPairwiseComp_16_BonaFide_CGI_Border.pdf
  frequency_barchart_pvalPairwiseComp_17_Imprinted_DMR.pdf
  frequency_barchart_pvalPairwiseComp_18_Imprinted_Promoter.pdf
  frequency_barchart_pvalPairwiseComp_19_CancerGene_Promoter.pdf
  frequency_barchart_pvalPairwiseComp_20_CellStateGene_Promoter.pdf
  frequency_barchart_pvalPairwiseComp_21_Tandem_Repeat.pdf
  frequency_barchart_pvalPairwiseComp_22_Repeat_DNA.pdf
  frequency_barchart_pvalPairwiseComp_23_Repeat_LINE.pdf
  frequency_barchart_pvalPairwiseComp_24_Repeat_LowComplex.pdf
  frequency_barchart_pvalPairwiseComp_25_Repeat_LTR.pdf
  frequency_barchart_pvalPairwiseComp_26_Repeat_Simple.pdf
  frequency_barchart_pvalPairwiseComp_27_Repeat_SINE.pdf
  frequency_barchart_pvalPairwiseComp_28_Tiling_regions_5kb.pdf
  frequency_barchart_pvalPairwiseComp_29_Tiling_regions_5kb_nonRepetitive.pdf
  frequency_barchart_pvalPairwiseComp_30_Tiling_regions_5kb_repetitive.pdf
  


• Significant regions frequency bar chart - signficant differences between all pairs of samples (q-value based)
  frequency_barchart_qvalPairwiseComp_1_Promoter_ensembl.pdf
  frequency_barchart_qvalPairwiseComp_2_Promoter_centered.pdf
  frequency_barchart_qvalPairwiseComp_3_Promoter_region.pdf
  frequency_barchart_qvalPairwiseComp_4_CpG_Island.pdf
  frequency_barchart_qvalPairwiseComp_5_BonaFide_CGI.pdf
  frequency_barchart_qvalPairwiseComp_6_CGI_Promoter.pdf
  frequency_barchart_qvalPairwiseComp_7_NonCGI_Promoter.pdf
  frequency_barchart_qvalPairwiseComp_8_NonGenic_CGI.pdf
  frequency_barchart_qvalPairwiseComp_9_Middle_Exon.pdf
  frequency_barchart_qvalPairwiseComp_10_3prim_UTR.pdf
  frequency_barchart_qvalPairwiseComp_11_Conserved_Region.pdf
  frequency_barchart_qvalPairwiseComp_12_Open_Chromatin.pdf
  frequency_barchart_qvalPairwiseComp_13_Enhancer_H3K4me2.pdf
  frequency_barchart_qvalPairwiseComp_14_CpG_Island_Shore.pdf
  frequency_barchart_qvalPairwiseComp_15_BonaFide_CGI_Shore.pdf
  frequency_barchart_qvalPairwiseComp_16_BonaFide_CGI_Border.pdf
  frequency_barchart_qvalPairwiseComp_17_Imprinted_DMR.pdf
  frequency_barchart_qvalPairwiseComp_18_Imprinted_Promoter.pdf
  frequency_barchart_qvalPairwiseComp_19_CancerGene_Promoter.pdf
  frequency_barchart_qvalPairwiseComp_20_CellStateGene_Promoter.pdf
  frequency_barchart_qvalPairwiseComp_21_Tandem_Repeat.pdf
  frequency_barchart_qvalPairwiseComp_22_Repeat_DNA.pdf
  frequency_barchart_qvalPairwiseComp_23_Repeat_LINE.pdf
  frequency_barchart_qvalPairwiseComp_24_Repeat_LowComplex.pdf
  frequency_barchart_qvalPairwiseComp_25_Repeat_LTR.pdf
  frequency_barchart_qvalPairwiseComp_26_Repeat_Simple.pdf
  frequency_barchart_qvalPairwiseComp_27_Repeat_SINE.pdf
  frequency_barchart_qvalPairwiseComp_28_Tiling_regions_5kb.pdf
  frequency_barchart_qvalPairwiseComp_29_Tiling_regions_5kb_nonRepetitive.pdf
  frequency_barchart_qvalPairwiseComp_30_Tiling_regions_5kb_repetitive.pdf
  


• Number of significant differences between samples:
