Exploratory Analysis

Sample Groups

The specified traits were tested based on criteria for defining sample groups. The table below summarizes these traits.

Trait Number of groups
sex 3
tissue 31
karyotype 2
tier 3
lineage 7
obtainedBy 5
dataVersion 3

Region Annotations

In addition to CpG sites, there are 4 sets of genomic regions to be covered in the analysis. The table below gives a summary of these annotations.

Annotation Description Regions in the Dataset
tiling n.a. 64574
genes n.a. 21548
promoters n.a. 18433
cpgislands n.a. 19509

Region length distributions

The plots below show region size distributions for the region types above.

Region type

Figure 1

Open PDF Figure 1

Distribution of region lengths

Number of sites per region

The plots below show the distributions of the number of sites per region type.

Region type

Figure 2

Open PDF Figure 2

Distribution of the number of sites per region

Region site distributions

The plots below show distributions of sites across the different region types.

Region type

Figure 3

Open PDF Figure 3

Distribution of sites across regions. relative coordinates of 0 and 1 corresponds to the start and end coordinates of that region respectively. Coordinates smaller than 0 and greater than 1 denote flanking regions normalized by region length.

Analysis of Sample Replicates

Sample replicates were compared. This section shows pairwise scatterplots for each sample replicate group on both site and region level.

replicate
site/region

Figure 4

Figure 4

Scatterplot for replicate methylation comparison. The transparency corresponds to point density. The 1% of the points in the sparsest populated plot regions are drawn explicitly.

The following table contains pearson correlation coefficients:

