RnBeads: uWGBS - prog_v08_um

Option	Value
analyze.sites	no
region.types	tiling, cpgislands, genes, promoters, ensembleRegBuildBPall, ensembleRegBuildBPallMerged
differential.permutations	0
differential.comparison.columns	cmp_ct_CMPvMEP, cmp_ct_CMPvGMP, cmp_ct_CMPvCLP, cmp_ct_MLP3vGMP, cmp_ct_CLPvMLP0, cmp_ct_CLPvMLP1, cmp_ct_CLPvMLP2, cmp_ct_CLPvMLP3, cmp_ct_MLP1vMLP2, cmp_ct_MLP2vMLP3, cmp_ct_MLP1vMLP3, cmp_ct_MLP0vMLP1, cmp_ct_MLP0vMLP2, cmp_ct_MLP0vMLP3, cmp_ct_HSCvMPP, cmp_ct_MPPvCMP, cmp_ct_HSCvML, cmp_ct_MYEvLYM, cmp_src_HSC_BMvCB, cmp_src_HSC_BMvFL, cmp_src_HSC_BMvPB, cmp_src_HSC_CBvFL, cmp_src_HSC_CBvPB, cmp_src_HSC_FLvPB, cmp_src_MPP_BMvCB, cmp_src_MPP_BMvPB, cmp_src_MPP_CBvPB, cmp_HSCvMPP_PB, cmp_HSCvMPP_CB, cmp_HSCvMPP_BM
differential.comparison.columns.all.pairwise	default
columns.pairing	default
differential.site.test.method	limma
covariate.adjustment.columns	sex, donorId, flowcell, cellSourceCurated, nominalCellNumber
differential.adjustment.sva	yes
differential.adjustment.celltype	yes
differential.enrichment	yes

	comparison	adjustment	covariateTable
1	CMP vs. MEP (based on cmp_ct_CMPvMEP)	sex,donorId,flowcell,nominalCellNumber	csv
2	CMP vs. GMP (based on cmp_ct_CMPvGMP)	donorId,flowcell,nominalCellNumber	csv
3	CLP vs. CMP (based on cmp_ct_CMPvCLP)	sex,donorId,flowcell,nominalCellNumber	csv
4	GMP vs. MLP3 (based on cmp_ct_MLP3vGMP)	donorId,flowcell,nominalCellNumber	csv
5	CLP vs. MLP0 (based on cmp_ct_CLPvMLP0)	donorId,flowcell,nominalCellNumber	csv
6	CLP vs. MLP1 (based on cmp_ct_CLPvMLP1)	sex,donorId,nominalCellNumber	csv
7	CLP vs. MLP2 (based on cmp_ct_CLPvMLP2)	sex,donorId,flowcell,nominalCellNumber	csv
8	CLP vs. MLP3 (based on cmp_ct_CLPvMLP3)	sex,donorId,flowcell,nominalCellNumber	csv
9	MLP1 vs. MLP2 (based on cmp_ct_MLP1vMLP2)	sex,donorId,flowcell,nominalCellNumber	csv
10	MLP2 vs. MLP3 (based on cmp_ct_MLP2vMLP3)	sex,donorId,flowcell,nominalCellNumber	csv
11	MLP1 vs. MLP3 (based on cmp_ct_MLP1vMLP3)	sex,donorId,flowcell,nominalCellNumber	csv
12	MLP0 vs. MLP1 (based on cmp_ct_MLP0vMLP1)	donorId,flowcell,nominalCellNumber	csv
13	MLP0 vs. MLP2 (based on cmp_ct_MLP0vMLP2)	donorId,flowcell,nominalCellNumber	csv
14	MLP0 vs. MLP3 (based on cmp_ct_MLP0vMLP3)	donorId,flowcell,nominalCellNumber	csv
15	HSC vs. MPP (based on cmp_ct_HSCvMPP)	flowcell,cellSourceCurated,nominalCellNumber	csv
16	CMP vs. MPP (based on cmp_ct_MPPvCMP)	flowcell,cellSourceCurated,nominalCellNumber	csv
17	HSC vs. ML (based on cmp_ct_HSCvML)	flowcell,cellSourceCurated,nominalCellNumber	csv
18	LYM vs. MYE (based on cmp_ct_MYEvLYM)	donorId,flowcell,nominalCellNumber	csv
19	BM vs. CB (based on cmp_src_HSC_BMvCB)	flowcell,nominalCellNumber	csv
20	BM vs. FL (based on cmp_src_HSC_BMvFL)	flowcell,nominalCellNumber	csv
21	BM vs. PB (based on cmp_src_HSC_BMvPB)	flowcell,nominalCellNumber	csv
22	CB vs. FL (based on cmp_src_HSC_CBvFL)	donorId,flowcell,nominalCellNumber	csv
23	CB vs. PB (based on cmp_src_HSC_CBvPB)	sex,donorId,nominalCellNumber	csv
24	FL vs. PB (based on cmp_src_HSC_FLvPB)	donorId,flowcell,nominalCellNumber	csv
25	BM vs. CB (based on cmp_src_MPP_BMvCB)	nominalCellNumber	csv
26	BM vs. PB (based on cmp_src_MPP_BMvPB)	flowcell,nominalCellNumber	csv
27	CB vs. PB (based on cmp_src_MPP_CBvPB)	donorId,flowcell,nominalCellNumber	csv
28	HSC vs. MPP (based on cmp_HSCvMPP_PB)	donorId,flowcell,nominalCellNumber	csv
29	HSC vs. MPP (based on cmp_HSCvMPP_CB)	sex,donorId,nominalCellNumber	csv
30	HSC vs. MPP (based on cmp_HSCvMPP_BM)	flowcell,nominalCellNumber	csv