  significant_differences_1_Promoter_ensembl.pdf
  significant_differences_2_Promoter_centered.pdf
  significant_differences_3_Promoter_region.pdf
  significant_differences_4_CpG_Island.pdf
  significant_differences_5_BonaFide_CGI.pdf
  significant_differences_6_CGI_Promoter.pdf
  significant_differences_7_NonCGI_Promoter.pdf
  significant_differences_8_NonGenic_CGI.pdf
  significant_differences_9_Middle_Exon.pdf
  significant_differences_10_3prim_UTR.pdf
  significant_differences_11_Conserved_Region.pdf
  significant_differences_12_Open_Chromatin.pdf
  significant_differences_13_Enhancer_H3K4me2.pdf
  significant_differences_14_CpG_Island_Shore.pdf
  significant_differences_15_BonaFide_CGI_Shore.pdf
  significant_differences_16_BonaFide_CGI_Border.pdf
  significant_differences_17_Imprinted_DMR.pdf
  significant_differences_18_Imprinted_Promoter.pdf
  significant_differences_19_CancerGene_Promoter.pdf
  significant_differences_20_CellStateGene_Promoter.pdf
  significant_differences_21_Tandem_Repeat.pdf
  significant_differences_22_Repeat_DNA.pdf
  significant_differences_23_Repeat_LINE.pdf
  significant_differences_24_Repeat_LowComplex.pdf
  significant_differences_25_Repeat_LTR.pdf
  significant_differences_26_Repeat_Simple.pdf
  significant_differences_27_Repeat_SINE.pdf
  significant_differences_28_Tiling_regions_5kb.pdf
  significant_differences_29_Tiling_regions_5kb_nonRepetitive.pdf
  significant_differences_30_Tiling_regions_5kb_repetitive.pdf
  


• Pairwise scatterplots including all regions with sufficient coverage:
  pairwise_scatterplots_1_Promoter_ensembl.png
  pairwise_scatterplots_2_Promoter_centered.png
  pairwise_scatterplots_3_Promoter_region.png
  pairwise_scatterplots_4_CpG_Island.png
  pairwise_scatterplots_5_BonaFide_CGI.png
  pairwise_scatterplots_6_CGI_Promoter.png
  pairwise_scatterplots_7_NonCGI_Promoter.png
  pairwise_scatterplots_8_NonGenic_CGI.png
  pairwise_scatterplots_9_Middle_Exon.png
  pairwise_scatterplots_10_3prim_UTR.png
  pairwise_scatterplots_11_Conserved_Region.png
  pairwise_scatterplots_12_Open_Chromatin.png
  pairwise_scatterplots_13_Enhancer_H3K4me2.png
  pairwise_scatterplots_14_CpG_Island_Shore.png
  pairwise_scatterplots_15_BonaFide_CGI_Shore.png
  pairwise_scatterplots_16_BonaFide_CGI_Border.png
  pairwise_scatterplots_17_Imprinted_DMR.png
  pairwise_scatterplots_18_Imprinted_Promoter.png
  pairwise_scatterplots_19_CancerGene_Promoter.png
  pairwise_scatterplots_20_CellStateGene_Promoter.png
  pairwise_scatterplots_21_Tandem_Repeat.png
  pairwise_scatterplots_22_Repeat_DNA.png
  pairwise_scatterplots_23_Repeat_LINE.png
  pairwise_scatterplots_24_Repeat_LowComplex.png
  pairwise_scatterplots_25_Repeat_LTR.png
  pairwise_scatterplots_26_Repeat_Simple.png
  pairwise_scatterplots_27_Repeat_SINE.png
  pairwise_scatterplots_28_Tiling_regions_5kb.png
  pairwise_scatterplots_29_Tiling_regions_5kb_nonRepetitive.png