sites tiling genes promoters cpgislands
wgEncodeHaibMethylRrbsA549Dm002p7dHaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsA549Dm002p7dHaibSitesRep2.bed.gz (A549) 0.9861 0.9885 0.993 0.9944 0.9961
wgEncodeHaibMethylRrbsAg04449UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsAg04449UwSitesRep2.bed.gz (AG04449) 0.8968 0.8853 0.8843 0.9296 0.9633
wgEncodeHaibMethylRrbsAg04450UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsAg04450UwSitesRep2.bed.gz (AG04450) 0.9612 0.9618 0.9676 0.9785 0.988
wgEncodeHaibMethylRrbsAg09309UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsAg09309UwSitesRep2.bed.gz (AG09309) 0.9668 0.9623 0.9526 0.976 0.988
wgEncodeHaibMethylRrbsAg09319UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsAg09319UwSitesRep2.bed.gz (AG09319) 0.9682 0.9624 0.9585 0.9767 0.9868
wgEncodeHaibMethylRrbsAg10803UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsAg10803UwSitesRep2.bed.gz (AG10803) 0.9622 0.9633 0.9727 0.9794 0.9888
wgEncodeHaibMethylRrbsAosmcDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsAosmcDukeSitesRep2.bed.gz (AoSMC) 0.9575 0.9524 0.9497 0.968 0.9848
wgEncodeHaibMethylRrbsBcadrenalglandh12803nBiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBcadrenalglandh12803nBiochainSitesRep2.bed.gz (BC_Adrenal_Gland_H12803N) 0.9812 0.9811 0.9858 0.9901 0.9938
wgEncodeHaibMethylRrbsBcbrainh11058nBiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBcbrainh11058nBiochainSitesRep2.bed.gz (BC_Brain_H11058N) 0.9705 0.9735 0.9829 0.9862 0.9893
wgEncodeHaibMethylRrbsBcbreast0203015BiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBcbreast0203015BiochainSitesRep2.bed.gz (BC_Breast_02-03015) 0.9568 0.9673 0.9766 0.9802 0.9852
wgEncodeHaibMethylRrbsBckidney0111002BiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBckidney0111002BiochainSitesRep2.bed.gz (BC_Kidney_01-11002) 0.9699 0.9716 0.9722 0.9822 0.9886
wgEncodeHaibMethylRrbsBcleftventriclen41BiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBcleftventriclen41BiochainSitesRep2.bed.gz (BC_Left_Ventricle_N41) 0.9688 0.9691 0.9801 0.9828 0.9892
wgEncodeHaibMethylRrbsBcleukocyteuhn00204BiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBcleukocyteuhn00204BiochainSitesRep2.bed.gz (BC_Leukocyte_UHN00204) 0.9779 0.9797 0.9855 0.9886 0.9925
wgEncodeHaibMethylRrbsBcliver0111002BiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBcliver0111002BiochainSitesRep2.bed.gz (BC_Liver_01-11002) 0.9611 0.9644 0.9663 0.9773 0.9847
wgEncodeHaibMethylRrbsBclung0111002BiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBclung0111002BiochainSitesRep2.bed.gz (BC_Lung_01-11002) 0.9714 0.9705 0.9725 0.9825 0.9887
wgEncodeHaibMethylRrbsBcpancreash12817nBiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBcpancreash12817nBiochainSitesRep2.bed.gz (BC_Pancreas_H12817N) 0.9577 0.9564 0.9619 0.9745 0.9843
wgEncodeHaibMethylRrbsBcpericardiumh12529nBiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBcpericardiumh12529nBiochainSitesRep2.bed.gz (BC_Pericardium_H12529N) 0.9754 0.9784 0.9855 0.9882 0.9916
wgEncodeHaibMethylRrbsBcplacentauhn00189BiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBcplacentauhn00189BiochainSitesRep2.bed.gz (BC_Placenta_UHN00189) 0.9642 0.9706 0.9771 0.9801 0.9855
wgEncodeHaibMethylRrbsBcskeletalmuscle0111002BiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBcskeletalmuscle0111002BiochainSitesRep2.bed.gz (BC_Skeletal_Muscle_01-11002) 0.96 0.963 0.9698 0.9768 0.9852
wgEncodeHaibMethylRrbsBcskeletalmuscleh12817nBiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBcskeletalmuscleh12817nBiochainSitesRep2.bed.gz (BC_Skeletal_Muscle_H12817N) 0.9649 0.9718 0.9838 0.9844 0.9895
wgEncodeHaibMethylRrbsBcskin0111002BiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBcskin0111002BiochainSitesRep2.bed.gz (BC_Skin_01-11002) 0.9776 0.9804 0.9871 0.9888 0.9909
wgEncodeHaibMethylRrbsBcstomach0111002BiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBcstomach0111002BiochainSitesRep2.bed.gz (BC_Stomach_01-11002) 0.9753 0.9778 0.9847 0.9875 0.991
wgEncodeHaibMethylRrbsBctestisn30BiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBctestisn30BiochainSitesRep2.bed.gz (BC_Testis_N30) 0.9779 0.9804 0.982 0.9841 0.9852
wgEncodeHaibMethylRrbsBcuterusbn0765BiochainSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBcuterusbn0765BiochainSitesRep2.bed.gz (BC_Uterus_BN0765) 0.9728 0.973 0.9805 0.9847 0.9902
wgEncodeHaibMethylRrbsBe2cHaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBe2cHaibSitesRep2.bed.gz (BE2_C) 0.9829 0.9854 0.9908 0.9929 0.9952
wgEncodeHaibMethylRrbsBjUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsBjUwSitesRep2.bed.gz (BJ) 0.9628 0.9605 0.9615 0.977 0.9877
wgEncodeHaibMethylRrbsCmkUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsCmkUwSitesRep2.bed.gz (CMK) 0.9777 0.9731 0.981 0.9891 0.9919
wgEncodeHaibMethylRrbsCaco2UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsCaco2UwSitesRep2.bed.gz (Caco-2) 0.951 0.9533 0.9643 0.976 0.9829
wgEncodeHaibMethylRrbsEcc1HaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsEcc1HaibSitesRep2.bed.gz (ECC-1) 0.9849 0.9889 0.9924 0.9932 0.9962
wgEncodeHaibMethylRrbsFibroblDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsFibroblDukeSitesRep2.bed.gz (Fibrobl) 0.9497 0.9491 0.9321 0.9619 0.9774
wgEncodeHaibMethylRrbsGm06990UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsGm06990UwSitesRep2.bed.gz (GM06990) 0.8649 0.8921 0.8807 0.9129 0.9396
wgEncodeHaibMethylRrbsGm12878HaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsGm12878HaibSitesRep2.bed.gz (GM12878) 0.9515 0.9575 0.9676 0.973 0.9813
wgEncodeHaibMethylRrbsGm12878ximatHaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsGm12878ximatHaibSitesRep2.bed.gz (GM12878-XiMat) 0.9166 0.9293 0.96 0.9664 0.9811
wgEncodeHaibMethylRrbsGm12891HaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsGm12891HaibSitesRep2.bed.gz (GM12891) 0.9626 0.9609 0.9632 0.9767 0.9854
wgEncodeHaibMethylRrbsGm12892HaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsGm12892HaibSitesRep2.bed.gz (GM12892) 0.961 0.9546 0.9514 0.9694 0.981
wgEncodeHaibMethylRrbsGm19239DukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsGm19239DukeSitesRep2.bed.gz (GM19239) 0.9634 0.9564 0.9399 0.9702 0.9849
wgEncodeHaibMethylRrbsGm19240DukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsGm19240DukeSitesRep2.bed.gz (GM19240) 0.9648 0.9663 0.9731 0.9804 0.9884