Differential methylation on the region level was computed based on a variety of metrics. Of particular interest for the following plots and analyses are the following quantities for each region: the mean methylation difference in a region of the two groups being and of quotient of mean methylation levelsas well as a p-value obtained from statistical testing (limma or t-test; depending on parameter settings). Additionally each region was assigned a rank based on each of these three criteria. A combined rank is computed as the maximum (i.e. worst) value among the three ranks. The smaller the combined rank for a region, the more evidence for differential methylation it exhibits. Regions were defined based on the region types specified in the analysis. This section includes scatterplots of the region group means as well as volcano plots of each pairwise comparison colored according to the combined rank of a given region.

The following rank cutfoffs have been automatically selected for the analysis of differentially methylated regions:

	tiling	cpgislands	genes	promoters	ensembleRegBuildBPall	ensembleRegBuildBPallMerged
CMP vs. MEP (based on cmp_ct_CMPvMEP)	0	0	0	0	0	0
CMP vs. GMP (based on cmp_ct_CMPvGMP)	0	0	0	0	0	0
CLP vs. CMP (based on cmp_ct_CMPvCLP)	0	0	0	0	0	0
GMP vs. MLP3 (based on cmp_ct_MLP3vGMP)	0	0	0	0	0	0
CLP vs. MLP0 (based on cmp_ct_CLPvMLP0)	0	0	0	0	0	0
CLP vs. MLP1 (based on cmp_ct_CLPvMLP1)	0	0	0	0	0	0
CLP vs. MLP2 (based on cmp_ct_CLPvMLP2)	0	0	0	0	0	0
CLP vs. MLP3 (based on cmp_ct_CLPvMLP3)	0	0	0	0	0	0
MLP1 vs. MLP2 (based on cmp_ct_MLP1vMLP2)	0	0	0	0	0	0
MLP2 vs. MLP3 (based on cmp_ct_MLP2vMLP3)	0	0	0	0	0	0
MLP1 vs. MLP3 (based on cmp_ct_MLP1vMLP3)	0	0	0	0	0	0
MLP0 vs. MLP1 (based on cmp_ct_MLP0vMLP1)	0	0	0	0	0	0
MLP0 vs. MLP2 (based on cmp_ct_MLP0vMLP2)	0	0	0	0	0	0
MLP0 vs. MLP3 (based on cmp_ct_MLP0vMLP3)	0	0	0	0	0	0
HSC vs. MPP (based on cmp_ct_HSCvMPP)	0	0	0	0	0	0
CMP vs. MPP (based on cmp_ct_MPPvCMP)	0	0	0	0	0	0
HSC vs. ML (based on cmp_ct_HSCvML)	0	0	0	0	0	0
LYM vs. MYE (based on cmp_ct_MYEvLYM)	0	0	0	0	0	0
BM vs. CB (based on cmp_src_HSC_BMvCB)	0	0	0	0	0	0
BM vs. FL (based on cmp_src_HSC_BMvFL)	0	0	0	0	0	0
BM vs. PB (based on cmp_src_HSC_BMvPB)	0	0	0	0	0	0
CB vs. FL (based on cmp_src_HSC_CBvFL)	0	0	0	0	0	0
CB vs. PB (based on cmp_src_HSC_CBvPB)	0	0	0	0	0	0
FL vs. PB (based on cmp_src_HSC_FLvPB)	0	0	0	0	0	0
BM vs. CB (based on cmp_src_MPP_BMvCB)	0	0	0	0	0	0
BM vs. PB (based on cmp_src_MPP_BMvPB)	0	0	0	0	0	0
CB vs. PB (based on cmp_src_MPP_CBvPB)	0	0	0	0	0	0
HSC vs. MPP (based on cmp_HSCvMPP_PB)	0	0	0	0	0	0
HSC vs. MPP (based on cmp_HSCvMPP_CB)	0	0	0	0	0	0
HSC vs. MPP (based on cmp_HSCvMPP_BM)	0	0	0	0	0	0

