Journal
G3
Publication Date
2016
Volume
6
Issue
4
Inclusive Pages
973-986
Document Type
Open Access Publication
DOI
10.1534/g3.115.025437
Rights and Permissions
Junchen Gu, et al. (2016) Mapping of Variable DNA Methylation Across Multiple Cell Types Defines a Dynamic Regulatory Landscape of the Human Genome. G3, 6(4): 973-986. doi: 10.1534/g3.115.025437
Recommended Citation
Gu, Junchen; Stevens, Michael; Xing, Xiaoyun; Li, Daofeng; Zhang, Bo; Payton, Jacqueline E.; Oltz, Eugene M.; Jarvis, James N.; Jiang, Kaiyu; Cicero, Theodore; Costello, Joseph F.; and Wang, Ting, "Mapping of variable DNA methylation across multiple cell types defines a dynamic regulatory landscape of the human genome." G3. 6, 4. 973-986. (2016).
https://digitalcommons.wustl.edu/open_access_pubs/4802
FigureS1.pdf (241 kB)
Characterization of autosomal CpG methylation patterns continued.
FigureS2.pdf (73 kB)
Overlap of constitutively methylated CpGs with repeats and constitutively unmethylated CpGs with CpG islands.
FigureS3.pdf (254 kB)
A complete browser view of the example in Figure 1D.
FigureS4.pdf (89 kB)
Characterization of variably methylated regions (VMRs) continued.
FigureS5.pdf (78 kB)
Known transcription factor binding motifs enriched in VMRs for each tissue type and their enrichment in (A) brain (B) blood (C) skin and (D) breast
FigureS6.pdf (133 kB)
Hypomethylated VMRs enrich for enhancer or active transcription histone modifications.
FigureS7.pdf (516 kB)
Hierarchy of functional enrichment of genes near hypomethtlated VMRs in fetal brain.
FigureS8.pdf (91 kB)
Functional enrichment of genes near hypomethylated VMRs.
FigureS9.pdf (1301 kB)
FOXD3 is potentially regulated by methylation level in nearby regions in brain.
FigureS10.pdf (1039 kB)
OLIG2 is potentially regulated by upstream VMRs in fetal brain.
FigureS11.pdf (192 kB)
KRT2 is potentially regulated by upstream VMRs in keratinocyte.
FigureS12.pdf (318 kB)
TYR is potentially regulated by VMRs in melanocyte.
FigureS13.pdf (97 kB)
Genes near hypomethylated VMRs show increased expression.
FigureS14.pdf (2081 kB)
Comparison between methylCRF predicted VMRs and WGBS predicted DMRs.
FigureS15.pdf (577 kB)
Characterization of regions identified specifically in each study.
FigureS16.pdf (363 kB)
Characterization of constitutively unmethylated regions (UMRs).
FigureS17.pdf (455 kB)
Saturation analysis on the identification of variably methylated CpGs.
TableS1.xlsx (34 kB)
Data used in this study.
TableS2.xlsx (42 kB)
CpG category number and percentage in the genome.
TableS3.xlsx (86 kB)
List of VMRs overlapping positive human VISTA.
TableS4.xlsx (191 kB)
GWAS variants located in VMRs by cell type.
TableS5.xlsx (27 kB)
GWAS variants in CpG context.
TableS6.xlsx (8 kB)
Concordance between WGBS and methylCRF.
TableS7.xlsx (34 kB)
Bases sequenced comparison between WGBS and methylCRF.
Characterization of autosomal CpG methylation patterns continued.
FigureS2.pdf (73 kB)
Overlap of constitutively methylated CpGs with repeats and constitutively unmethylated CpGs with CpG islands.
FigureS3.pdf (254 kB)
A complete browser view of the example in Figure 1D.
FigureS4.pdf (89 kB)
Characterization of variably methylated regions (VMRs) continued.
FigureS5.pdf (78 kB)
Known transcription factor binding motifs enriched in VMRs for each tissue type and their enrichment in (A) brain (B) blood (C) skin and (D) breast
FigureS6.pdf (133 kB)
Hypomethylated VMRs enrich for enhancer or active transcription histone modifications.
FigureS7.pdf (516 kB)
Hierarchy of functional enrichment of genes near hypomethtlated VMRs in fetal brain.
FigureS8.pdf (91 kB)
Functional enrichment of genes near hypomethylated VMRs.
FigureS9.pdf (1301 kB)
FOXD3 is potentially regulated by methylation level in nearby regions in brain.
FigureS10.pdf (1039 kB)
OLIG2 is potentially regulated by upstream VMRs in fetal brain.
FigureS11.pdf (192 kB)
KRT2 is potentially regulated by upstream VMRs in keratinocyte.
FigureS12.pdf (318 kB)
TYR is potentially regulated by VMRs in melanocyte.
FigureS13.pdf (97 kB)
Genes near hypomethylated VMRs show increased expression.
FigureS14.pdf (2081 kB)
Comparison between methylCRF predicted VMRs and WGBS predicted DMRs.
FigureS15.pdf (577 kB)
Characterization of regions identified specifically in each study.
FigureS16.pdf (363 kB)
Characterization of constitutively unmethylated regions (UMRs).
FigureS17.pdf (455 kB)
Saturation analysis on the identification of variably methylated CpGs.
TableS1.xlsx (34 kB)
Data used in this study.
TableS2.xlsx (42 kB)
CpG category number and percentage in the genome.
TableS3.xlsx (86 kB)
List of VMRs overlapping positive human VISTA.
TableS4.xlsx (191 kB)
GWAS variants located in VMRs by cell type.
TableS5.xlsx (27 kB)
GWAS variants in CpG context.
TableS6.xlsx (8 kB)
Concordance between WGBS and methylCRF.
TableS7.xlsx (34 kB)
Bases sequenced comparison between WGBS and methylCRF.