wgEncodeHaibMethylRrbsH1hescHaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsH1hescHaibSitesRep2.bed.gz (H1-hESC) 0.983 0.982 0.9844 0.9906 0.9946
wgEncodeHaibMethylRrbsHaeUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHaeUwSitesRep2.bed.gz (HAEpiC) 0.9206 0.927 0.9413 0.9503 0.966
wgEncodeHaibMethylRrbsHcfUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHcfUwSitesRep2.bed.gz (HCF) 0.971 0.9569 0.9277 0.9689 0.9861
wgEncodeHaibMethylRrbsHcmUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHcmUwSitesRep2.bed.gz (HCM) 0.9447 0.9477 0.9565 0.9673 0.9785
wgEncodeHaibMethylRrbsHcpeUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHcpeUwSitesRep2.bed.gz (HCPEpiC) 0.9596 0.961 0.9658 0.9766 0.9874
wgEncodeHaibMethylRrbsHct116StanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHct116StanfordSitesRep2.bed.gz (HCT-116) 0.9741 0.9644 0.9595 0.9781 0.9855
wgEncodeHaibMethylRrbsHeeUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHeeUwSitesRep2.bed.gz (HEEpiC) 0.9648 0.9656 0.9678 0.9785 0.9862
wgEncodeHaibMethylRrbsHek293StanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHek293StanfordSitesRep2.bed.gz (HEK293) 0.9747 0.9646 0.9698 0.9823 0.99
wgEncodeHaibMethylRrbsHek293StanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHek293UwSitesRep1.bed.gz (HEK293) 0.8907 0.894 0.8977 0.9054 0.9059
wgEncodeHaibMethylRrbsHek293StanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHek293UwSitesRep2.bed.gz (HEK293) 0.887 0.8883 0.8986 0.9074 0.9083
wgEncodeHaibMethylRrbsHek293StanfordSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsHek293UwSitesRep1.bed.gz (HEK293) 0.8847 0.8887 0.9032 0.9068 0.9074
wgEncodeHaibMethylRrbsHek293StanfordSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsHek293UwSitesRep2.bed.gz (HEK293) 0.9024 0.8998 0.904 0.9142 0.9159
wgEncodeHaibMethylRrbsHek293UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHek293UwSitesRep2.bed.gz (HEK293) 0.9717 0.9659 0.9593 0.9794 0.9872
wgEncodeHaibMethylRrbsHipeUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHipeUwSitesRep2.bed.gz (HIPEpiC) 0.9545 0.9538 0.9555 0.9688 0.9832
wgEncodeHaibMethylRrbsHl60UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHl60UwSitesRep2.bed.gz (HL-60) 0.9472 0.9655 0.9717 0.9765 0.9787
wgEncodeHaibMethylRrbsHmecUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHmecUwSitesRep2.bed.gz (HMEC) 0.9742 0.9666 0.9612 0.9801 0.9883
wgEncodeHaibMethylRrbsHnpceUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHnpceUwSitesRep2.bed.gz (HNPCEpiC) 0.9379 0.9349 0.9503 0.9628 0.9744
wgEncodeHaibMethylRrbsHpaeUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHpaeUwSitesRep2.bed.gz (HPAEpiC) 0.9743 0.9705 0.9635 0.98 0.9888
wgEncodeHaibMethylRrbsHrceUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHrceUwSitesRep2.bed.gz (HRCEpiC) 0.9636 0.9585 0.9459 0.9742 0.9835
wgEncodeHaibMethylRrbsHreUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHreUwSitesRep2.bed.gz (HRE) 0.9746 0.9763 0.9747 0.9839 0.9903
wgEncodeHaibMethylRrbsHrpeUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHrpeUwSitesRep2.bed.gz (HRPEpiC) 0.975 0.9782 0.9818 0.9856 0.9872
wgEncodeHaibMethylRrbsHsmmDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHsmmDukeSitesRep2.bed.gz (HSMM) 0.9396 0.9445 0.9482 0.9644 0.9722
wgEncodeHaibMethylRrbsHsmmDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHsmmDukeSitesRep3.bed.gz (HSMM) 0.944 0.9542 0.9597 0.9682 0.9761
wgEncodeHaibMethylRrbsHsmmDukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsHsmmDukeSitesRep3.bed.gz (HSMM) 0.9275 0.9369 0.9394 0.9585 0.972
wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep2.bed.gz (HSMM_FSHD) 0.9129 0.9086 0.9422 0.9457 0.9469
wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep3.bed.gz (HSMM_FSHD) 0.8994 0.9071 0.9266 0.9367 0.9485
wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsHsmmfshdDukeSitesRep3.bed.gz (HSMM_FSHD) 0.8762 0.8771 0.9028 0.9223 0.9357
wgEncodeHaibMethylRrbsHsmmtDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHsmmtDukeSitesRep2.bed.gz (HSMMtube) 0.9689 0.9736 0.9749 0.9827 0.9888
wgEncodeHaibMethylRrbsHsmmtDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHsmmtDukeSitesRep3.bed.gz (HSMMtube) 0.9494 0.9592 0.9679 0.9724 0.9794
wgEncodeHaibMethylRrbsHsmmtDukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsHsmmtDukeSitesRep3.bed.gz (HSMMtube) 0.9478 0.9593 0.9683 0.9728 0.9769
wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep2.bed.gz (HSMMtube_FSHD) 0.9137 0.9083 0.9453 0.948 0.9438
wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep3.bed.gz (HSMMtube_FSHD) 0.9468 0.9494 0.9657 0.9694 0.9709
wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsHsmmtubefshdDukeSitesRep3.bed.gz (HSMMtube_FSHD) 0.9392 0.9422 0.9617 0.9661 0.9665
wgEncodeHaibMethylRrbsHtr8DukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHtr8DukeSitesRep3.bed.gz (HTR8svn) 0.933 0.9172 0.9471 0.9587 0.9665
wgEncodeHaibMethylRrbsHelas3HaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHelas3HaibSitesRep2.bed.gz (HeLa-S3) 0.9743 0.9672 0.9731 0.9854 0.9915
wgEncodeHaibMethylRrbsHepg2DukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHepg2DukeSitesRep2.bed.gz (HepG2) 0.9773 0.9801 0.983 0.9885 0.993
wgEncodeHaibMethylRrbsHepg2DukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHepg2HaibSitesRep1.bed.gz (HepG2) 0.9711 0.9702 0.9701 0.9826 0.99
wgEncodeHaibMethylRrbsHepg2DukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHepg2HaibSitesRep2.bed.gz (HepG2) 0.971 0.9717 0.9702 0.982 0.9891
wgEncodeHaibMethylRrbsHepg2DukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsHepg2HaibSitesRep1.bed.gz (HepG2) 0.969 0.9673 0.9666 0.9805 0.9882
wgEncodeHaibMethylRrbsHepg2DukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsHepg2HaibSitesRep2.bed.gz (HepG2) 0.9684 0.9698 0.969 0.9801 0.9883
wgEncodeHaibMethylRrbsHepg2HaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHepg2HaibSitesRep2.bed.gz (HepG2) 0.9742 0.9715 0.9732 0.9839 0.9916
wgEncodeHaibMethylRrbsHepatocytesDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsHepatocytesDukeSitesRep2.bed.gz (Hepatocytes) 0.9593 0.9607 0.9734 0.9743 0.9743
wgEncodeHaibMethylRrbsImr90UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsImr90UwSitesRep2.bed.gz (IMR90) 0.9617 0.957 0.9269 0.9675 0.984
wgEncodeHaibMethylRrbsJurkatUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsJurkatUwSitesRep2.bed.gz (Jurkat) 0.9633 0.9276 0.9226 0.957 0.9713