comparison
regions
differential methylation measure

Figure 1

Scatterplot for differential methylation (regions). If the selected criterion is not rankGradient: The transparency corresponds to point density. The 1% of the points in the sparsest populated plot regions are drawn explicitly. Additionally, the colored points represent differentially methylated regions (according to the selected criterion). If the selected criterion is rankGradient: median combined ranks accross hexagonal bins are shown as a gradient according to the color legend.

comparison
regions
difference metric
significance metric

Figure 2

Volcano plot for differential methylation quantified by various metrics. Color scale according to combined ranking.

Differential Methylation Tables

A tabular overview of measures for differential methylation on the region level for the individual comparisons are provided in this section.

id: region id
Chromosome: chromosome of the region
Start: start coordinate of the region
End: end coordinate of the region
mean.g1,mean.g2: (where g1 and g2 is replaced by the respective group names in the table) mean methylation in each of the two groups
mean.diff: difference in methylation means between the two groups: mean.g1-mean.g2. In case of paired analysis, it is the mean of the pairwise differences.
mean.quot.log2: log2 of the quotient in methylation: log2((mean.g1+epsilon)/(mean.g2+epsilon)), where epsilon:=0.01. In case of paired analysis, it is the mean of the pairwise quotients.
diffmeth.p.val: p-value obtained from linear models employed in the limma package (or alternatively from a two-sided Welch t-test; which type of p-value is computed is specified in the differential.site.test.method option).
max.g1,max.g2: maximum methylation level in group 1 and 2 respectively
min.g1,min.g2: minimum methylation level in group 1 and 2 respectively
sd.g1,sd.g2: standard deviation of methylation levels
min.diff: Minimum of 0 and the smallest pairwise difference between samples of the two groups
diffmeth.p.adj.fdr: FDR adjusted p-value of all sites
combinedRank: mean.diff, mean.quot.log2 and diffmeth.p.val are ranked for all regions. This aggregates them using the maximum, i.e. worst rank of a site among the three measures
num.na.g1,num.na.g2: number of NA methylation values for groups 1 and 2 respectively
mean.covg.g1,mean.covg.g2: mean coverage of groups 1 and 2 respectively (In case of Infinium array methylation data, coverage is defined as combined beadcount.)
min.covg.g1,min.covg.g2: minimum coverage of groups 1 and 2 respectively
max.covg.g1,max.covg.g2: maximum coverage of groups 1 and 2 respectively
covg.thresh.nsamples.g1,covg.thresh.nsamples.g2: number of samples in group 1 and 2 respectively exceeding the coverage threshold (1) for this region.