  pairwise_scatterplots_30_Tiling_regions_5kb_repetitive.png
  


• Pairwise correlations between samples:
  sample_correlation_table_1_Promoter_ensembl.txt
  sample_correlation_table_2_Promoter_centered.txt
  sample_correlation_table_3_Promoter_region.txt
  sample_correlation_table_4_CpG_Island.txt
  sample_correlation_table_5_BonaFide_CGI.txt
  sample_correlation_table_6_CGI_Promoter.txt
  sample_correlation_table_7_NonCGI_Promoter.txt
  sample_correlation_table_8_NonGenic_CGI.txt
  sample_correlation_table_9_Middle_Exon.txt
  sample_correlation_table_10_3prim_UTR.txt
  sample_correlation_table_11_Conserved_Region.txt
  sample_correlation_table_12_Open_Chromatin.txt
  sample_correlation_table_13_Enhancer_H3K4me2.txt
  sample_correlation_table_14_CpG_Island_Shore.txt
  sample_correlation_table_15_BonaFide_CGI_Shore.txt
  sample_correlation_table_16_BonaFide_CGI_Border.txt
  sample_correlation_table_17_Imprinted_DMR.txt
  sample_correlation_table_18_Imprinted_Promoter.txt
  sample_correlation_table_19_CancerGene_Promoter.txt
  sample_correlation_table_20_CellStateGene_Promoter.txt
  sample_correlation_table_21_Tandem_Repeat.txt
  sample_correlation_table_22_Repeat_DNA.txt
  sample_correlation_table_23_Repeat_LINE.txt
  sample_correlation_table_24_Repeat_LowComplex.txt
  sample_correlation_table_25_Repeat_LTR.txt
  sample_correlation_table_26_Repeat_Simple.txt
  sample_correlation_table_27_Repeat_SINE.txt
  sample_correlation_table_28_Tiling_regions_5kb.txt
  sample_correlation_table_29_Tiling_regions_5kb_nonRepetitive.txt
  sample_correlation_table_30_Tiling_regions_5kb_repetitive.txt
  


• Clustering diagrams by samples:
  clustering_by_samples_1_Promoter_ensembl.pdf
  clustering_by_samples_2_Promoter_centered.pdf
  clustering_by_samples_3_Promoter_region.pdf
  clustering_by_samples_4_CpG_Island.pdf
  clustering_by_samples_5_BonaFide_CGI.pdf
  clustering_by_samples_6_CGI_Promoter.pdf
  clustering_by_samples_7_NonCGI_Promoter.pdf
  clustering_by_samples_8_NonGenic_CGI.pdf
  clustering_by_samples_9_Middle_Exon.pdf
  clustering_by_samples_10_3prim_UTR.pdf
  clustering_by_samples_11_Conserved_Region.pdf
  clustering_by_samples_12_Open_Chromatin.pdf
  clustering_by_samples_13_Enhancer_H3K4me2.pdf
  clustering_by_samples_14_CpG_Island_Shore.pdf
  clustering_by_samples_15_BonaFide_CGI_Shore.pdf
  clustering_by_samples_16_BonaFide_CGI_Border.pdf
  clustering_by_samples_17_Imprinted_DMR.pdf
  clustering_by_samples_18_Imprinted_Promoter.pdf
  clustering_by_samples_19_CancerGene_Promoter.pdf
  clustering_by_samples_20_CellStateGene_Promoter.pdf
  clustering_by_samples_21_Tandem_Repeat.pdf
  clustering_by_samples_22_Repeat_DNA.pdf
  clustering_by_samples_23_Repeat_LINE.pdf
  clustering_by_samples_24_Repeat_LowComplex.pdf
  clustering_by_samples_25_Repeat_LTR.pdf
  clustering_by_samples_26_Repeat_Simple.pdf
  clustering_by_samples_27_Repeat_SINE.pdf