wgEncodeHaibMethylRrbsK562HaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsK562HaibSitesRep2.bed.gz (K562) 0.9793 0.9852 0.9859 0.9902 0.9935
wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep2.bed.gz (LNCaP) 0.9712 0.9618 0.9515 0.9732 0.9837
wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsLncapDukeSitesRep1.bed.gz (LNCaP) 0.9503 0.9402 0.9411 0.9594 0.9732
wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsLncapDukeSitesRep2.bed.gz (LNCaP) 0.9648 0.9549 0.9475 0.9685 0.9815
wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsLncapUwSitesRep1.bed.gz (LNCaP) 0.9505 0.9408 0.9342 0.9589 0.9716
wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsLncapUwSitesRep2.bed.gz (LNCaP) 0.9529 0.9462 0.9362 0.9596 0.9718
wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsLncapDukeSitesRep1.bed.gz (LNCaP) 0.9585 0.9543 0.9558 0.9707 0.9796
wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsLncapDukeSitesRep2.bed.gz (LNCaP) 0.9701 0.9713 0.9779 0.9831 0.9891
wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsLncapUwSitesRep1.bed.gz (LNCaP) 0.9603 0.963 0.9736 0.9774 0.9819
wgEncodeHaibMethylRrbsLncapAndroDukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsLncapUwSitesRep2.bed.gz (LNCaP) 0.9582 0.964 0.9718 0.9756 0.9812
wgEncodeHaibMethylRrbsLncapDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsLncapDukeSitesRep2.bed.gz (LNCaP) 0.9451 0.9382 0.9405 0.9589 0.9704
wgEncodeHaibMethylRrbsLncapDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsLncapUwSitesRep1.bed.gz (LNCaP) 0.9375 0.9354 0.9389 0.954 0.9621
wgEncodeHaibMethylRrbsLncapDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsLncapUwSitesRep2.bed.gz (LNCaP) 0.9328 0.9303 0.9331 0.9492 0.9594
wgEncodeHaibMethylRrbsLncapDukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsLncapUwSitesRep1.bed.gz (LNCaP) 0.9652 0.9669 0.975 0.9811 0.9865
wgEncodeHaibMethylRrbsLncapDukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsLncapUwSitesRep2.bed.gz (LNCaP) 0.9662 0.9696 0.9761 0.9812 0.9868
wgEncodeHaibMethylRrbsLncapUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsLncapUwSitesRep2.bed.gz (LNCaP) 0.9704 0.9744 0.9838 0.9864 0.9898
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep1.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep2.bedRrbs.gz (MCF-7) 0.9884 0.9872 0.9926 0.9949 0.9972
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep1.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7DukeSitesRep1.bed.gz (MCF-7) 0.9612 0.9481 0.9679 0.9746 0.9801
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep1.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7DukeSitesRep2.bed.gz (MCF-7) 0.959 0.942 0.9559 0.969 0.9766
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep1.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep1.bedRrbs.gz (MCF-7) 0.9811 0.9785 0.9874 0.9904 0.9932
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep1.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep2.bedRrbs.gz (MCF-7) 0.9867 0.9857 0.9922 0.9941 0.9964
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep1.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7StanfordSitesRep1.bed.gz (MCF-7) 0.9511 0.9333 0.9359 0.9581 0.9691
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep1.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7StanfordSitesRep2.bed.gz (MCF-7) 0.9506 0.9394 0.9521 0.9626 0.9701
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep1.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep1.bed.gz (MCF-7) 0.9623 0.9461 0.9341 0.9639 0.9768
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep1.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep2.bed.gz (MCF-7) 0.956 0.9467 0.9545 0.9676 0.9755
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep2.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7DukeSitesRep1.bed.gz (MCF-7) 0.9628 0.9496 0.9699 0.9757 0.9808
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep2.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7DukeSitesRep2.bed.gz (MCF-7) 0.9605 0.9432 0.9581 0.9696 0.9775
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep2.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep1.bedRrbs.gz (MCF-7) 0.9829 0.98 0.9882 0.9909 0.9939
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep2.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep2.bedRrbs.gz (MCF-7) 0.9883 0.988 0.9938 0.995 0.997
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep2.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7StanfordSitesRep1.bed.gz (MCF-7) 0.9529 0.9365 0.9396 0.9598 0.9695
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep2.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7StanfordSitesRep2.bed.gz (MCF-7) 0.952 0.942 0.9552 0.9642 0.9704
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep2.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep1.bed.gz (MCF-7) 0.965 0.9491 0.9373 0.9664 0.9782
wgEncodeHaibMethylRrbsMcf7CtcfshrnaDukeSitesRep2.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep2.bed.gz (MCF-7) 0.9579 0.9476 0.954 0.968 0.9762
wgEncodeHaibMethylRrbsMcf7DukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf7DukeSitesRep2.bed.gz (MCF-7) 0.9837 0.9789 0.9821 0.9898 0.9937
wgEncodeHaibMethylRrbsMcf7DukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep1.bedRrbs.gz (MCF-7) 0.9617 0.9455 0.9655 0.9743 0.9799
wgEncodeHaibMethylRrbsMcf7DukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep2.bedRrbs.gz (MCF-7) 0.9649 0.9525 0.9712 0.9773 0.9815
wgEncodeHaibMethylRrbsMcf7DukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf7StanfordSitesRep1.bed.gz (MCF-7) 0.9488 0.921 0.9303 0.9529 0.9645
wgEncodeHaibMethylRrbsMcf7DukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf7StanfordSitesRep2.bed.gz (MCF-7) 0.9492 0.9316 0.9466 0.9584 0.966
wgEncodeHaibMethylRrbsMcf7DukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep1.bed.gz (MCF-7) 0.9581 0.9381 0.9331 0.9632 0.9732
wgEncodeHaibMethylRrbsMcf7DukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep2.bed.gz (MCF-7) 0.9528 0.9365 0.9482 0.964 0.9734
wgEncodeHaibMethylRrbsMcf7DukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep1.bedRrbs.gz (MCF-7) 0.9629 0.9432 0.9568 0.9702 0.9786
wgEncodeHaibMethylRrbsMcf7DukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep2.bedRrbs.gz (MCF-7) 0.9636 0.9471 0.9603 0.9718 0.9788
wgEncodeHaibMethylRrbsMcf7DukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsMcf7StanfordSitesRep1.bed.gz (MCF-7) 0.9451 0.9198 0.9329 0.9516 0.9622