The tables for the individual comparisons can be found here:

	tiling	cpgislands	genes	promoters	ensembleRegBuildBPall	ensembleRegBuildBPallMerged
CMP vs. MEP (based on cmp_ct_CMPvMEP)	csv	csv	csv	csv	csv	csv
CMP vs. GMP (based on cmp_ct_CMPvGMP)	csv	csv	csv	csv	csv	csv
CLP vs. CMP (based on cmp_ct_CMPvCLP)	csv	csv	csv	csv	csv	csv
GMP vs. MLP3 (based on cmp_ct_MLP3vGMP)	csv	csv	csv	csv	csv	csv
CLP vs. MLP0 (based on cmp_ct_CLPvMLP0)	csv	csv	csv	csv	csv	csv
CLP vs. MLP1 (based on cmp_ct_CLPvMLP1)	csv	csv	csv	csv	csv	csv
CLP vs. MLP2 (based on cmp_ct_CLPvMLP2)	csv	csv	csv	csv	csv	csv
CLP vs. MLP3 (based on cmp_ct_CLPvMLP3)	csv	csv	csv	csv	csv	csv
MLP1 vs. MLP2 (based on cmp_ct_MLP1vMLP2)	csv	csv	csv	csv	csv	csv
MLP2 vs. MLP3 (based on cmp_ct_MLP2vMLP3)	csv	csv	csv	csv	csv	csv
MLP1 vs. MLP3 (based on cmp_ct_MLP1vMLP3)	csv	csv	csv	csv	csv	csv
MLP0 vs. MLP1 (based on cmp_ct_MLP0vMLP1)	csv	csv	csv	csv	csv	csv
MLP0 vs. MLP2 (based on cmp_ct_MLP0vMLP2)	csv	csv	csv	csv	csv	csv
MLP0 vs. MLP3 (based on cmp_ct_MLP0vMLP3)	csv	csv	csv	csv	csv	csv
HSC vs. MPP (based on cmp_ct_HSCvMPP)	csv	csv	csv	csv	csv	csv
CMP vs. MPP (based on cmp_ct_MPPvCMP)	csv	csv	csv	csv	csv	csv
HSC vs. ML (based on cmp_ct_HSCvML)	csv	csv	csv	csv	csv	csv
LYM vs. MYE (based on cmp_ct_MYEvLYM)	csv	csv	csv	csv	csv	csv
BM vs. CB (based on cmp_src_HSC_BMvCB)	csv	csv	csv	csv	csv	csv
BM vs. FL (based on cmp_src_HSC_BMvFL)	csv	csv	csv	csv	csv	csv
BM vs. PB (based on cmp_src_HSC_BMvPB)	csv	csv	csv	csv	csv	csv
CB vs. FL (based on cmp_src_HSC_CBvFL)	csv	csv	csv	csv	csv	csv
CB vs. PB (based on cmp_src_HSC_CBvPB)	csv	csv	csv	csv	csv	csv
FL vs. PB (based on cmp_src_HSC_FLvPB)	csv	csv	csv	csv	csv	csv
BM vs. CB (based on cmp_src_MPP_BMvCB)	csv	csv	csv	csv	csv	csv
BM vs. PB (based on cmp_src_MPP_BMvPB)	csv	csv	csv	csv	csv	csv
CB vs. PB (based on cmp_src_MPP_CBvPB)	csv	csv	csv	csv	csv	csv
HSC vs. MPP (based on cmp_HSCvMPP_PB)	csv	csv	csv	csv	csv	csv
HSC vs. MPP (based on cmp_HSCvMPP_CB)	csv	csv	csv	csv	csv	csv
HSC vs. MPP (based on cmp_HSCvMPP_BM)	csv	csv	csv	csv	csv	csv

Enrichment Analysis

Enrichment Analysis was conducted. The wordclouds and tables below contains significant GO terms as determined by a hypergeometric test.

comparison
Hypermethylation/hypomethylation
ontology
regions
differential methylation measure

Figure 3

Wordclouds for GO enrichment terms.

comparison
Hypermethylation/hypomethylation
ontology
regions
differential methylation measure