  clustering_by_samples_28_Tiling_regions_5kb.pdf
  clustering_by_samples_29_Tiling_regions_5kb_nonRepetitive.pdf
  clustering_by_samples_30_Tiling_regions_5kb_repetitive.pdf
  


• Clustering diagrams by regions:
  clustering_by_regions_1_Promoter_ensembl.png
  clustering_by_regions_2_Promoter_centered.png
  clustering_by_regions_3_Promoter_region.png
  clustering_by_regions_4_CpG_Island.png
  clustering_by_regions_5_BonaFide_CGI.png
  clustering_by_regions_6_CGI_Promoter.png
  clustering_by_regions_7_NonCGI_Promoter.png
  clustering_by_regions_8_NonGenic_CGI.png
  clustering_by_regions_9_Middle_Exon.png
  clustering_by_regions_10_3prim_UTR.png
  clustering_by_regions_11_Conserved_Region.png
  clustering_by_regions_12_Open_Chromatin.png
  clustering_by_regions_13_Enhancer_H3K4me2.png
  clustering_by_regions_14_CpG_Island_Shore.png
  clustering_by_regions_15_BonaFide_CGI_Shore.png
  clustering_by_regions_16_BonaFide_CGI_Border.png
  clustering_by_regions_17_Imprinted_DMR.png
  clustering_by_regions_18_Imprinted_Promoter.png
  clustering_by_regions_19_CancerGene_Promoter.png
  clustering_by_regions_20_CellStateGene_Promoter.png
  clustering_by_regions_21_Tandem_Repeat.png
  clustering_by_regions_22_Repeat_DNA.png
  clustering_by_regions_23_Repeat_LINE.png
  clustering_by_regions_24_Repeat_LowComplex.png
  clustering_by_regions_25_Repeat_LTR.png
  clustering_by_regions_26_Repeat_Simple.png
  clustering_by_regions_27_Repeat_SINE.png
  clustering_by_regions_28_Tiling_regions_5kb.png
  clustering_by_regions_29_Tiling_regions_5kb_nonRepetitive.png
  clustering_by_regions_30_Tiling_regions_5kb_repetitive.png
  


• Clustering diagrams by regions and samples:
  clustering_by_regions,samples_1_Promoter_ensembl.png
  clustering_by_regions,samples_2_Promoter_centered.png
  clustering_by_regions,samples_3_Promoter_region.png
  clustering_by_regions,samples_4_CpG_Island.png
  clustering_by_regions,samples_5_BonaFide_CGI.png
  clustering_by_regions,samples_6_CGI_Promoter.png
  clustering_by_regions,samples_7_NonCGI_Promoter.png
  clustering_by_regions,samples_8_NonGenic_CGI.png
  clustering_by_regions,samples_9_Middle_Exon.png
  clustering_by_regions,samples_10_3prim_UTR.png
  clustering_by_regions,samples_11_Conserved_Region.png
  clustering_by_regions,samples_12_Open_Chromatin.png
  clustering_by_regions,samples_13_Enhancer_H3K4me2.png
  clustering_by_regions,samples_14_CpG_Island_Shore.png
  clustering_by_regions,samples_15_BonaFide_CGI_Shore.png
  clustering_by_regions,samples_16_BonaFide_CGI_Border.png
  clustering_by_regions,samples_17_Imprinted_DMR.png
  clustering_by_regions,samples_18_Imprinted_Promoter.png
  clustering_by_regions,samples_19_CancerGene_Promoter.png
  clustering_by_regions,samples_20_CellStateGene_Promoter.png
  clustering_by_regions,samples_21_Tandem_Repeat.png
  clustering_by_regions,samples_22_Repeat_DNA.png
  clustering_by_regions,samples_23_Repeat_LINE.png