wgEncodeHaibMethylRrbsMcf7DukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsMcf7StanfordSitesRep2.bed.gz (MCF-7) 0.9487 0.93 0.9399 0.955 0.9644
wgEncodeHaibMethylRrbsMcf7DukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep1.bed.gz (MCF-7) 0.9577 0.9392 0.9397 0.9641 0.9733
wgEncodeHaibMethylRrbsMcf7DukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep2.bed.gz (MCF-7) 0.9567 0.9387 0.9453 0.9636 0.9733
wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep1.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep2.bedRrbs.gz (MCF-7) 0.9844 0.9824 0.9896 0.9923 0.9946
wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep1.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7StanfordSitesRep1.bed.gz (MCF-7) 0.945 0.9315 0.933 0.9533 0.964
wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep1.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7StanfordSitesRep2.bed.gz (MCF-7) 0.9506 0.9431 0.9535 0.9624 0.9672
wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep1.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep1.bed.gz (MCF-7) 0.9646 0.947 0.9349 0.9661 0.9786
wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep1.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep2.bed.gz (MCF-7) 0.9653 0.9552 0.9616 0.9742 0.981
wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep2.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7StanfordSitesRep1.bed.gz (MCF-7) 0.9534 0.9393 0.9406 0.9602 0.9692
wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep2.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7StanfordSitesRep2.bed.gz (MCF-7) 0.9543 0.9459 0.9564 0.9655 0.971
wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep2.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep1.bed.gz (MCF-7) 0.9673 0.9522 0.9394 0.9681 0.9794
wgEncodeHaibMethylRrbsMcf7RandshrnaDukeSitesRep2.bedRrbs.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep2.bed.gz (MCF-7) 0.962 0.9525 0.958 0.9716 0.9787
wgEncodeHaibMethylRrbsMcf7StanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf7StanfordSitesRep2.bed.gz (MCF-7) 0.983 0.9726 0.9656 0.9845 0.992
wgEncodeHaibMethylRrbsMcf7StanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep1.bed.gz (MCF-7) 0.9449 0.9395 0.9376 0.9541 0.9617
wgEncodeHaibMethylRrbsMcf7StanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep2.bed.gz (MCF-7) 0.9341 0.9202 0.9098 0.9401 0.9529
wgEncodeHaibMethylRrbsMcf7StanfordSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep1.bed.gz (MCF-7) 0.9421 0.9325 0.9167 0.9476 0.9582
wgEncodeHaibMethylRrbsMcf7StanfordSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep2.bed.gz (MCF-7) 0.9396 0.9345 0.9341 0.9512 0.9566
wgEncodeHaibMethylRrbsMcf7UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf7UwSitesRep2.bed.gz (MCF-7) 0.9733 0.9522 0.9307 0.9701 0.9831
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep2.bed.gz (MCF10A-Er-Src) 0.9738 0.9758 0.9833 0.9876 0.9907
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep3.bed.gz (MCF10A-Er-Src) 0.9742 0.9745 0.9826 0.9864 0.9907
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep1.bed.gz (MCF10A-Er-Src) 0.9763 0.9777 0.9826 0.9884 0.9915
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep2.bed.gz (MCF10A-Er-Src) 0.9742 0.9745 0.9786 0.9857 0.9898
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep3.bed.gz (MCF10A-Er-Src) 0.9748 0.9758 0.9809 0.9871 0.9907
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep3.bed.gz (MCF10A-Er-Src) 0.9749 0.9779 0.985 0.9884 0.9917
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep1.bed.gz (MCF10A-Er-Src) 0.9757 0.9783 0.985 0.9885 0.9918
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep2.bed.gz (MCF10A-Er-Src) 0.9734 0.9749 0.9803 0.9861 0.9894
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep3.bed.gz (MCF10A-Er-Src) 0.974 0.9765 0.9829 0.987 0.9906
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep3.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep1.bed.gz (MCF10A-Er-Src) 0.9763 0.9779 0.9853 0.9881 0.992
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep3.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep2.bed.gz (MCF10A-Er-Src) 0.9738 0.9749 0.9808 0.9854 0.9902
wgEncodeHaibMethylRrbsMcf10aesStanfordSitesRep3.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep3.bed.gz (MCF10A-Er-Src) 0.9746 0.9765 0.9827 0.9869 0.9909
wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep2.bed.gz (MCF10A-Er-Src) 0.9758 0.9773 0.9818 0.9873 0.9902
wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep3.bed.gz (MCF10A-Er-Src) 0.9765 0.9781 0.9833 0.9884 0.9915
wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsMcf10aesTamStanfordSitesRep3.bed.gz (MCF10A-Er-Src) 0.9739 0.976 0.9826 0.9871 0.9903
wgEncodeHaibMethylRrbsMelanoSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMelanoSitesRep2.bed.gz (Melano) 0.9226 0.9279 0.9265 0.951 0.9719
wgEncodeHaibMethylRrbsMelanoSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMelanoSitesRep3.bed.gz (Melano) 0.7968 0.7972 0.8185 0.851 0.8937
wgEncodeHaibMethylRrbsMelanoSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsMelanoSitesRep3.bed.gz (Melano) 0.8147 0.8437 0.8675 0.8784 0.9148
wgEncodeHaibMethylRrbsMyometrDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsMyometrDukeSitesRep2.bed.gz (Myometr) 0.6621 0.5597 0.6715 0.7097 0.772
wgEncodeHaibMethylRrbsNb4UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsNb4UwSitesRep2.bed.gz (NB4) 0.9744 0.9733 0.9782 0.986 0.9907
wgEncodeHaibMethylRrbsNhaDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsNhaDukeSitesRep2.bed.gz (NH-A) 0.9161 0.912 0.9209 0.9415 0.9604
wgEncodeHaibMethylRrbsNhaDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsNhaUwSitesRep1.bed.gz (NH-A) 0.9279 0.9296 0.9357 0.9515 0.9679
wgEncodeHaibMethylRrbsNhaDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsNhaUwSitesRep2.bed.gz (NH-A) 0.9273 0.9281 0.9347 0.9507 0.9687
wgEncodeHaibMethylRrbsNhaDukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsNhaUwSitesRep1.bed.gz (NH-A) 0.959 0.9483 0.9548 0.9704 0.9803
wgEncodeHaibMethylRrbsNhaDukeSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsNhaUwSitesRep2.bed.gz (NH-A) 0.9577 0.9503 0.9624 0.9723 0.9784
wgEncodeHaibMethylRrbsNhaUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsNhaUwSitesRep2.bed.gz (NH-A) 0.9745 0.9749 0.9784 0.9839 0.9894
wgEncodeHaibMethylRrbsNhbeUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsNhbeUwSitesRep2.bed.gz (NHBE) 0.9632 0.9633 0.9615 0.9775 0.9845
wgEncodeHaibMethylRrbsNhdfneoUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsNhdfneoUwSitesRep2.bed.gz (NHDF-neo) 0.9695 0.9667 0.9664 0.9801 0.9891
wgEncodeHaibMethylRrbsNt2d1StanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsNt2d1StanfordSitesRep2.bed.gz (NT2-D1) 0.9792 0.9754 0.9594 0.9824 0.9895
wgEncodeHaibMethylRrbsNt2d1StanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsNt2d1UwSitesRep1.bed.gz (NT2-D1) 0.9576 0.9596 0.9623 0.9618 0.9684
wgEncodeHaibMethylRrbsNt2d1StanfordSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsNt2d1UwSitesRep2.bed.gz (NT2-D1) 0.954 0.954 0.9432 0.9579 0.9659
wgEncodeHaibMethylRrbsNt2d1StanfordSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsNt2d1UwSitesRep1.bed.gz (NT2-D1) 0.9601 0.9614 0.9412 0.9625 0.9689
wgEncodeHaibMethylRrbsNt2d1StanfordSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsNt2d1UwSitesRep2.bed.gz (NT2-D1) 0.9616 0.9664 0.9702 0.9693 0.9732
wgEncodeHaibMethylRrbsNt2d1UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsNt2d1UwSitesRep2.bed.gz (NT2-D1) 0.9835 0.9776 0.9548 0.9829 0.9885
wgEncodeHaibMethylRrbsOsteoblDukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsOsteoblDukeSitesRep2.bed.gz (Osteobl) 0.9687 0.9648 0.9654 0.9775 0.9894
wgEncodeHaibMethylRrbsPanc1HaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsPanc1HaibSitesRep2.bed.gz (PANC-1) 0.9857 0.9855 0.9905 0.9931 0.9965
wgEncodeHaibMethylRrbsPanc1HaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsPanc1UwSitesRep1.bed.gz (PANC-1) 0.9285 0.8982 0.9364 0.9523 0.9707
wgEncodeHaibMethylRrbsPanc1HaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsPanc1UwSitesRep2.bed.gz (PANC-1) 0.9525 0.962 0.9769 0.9816 0.9906
wgEncodeHaibMethylRrbsPanc1HaibSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsPanc1UwSitesRep1.bed.gz (PANC-1) 0.9301 0.8988 0.935 0.9512 0.9716
wgEncodeHaibMethylRrbsPanc1HaibSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsPanc1UwSitesRep2.bed.gz (PANC-1) 0.9526 0.9611 0.9748 0.9805 0.9908
wgEncodeHaibMethylRrbsPanc1UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsPanc1UwSitesRep2.bed.gz (PANC-1) 0.9207 0.914 0.9431 0.9571 0.975
wgEncodeHaibMethylRrbsPfsk1HaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsPfsk1HaibSitesRep2.bed.gz (PFSK-1) 0.9785 0.982 0.9902 0.992 0.995
wgEncodeHaibMethylRrbsPanisletsSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsPanisletsSitesRep2.bed.gz (PanIslets) 0.9085 0.9049 0.8901 0.9308 0.9441
wgEncodeHaibMethylRrbsPanisletsSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsPanisletsSitesRep3.bed.gz (PanIslets) 0.938 0.9428 0.9411 0.9588 0.9695
wgEncodeHaibMethylRrbsPanisletsSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsPanisletsSitesRep4.bed.gz (PanIslets) 0.9044 0.9029 0.9017 0.9308 0.9446
wgEncodeHaibMethylRrbsPanisletsSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsPanisletsSitesRep5.bed.gz (PanIslets) 0.9081 0.9051 0.9012 0.9329 0.9483
wgEncodeHaibMethylRrbsPanisletsSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsPanisletsSitesRep3.bed.gz (PanIslets) 0.9441 0.9425 0.9396 0.9572 0.966
wgEncodeHaibMethylRrbsPanisletsSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsPanisletsSitesRep4.bed.gz (PanIslets) 0.9684 0.9739 0.9686 0.9799 0.9859
wgEncodeHaibMethylRrbsPanisletsSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsPanisletsSitesRep5.bed.gz (PanIslets) 0.9693 0.9742 0.9681 0.9808 0.9854
wgEncodeHaibMethylRrbsPanisletsSitesRep3.bed.gz vs. wgEncodeHaibMethylRrbsPanisletsSitesRep4.bed.gz (PanIslets) 0.943 0.942 0.9502 0.958 0.9671
wgEncodeHaibMethylRrbsPanisletsSitesRep3.bed.gz vs. wgEncodeHaibMethylRrbsPanisletsSitesRep5.bed.gz (PanIslets) 0.9438 0.9425 0.9495 0.9588 0.9697
wgEncodeHaibMethylRrbsPanisletsSitesRep4.bed.gz vs. wgEncodeHaibMethylRrbsPanisletsSitesRep5.bed.gz (PanIslets) 0.9717 0.9779 0.98 0.9845 0.9884
wgEncodeHaibMethylRrbsPrecUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsPrecUwSitesRep2.bed.gz (PrEC) 0.9725 0.971 0.9671 0.9816 0.9892
wgEncodeHaibMethylRrbsProgfibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsProgfibSitesRep2.bed.gz (ProgFib) 0.9641 0.9662 0.971 0.9806 0.9887
wgEncodeHaibMethylRrbsRptecSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsRptecSitesRep2.bed.gz (RPTEC) 0.9593 0.9562 0.95 0.9727 0.9835
wgEncodeHaibMethylRrbsSaecUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsSaecUwSitesRep2.bed.gz (SAEC) 0.9779 0.9798 0.9825 0.9878 0.9931
wgEncodeHaibMethylRrbsSknmcHaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsSknmcHaibSitesRep2.bed.gz (SK-N-MC) 0.9757 0.9805 0.9842 0.9876 0.9912
wgEncodeHaibMethylRrbsSknshHaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsSknshHaibSitesRep2.bed.gz (SK-N-SH) 0.9849 0.9879 0.9927 0.9943 0.9964
wgEncodeHaibMethylRrbsSknshraUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsSknshraUwSitesRep2.bed.gz (SK-N-SH_RA) 0.9597 0.945 0.9603 0.9743 0.985
wgEncodeHaibMethylRrbsSkmcUwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsSkmcUwSitesRep2.bed.gz (SKMC) 0.9747 0.9718 0.9746 0.9847 0.9914
wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep2.bed.gz (T-47D) 0.9735 0.9741 0.9809 0.9843 0.9902
wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsT47dEstradia24hhHaibSitesRep1.bed.gz (T-47D) 0.9837 0.9869 0.9908 0.9926 0.9948
wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsT47dEstradia24hhHaibSitesRep2.bed.gz (T-47D) 0.9772 0.9779 0.9845 0.9874 0.9922
wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsT47dEstradia24hhHaibSitesRep1.bed.gz (T-47D) 0.9756 0.9768 0.9832 0.9857 0.9917
wgEncodeHaibMethylRrbsT47dDm002p24hHaibSitesRep2.bed.gz vs. wgEncodeHaibMethylRrbsT47dEstradia24hhHaibSitesRep2.bed.gz (T-47D) 0.9823 0.9827 0.9894 0.9912 0.9953
wgEncodeHaibMethylRrbsT47dEstradia24hhHaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsT47dEstradia24hhHaibSitesRep2.bed.gz (T-47D) 0.9788 0.9797 0.9863 0.9883 0.9932
wgEncodeHaibMethylRrbsU87HaibSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsU87HaibSitesRep2.bed.gz (U87) 0.9777 0.9865 0.9887 0.9906 0.9939
wgEncodeHaibMethylRrbsUch1DukeSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsUch1DukeSitesRep2.bed.gz (UCH-1) 0.933 0.9292 0.934 0.9505 0.9722
wgEncodeHaibMethylRrbsOvcar3UwSitesRep1.bed.gz vs. wgEncodeHaibMethylRrbsOvcar3UwSitesRep2.bed.gz (ovcar-3) 0.9547 0.9673 0.9432 0.9704 0.9797