  clustering_by_regions,samples_24_Repeat_LowComplex.png
  clustering_by_regions,samples_25_Repeat_LTR.png
  clustering_by_regions,samples_26_Repeat_Simple.png
  clustering_by_regions,samples_27_Repeat_SINE.png
  clustering_by_regions,samples_28_Tiling_regions_5kb.png
  clustering_by_regions,samples_29_Tiling_regions_5kb_nonRepetitive.png
  clustering_by_regions,samples_30_Tiling_regions_5kb_repetitive.png
  

UCSC Genome Browser Tracks

• Methylated/unmethylated and enriched/depeleted regions - general tracks:
  genome_browser_track_overview_Promoter_ensembl.bed.gz
  genome_browser_track_overview_Promoter_centered.bed.gz
  genome_browser_track_overview_Promoter_region.bed.gz
  genome_browser_track_overview_CpG_Island.bed.gz
  genome_browser_track_overview_BonaFide_CGI.bed.gz
  genome_browser_track_overview_CGI_Promoter.bed.gz
  genome_browser_track_overview_NonCGI_Promoter.bed.gz
  genome_browser_track_overview_NonGenic_CGI.bed.gz
  genome_browser_track_overview_Middle_Exon.bed.gz
  genome_browser_track_overview_3prim_UTR.bed.gz
  genome_browser_track_overview_Conserved_Region.bed.gz
  genome_browser_track_overview_Open_Chromatin.bed.gz
  genome_browser_track_overview_Enhancer_H3K4me2.bed.gz
  genome_browser_track_overview_CpG_Island_Shore.bed.gz
  genome_browser_track_overview_BonaFide_CGI_Shore.bed.gz
  genome_browser_track_overview_BonaFide_CGI_Border.bed.gz
  genome_browser_track_overview_Imprinted_DMR.bed.gz
  genome_browser_track_overview_Imprinted_Promoter.bed.gz
  genome_browser_track_overview_CancerGene_Promoter.bed.gz
  genome_browser_track_overview_CellStateGene_Promoter.bed.gz
  genome_browser_track_overview_Tandem_Repeat.bed.gz
  genome_browser_track_overview_Repeat_DNA.bed.gz
  genome_browser_track_overview_Repeat_LINE.bed.gz
  genome_browser_track_overview_Repeat_LowComplex.bed.gz
  genome_browser_track_overview_Repeat_LTR.bed.gz
  genome_browser_track_overview_Repeat_Simple.bed.gz
  genome_browser_track_overview_Repeat_SINE.bed.gz
  genome_browser_track_overview_Tiling_regions_5kb.bed.gz
  genome_browser_track_overview_Tiling_regions_5kb_nonRepetitive.bed.gz
  genome_browser_track_overview_Tiling_regions_5kb_repetitive.bed.gz
  


• Methylated/unmethylated and enriched/depeleted regions - detailed & stringent tracks:
  genome_browser_track_precise_Promoter_ensembl.bed.gz
  genome_browser_track_precise_Promoter_centered.bed.gz
  genome_browser_track_precise_Promoter_region.bed.gz
  genome_browser_track_precise_CpG_Island.bed.gz
  genome_browser_track_precise_BonaFide_CGI.bed.gz
  genome_browser_track_precise_CGI_Promoter.bed.gz
  genome_browser_track_precise_NonCGI_Promoter.bed.gz
  genome_browser_track_precise_NonGenic_CGI.bed.gz
  genome_browser_track_precise_Middle_Exon.bed.gz
  genome_browser_track_precise_3prim_UTR.bed.gz
  genome_browser_track_precise_Conserved_Region.bed.gz
  genome_browser_track_precise_Open_Chromatin.bed.gz
  genome_browser_track_precise_Enhancer_H3K4me2.bed.gz
  genome_browser_track_precise_CpG_Island_Shore.bed.gz
  genome_browser_track_precise_BonaFide_CGI_Shore.bed.gz
  genome_browser_track_precise_BonaFide_CGI_Border.bed.gz
  genome_browser_track_precise_Imprinted_DMR.bed.gz
  genome_browser_track_precise_Imprinted_Promoter.bed.gz
  genome_browser_track_precise_CancerGene_Promoter.bed.gz
  genome_browser_track_precise_CellStateGene_Promoter.bed.gz
  genome_browser_track_precise_Tandem_Repeat.bed.gz
  genome_browser_track_precise_Repeat_DNA.bed.gz
  genome_browser_track_precise_Repeat_LINE.bed.gz
  genome_browser_track_precise_Repeat_LowComplex.bed.gz
  genome_browser_track_precise_Repeat_LTR.bed.gz
  genome_browser_track_precise_Repeat_Simple.bed.gz
  genome_browser_track_precise_Repeat_SINE.bed.gz
  genome_browser_track_precise_Tiling_regions_5kb.bed.gz
  genome_browser_track_precise_Tiling_regions_5kb_nonRepetitive.bed.gz
  genome_browser_track_precise_Tiling_regions_5kb_repetitive.bed.gz
  


• Sample-specifically altered regions compared to all other samples (p-value based):
  genome_browser_track_pvalCompVsAll_Promoter_ensembl.bed.gz
  genome_browser_track_pvalCompVsAll_Promoter_centered.bed.gz
  genome_browser_track_pvalCompVsAll_Promoter_region.bed.gz
  genome_browser_track_pvalCompVsAll_CpG_Island.bed.gz
  genome_browser_track_pvalCompVsAll_BonaFide_CGI.bed.gz
  genome_browser_track_pvalCompVsAll_CGI_Promoter.bed.gz
  genome_browser_track_pvalCompVsAll_NonCGI_Promoter.bed.gz
  genome_browser_track_pvalCompVsAll_NonGenic_CGI.bed.gz
  genome_browser_track_pvalCompVsAll_Middle_Exon.bed.gz
  genome_browser_track_pvalCompVsAll_3prim_UTR.bed.gz
  genome_browser_track_pvalCompVsAll_Conserved_Region.bed.gz
  genome_browser_track_pvalCompVsAll_Open_Chromatin.bed.gz
  genome_browser_track_pvalCompVsAll_Enhancer_H3K4me2.bed.gz
  genome_browser_track_pvalCompVsAll_CpG_Island_Shore.bed.gz
  genome_browser_track_pvalCompVsAll_BonaFide_CGI_Shore.bed.gz
  genome_browser_track_pvalCompVsAll_BonaFide_CGI_Border.bed.gz
  genome_browser_track_pvalCompVsAll_Imprinted_DMR.bed.gz
  genome_browser_track_pvalCompVsAll_Imprinted_Promoter.bed.gz
  genome_browser_track_pvalCompVsAll_CancerGene_Promoter.bed.gz
  genome_browser_track_pvalCompVsAll_CellStateGene_Promoter.bed.gz
  genome_browser_track_pvalCompVsAll_Tandem_Repeat.bed.gz
  genome_browser_track_pvalCompVsAll_Repeat_DNA.bed.gz
  genome_browser_track_pvalCompVsAll_Repeat_LINE.bed.gz
  genome_browser_track_pvalCompVsAll_Repeat_LowComplex.bed.gz
  genome_browser_track_pvalCompVsAll_Repeat_LTR.bed.gz
  genome_browser_track_pvalCompVsAll_Repeat_Simple.bed.gz
  genome_browser_track_pvalCompVsAll_Repeat_SINE.bed.gz
  genome_browser_track_pvalCompVsAll_Tiling_regions_5kb.bed.gz
  genome_browser_track_pvalCompVsAll_Tiling_regions_5kb_nonRepetitive.bed.gz
  genome_browser_track_pvalCompVsAll_Tiling_regions_5kb_repetitive.bed.gz
  