Low-dimensional Representation

Dimension reduction is used to visually inspect the dataset for a strong signal in the methylation values that is related to samples' clinical or batch processing annotation. RnBeads implements two methods for dimension reduction - principal component analysis (PCA) and multidimensional scaling (MDS).

One or more of the methylation matrices was augmented before applying the dimension reduction techniques because it contains missing values. The column Missing lists the number of dimensions ignored due to missing values. In the case of MDS, dimensions are ignored only if they contain missing values for all samples. In contrast, sites or regions with missing values in any sample are ignored prior to PCA.

Sites/regions Technique Dimensions Missing Selected
sites MDS 815439 0 815439
sites PCA 815439 627408 188031
tiling MDS 64574 0 64574
tiling PCA 64574 39365 25209
genes MDS 21548 0 21548
genes PCA 21548 6333 15215
promoters MDS 18433 0 18433
promoters PCA 18433 5905 12528
cpgislands MDS 19509 0 19509
cpgislands PCA 19509 5839 13670

Multidimensional Scaling

The scatter plot below visualizes the samples transformed into a two-dimensional space using MDS.

Location type
Distance
Sample representation
Sample color

Figure 5

Open PDF Figure 5

Scatter plot showing samples after performing Kruskal's non-metric mutidimensional scaling.

Principal Component Analysis

Similarly, the figure below shows the values of selected principal components in a scatter plot.

Location type
Principal components
Sample representation
Sample color

Figure 6

Open PDF Figure 6

Scatter plot showing the samples' coordinates on principal components.

The figure below shows the cumulative distribution functions of variance explained by the principal components.

Location type

Figure 7

Open PDF Figure 7

Cumulative distribution function of percentange of variance explained.

The table below gives for each location type a number of principal components that explain at least 95 percent of the total variance. The full tables of variances explained by all components are available in comma-separated values files accompanying this report.

Location Type Number of Components Full Table File
sites 69 csv
tiling 66 csv
genes 68 csv
promoters 46 csv
cpgislands 40 csv

Batch Effects

In this section, different properties of the dataset are tested for significant associations. The properties can include sample coordinates in the principal component space, phenotype traits and intensities of control probes. The tests used to calculate a p-value given two properties depend on the essence of the data:

Note that the p-values presented in this report are not corrected for multiple testing.

Associations between Principal Components and Traits

The computed sample coordinates in the principal component space were tested for association with the specified traits. Below is a list of the traits and the tests performed.

Trait Test
sex Kruskal-Wallis
tissue Kruskal-Wallis
karyotype Wilcoxon
tier Correlation
lineage Kruskal-Wallis
obtainedBy Kruskal-Wallis
dataVersion Kruskal-Wallis

The next figure shows the computed correlations between the first 8 principal components and the sample traits.

Region type

Figure 8

Open PDF Figure 8

Heatmap presenting a table of correlations. Grey cells, if present, denote missing values.

The values presented in the figure above are avaialable in CSV (comma-separated value) files accompanying this report.

Location type Table file
sites csv
tiling csv
genes csv
promoters csv
cpgislands csv

The heatmap below summarizes the results of permutation tests performed for associations. Significant p-values (values less than 0.01) are displayed in pink background.

Region type

Figure 9

Open PDF Figure 9

Heatmap presenting a table of p-values. Significant p-values (less than 0.01) are printed in pink boxes. Non-significant values are represented by blue boxes. Bright grey cells, if present, denote missing values.

The full tables of p-values for each location type are available in CSV (comma-separated value) files below.

Location Type File Name
sites csv
tiling csv
genes csv
promoters csv
cpgislands csv

Associations between Traits

This section summarizes the associations between pairs of traits.

The figure below visualizes the tests that were performed on trait pairs based on the description provided above. In addition, the calculated p-values for associations between traits are shown. Significant p-values (values less than 0.01) are displayed in pink background. The full table of p-values is available in a dedicated file that accompanies this report.

Heatmap of

Figure 10

Open PDF Figure 10

(1) Table of performed tests on pairs of traits. Test names (Correlation + permutation test, Fisher's exact test, Wilcoxon rank sum test and/or Kruskal-Wallis one-way analysis of variance) are color-coded according to the legend given above.
(2) Table of resulting p-values from the performed tests on pairs of traits. Significant p-values (less than 0.01) are printed in pink boxes Non-significant values are represented by blue boxes. White cells, if present, denote missing values.

Methylation Value Distributions

Methylation value distributions were assessed based on selected sample groups. This was done on site and region levels. This section contains the generated density plots.

Methylation Value Densities of Sample Groups

The plots below compare the distributions of methylation values in different sample groups, as defined by the traits listed above.

Sample trait
Methylation of

Figure 11

Open PDF Figure 11

Beta value density estimation according to sample grouping.

Clustering

The figure below shows clustering of samples using several algorithms and distance metrics.

Site/region level
Dissimilarity metric
Agglomeration strategy (linkage)
Sample color based on

Figure 12

Figure 12

Hierarchical clustering of samples based on all methylation values. The heatmap displays methylation percentiles per sample. The legend for sample coloring can be found in the figure below.

Site/region level
Dissimilarity metric
Agglomeration strategy (linkage)
Sample color based on
Site/region color based on
Visualize

Figure 13

Figure 13

Hierarchical clustering of samples based on all methylation values. The heatmap displays only selected sites/regions with the highest variance across all samples. The legend for locus and sample coloring can be found in the figure below.

Site/region level
Sample color based on
Site/region color based on

Figure 14

Open PDF Figure 14

Probe and sample colors used in the heatmaps in the previous figures.

Identified Clusters

Using the average silhouette value as a measure of cluster assignment [1], it is possible to infer the number of clusters produced by each of the studied methods. The figure below shows the corresponding mean silhouette value for every observed separation into clusters.

Site/region level
Dissimilarity metric

Figure 15

Open PDF Figure 15

Line plot visualizing mean silhouette values of the clustering algorithm outcomes for each applicable value of K (number of clusters).

The table below summarizes the number of clusters identified by the algorithms.

Site/region level

Metric Algorithm Clusters
correlation-based hierarchical (average linkage) 27
correlation-based hierarchical (complete linkage) 82
correlation-based hierarchical (median linkage) 34
Manhattan distance hierarchical (average linkage) 2
Manhattan distance hierarchical (complete linkage) 2
Manhattan distance hierarchical (median linkage) 2
Euclidean distance hierarchical (average linkage) 23
Euclidean distance hierarchical (complete linkage) 29
Euclidean distance hierarchical (median linkage) 33

Clusters and Traits

The figure below shows associations between clusterings and the examined traits. Associations are quantified using the adjusted Rand index [2]. Rand indices near 1 indicate high agreement while values close to -1 indicate seperation. The full table of all computed indices is stored in the following comma separated files:

Site/region level
Dissimilarity metric

Figure 16

Open PDF Figure 16

Heatmap visualizing Rand indices computed between sample traits (rows) and clustering algorithm outcomes (columns).

Regional Methylation Profiles

Methylation profiles were computed for the specified region types. Composite plots are shown

Region type
Sample trait

Figure 17

Open PDF Figure 17

Regional methylation profiles (composite plots) according to sample groups. For each region in the corresponding region type, relative coordinates of 0 and 1 corresponds to the start and end coordinates of that region respectively. Coordinates smaller than 0 and greater than 1 denote flanking regions normalized by region length. Scatterplot smoothers for each sample and sample group were fit. Horizontal lines indicate region boundaries. For smoothing, generalized additive models with cubic spine smoothing were used. Deviation bands indicate 95% confidence intervals

References

  1. Rousseeuw, P. J. (1987) Silhouettes: A graphical aid to the interpretation and validation of cluster analysis. Journal of Computational and Applied Mathematics, 20, 53-65
  2. Hubert, L. and Arabie, P. (1985) Comparing partitions. Journal of Classification, 2(1), 193-218