• Sample-specifically altered regions compared to all other samples (q-value based):
  genome_browser_track_qvalCompVsAll_Promoter_ensembl.bed.gz
  genome_browser_track_qvalCompVsAll_Promoter_centered.bed.gz
  genome_browser_track_qvalCompVsAll_Promoter_region.bed.gz
  genome_browser_track_qvalCompVsAll_CpG_Island.bed.gz
  genome_browser_track_qvalCompVsAll_BonaFide_CGI.bed.gz
  genome_browser_track_qvalCompVsAll_CGI_Promoter.bed.gz
  genome_browser_track_qvalCompVsAll_NonCGI_Promoter.bed.gz
  genome_browser_track_qvalCompVsAll_NonGenic_CGI.bed.gz
  genome_browser_track_qvalCompVsAll_Middle_Exon.bed.gz
  genome_browser_track_qvalCompVsAll_3prim_UTR.bed.gz
  genome_browser_track_qvalCompVsAll_Conserved_Region.bed.gz
  genome_browser_track_qvalCompVsAll_Open_Chromatin.bed.gz
  genome_browser_track_qvalCompVsAll_Enhancer_H3K4me2.bed.gz
  genome_browser_track_qvalCompVsAll_CpG_Island_Shore.bed.gz
  genome_browser_track_qvalCompVsAll_BonaFide_CGI_Shore.bed.gz
  genome_browser_track_qvalCompVsAll_BonaFide_CGI_Border.bed.gz
  genome_browser_track_qvalCompVsAll_Imprinted_DMR.bed.gz
  genome_browser_track_qvalCompVsAll_Imprinted_Promoter.bed.gz
  genome_browser_track_qvalCompVsAll_CancerGene_Promoter.bed.gz
  genome_browser_track_qvalCompVsAll_CellStateGene_Promoter.bed.gz
  genome_browser_track_qvalCompVsAll_Tandem_Repeat.bed.gz
  genome_browser_track_qvalCompVsAll_Repeat_DNA.bed.gz
  genome_browser_track_qvalCompVsAll_Repeat_LINE.bed.gz
  genome_browser_track_qvalCompVsAll_Repeat_LowComplex.bed.gz
  genome_browser_track_qvalCompVsAll_Repeat_LTR.bed.gz
  genome_browser_track_qvalCompVsAll_Repeat_Simple.bed.gz
  genome_browser_track_qvalCompVsAll_Repeat_SINE.bed.gz
  genome_browser_track_qvalCompVsAll_Tiling_regions_5kb.bed.gz
  genome_browser_track_qvalCompVsAll_Tiling_regions_5kb_nonRepetitive.bed.gz
  genome_browser_track_qvalCompVsAll_Tiling_regions_5kb_repetitive.bed.gz
  


• Signficant differences between all pairs of samples (p-value based):
  genome_browser_track_pvalPairwiseComp_Promoter_ensembl.bed.gz
  genome_browser_track_pvalPairwiseComp_Promoter_centered.bed.gz
  genome_browser_track_pvalPairwiseComp_Promoter_region.bed.gz
  genome_browser_track_pvalPairwiseComp_CpG_Island.bed.gz
  genome_browser_track_pvalPairwiseComp_BonaFide_CGI.bed.gz
  genome_browser_track_pvalPairwiseComp_CGI_Promoter.bed.gz
  genome_browser_track_pvalPairwiseComp_NonCGI_Promoter.bed.gz
  genome_browser_track_pvalPairwiseComp_NonGenic_CGI.bed.gz
  genome_browser_track_pvalPairwiseComp_Middle_Exon.bed.gz
  genome_browser_track_pvalPairwiseComp_3prim_UTR.bed.gz
  genome_browser_track_pvalPairwiseComp_Conserved_Region.bed.gz
  genome_browser_track_pvalPairwiseComp_Open_Chromatin.bed.gz
  genome_browser_track_pvalPairwiseComp_Enhancer_H3K4me2.bed.gz
  genome_browser_track_pvalPairwiseComp_CpG_Island_Shore.bed.gz
  genome_browser_track_pvalPairwiseComp_BonaFide_CGI_Shore.bed.gz
  genome_browser_track_pvalPairwiseComp_BonaFide_CGI_Border.bed.gz
  genome_browser_track_pvalPairwiseComp_Imprinted_DMR.bed.gz
  genome_browser_track_pvalPairwiseComp_Imprinted_Promoter.bed.gz
  genome_browser_track_pvalPairwiseComp_CancerGene_Promoter.bed.gz
  genome_browser_track_pvalPairwiseComp_CellStateGene_Promoter.bed.gz
  genome_browser_track_pvalPairwiseComp_Tandem_Repeat.bed.gz
  genome_browser_track_pvalPairwiseComp_Repeat_DNA.bed.gz
  genome_browser_track_pvalPairwiseComp_Repeat_LINE.bed.gz
  genome_browser_track_pvalPairwiseComp_Repeat_LowComplex.bed.gz
  genome_browser_track_pvalPairwiseComp_Repeat_LTR.bed.gz
  genome_browser_track_pvalPairwiseComp_Repeat_Simple.bed.gz
  genome_browser_track_pvalPairwiseComp_Repeat_SINE.bed.gz
  genome_browser_track_pvalPairwiseComp_Tiling_regions_5kb.bed.gz
  genome_browser_track_pvalPairwiseComp_Tiling_regions_5kb_nonRepetitive.bed.gz
  genome_browser_track_pvalPairwiseComp_Tiling_regions_5kb_repetitive.bed.gz
  


• Signficant differences between all pairs of samples (q-value based):
  genome_browser_track_qvalPairwiseComp_Promoter_ensembl.bed.gz
  genome_browser_track_qvalPairwiseComp_Promoter_centered.bed.gz
  genome_browser_track_qvalPairwiseComp_Promoter_region.bed.gz
  genome_browser_track_qvalPairwiseComp_CpG_Island.bed.gz
  genome_browser_track_qvalPairwiseComp_BonaFide_CGI.bed.gz
  genome_browser_track_qvalPairwiseComp_CGI_Promoter.bed.gz
  genome_browser_track_qvalPairwiseComp_NonCGI_Promoter.bed.gz
  genome_browser_track_qvalPairwiseComp_NonGenic_CGI.bed.gz
  genome_browser_track_qvalPairwiseComp_Middle_Exon.bed.gz
  genome_browser_track_qvalPairwiseComp_3prim_UTR.bed.gz
  genome_browser_track_qvalPairwiseComp_Conserved_Region.bed.gz
  genome_browser_track_qvalPairwiseComp_Open_Chromatin.bed.gz
  genome_browser_track_qvalPairwiseComp_Enhancer_H3K4me2.bed.gz
  genome_browser_track_qvalPairwiseComp_CpG_Island_Shore.bed.gz
  genome_browser_track_qvalPairwiseComp_BonaFide_CGI_Shore.bed.gz
  genome_browser_track_qvalPairwiseComp_BonaFide_CGI_Border.bed.gz
  genome_browser_track_qvalPairwiseComp_Imprinted_DMR.bed.gz
  genome_browser_track_qvalPairwiseComp_Imprinted_Promoter.bed.gz
  genome_browser_track_qvalPairwiseComp_CancerGene_Promoter.bed.gz
  genome_browser_track_qvalPairwiseComp_CellStateGene_Promoter.bed.gz
  genome_browser_track_qvalPairwiseComp_Tandem_Repeat.bed.gz
  genome_browser_track_qvalPairwiseComp_Repeat_DNA.bed.gz
  genome_browser_track_qvalPairwiseComp_Repeat_LINE.bed.gz
  genome_browser_track_qvalPairwiseComp_Repeat_LowComplex.bed.gz
  genome_browser_track_qvalPairwiseComp_Repeat_LTR.bed.gz
  genome_browser_track_qvalPairwiseComp_Repeat_Simple.bed.gz
  genome_browser_track_qvalPairwiseComp_Repeat_SINE.bed.gz
  genome_browser_track_qvalPairwiseComp_Tiling_regions_5kb.bed.gz
  genome_browser_track_qvalPairwiseComp_Tiling_regions_5kb_nonRepetitive.bed.gz
  genome_browser_track_qvalPairwiseComp_Tiling_regions_5kb_repetitive.bed.gz