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0060324	0.0018	36.0623	0.0641	2	53	face development
GO:0071049	0.0024	871.2778	0.0024	1	2	nuclear retention of pre-mRNA with aberrant 3'-ends at the site of transcription
GO:0002824	0.003	27.8396	0.0823	2	68	positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
GO:0019318	0.0032	11.7184	0.3025	3	250	hexose metabolic process
GO:0033091	0.0036	435.6111	0.0036	1	3	positive regulation of immature T cell proliferation
GO:0033133	0.0036	435.6111	0.0036	1	3	positive regulation of glucokinase activity
GO:0044375	0.0036	435.6111	0.0036	1	3	regulation of peroxisome size
GO:0006094	0.0041	23.5385	0.0968	2	80	gluconeogenesis
GO:0015746	0.0048	290.3889	0.0048	1	4	citrate transport
GO:0016557	0.0048	290.3889	0.0048	1	4	peroxisome membrane biogenesis
GO:0060528	0.0048	290.3889	0.0048	1	4	secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development
GO:0070427	0.0048	290.3889	0.0048	1	4	nucleotide-binding oligomerization domain containing 1 signaling pathway
GO:0070673	0.0048	290.3889	0.0048	1	4	response to interleukin-18
GO:0071034	0.0048	290.3889	0.0048	1	4	CUT catabolic process
GO:0071224	0.0048	290.3889	0.0048	1	4	cellular response to peptidoglycan
GO:1903142	0.0048	290.3889	0.0048	1	4	positive regulation of establishment of endothelial barrier
GO:0046364	0.005	21.3379	0.1065	2	88	monosaccharide biosynthetic process
GO:0000467	0.006	217.7778	0.006	1	5	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0070671	0.006	217.7778	0.006	1	5	response to interleukin-12
GO:0071038	0.006	217.7778	0.006	1	5	nuclear polyadenylation-dependent tRNA catabolic process
GO:0071051	0.006	217.7778	0.006	1	5	polyadenylation-dependent snoRNA 3'-end processing
GO:0071225	0.006	217.7778	0.006	1	5	cellular response to muramyl dipeptide
GO:0010906	0.0066	18.3341	0.1234	2	102	regulation of glucose metabolic process
GO:0043144	0.0072	174.2111	0.0073	1	6	snoRNA processing
GO:0043634	0.0072	174.2111	0.0073	1	6	polyadenylation-dependent ncRNA catabolic process
GO:0045627	0.0072	174.2111	0.0073	1	6	positive regulation of T-helper 1 cell differentiation
GO:0071029	0.0072	174.2111	0.0073	1	6	nuclear ncRNA surveillance
GO:0071035	0.0072	174.2111	0.0073	1	6	nuclear polyadenylation-dependent rRNA catabolic process
GO:0060770	0.0084	145.1667	0.0085	1	7	negative regulation of epithelial cell proliferation involved in prostate gland development
GO:0070131	0.0084	145.1667	0.0085	1	7	positive regulation of mitochondrial translation
GO:0002819	0.0087	15.9274	0.1416	2	117	regulation of adaptive immune response
GO:0034475	0.0096	124.4206	0.0097	1	8	U4 snRNA 3'-end processing

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0009889	7e-04	5.4031	4.3141	11	3985	regulation of biosynthetic process
GO:0019046	0.0011	Inf	0.0011	1	1	release from viral latency
GO:2000326	0.0011	Inf	0.0011	1	1	negative regulation of ligand-dependent nuclear receptor transcription coactivator activity
GO:0019219	0.0022	4.5566	4.0641	10	3754	regulation of nucleobase-containing compound metabolic process
GO:1901253	0.0022	980.3125	0.0022	1	2	negative regulation of intracellular transport of viral material
GO:0007500	0.0032	490.125	0.0032	1	3	mesodermal cell fate determination
GO:0034645	0.0035	4.2362	5.1412	11	4749	cellular macromolecule biosynthetic process
GO:0032481	0.0035	26.01	0.0888	2	82	positive regulation of type I interferon production
GO:0006355	0.0038	4.2209	3.5834	9	3310	regulation of transcription, DNA-templated
GO:2001141	0.004	4.1648	3.6213	9	3345	regulation of RNA biosynthetic process
GO:0006990	0.0043	326.7292	0.0043	1	4	positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response
GO:0032747	0.0054	245.0312	0.0054	1	5	positive regulation of interleukin-23 production
GO:0097659	0.0055	3.943	3.7793	9	3491	nucleic acid-templated transcription
GO:0010467	0.0055	3.9205	5.4227	11	5009	gene expression
GO:1901576	0.0056	4.0353	6.3462	12	5862	organic substance biosynthetic process
GO:0090045	0.0076	163.3333	0.0076	1	7	positive regulation of deacetylase activity
GO:1900246	0.0086	139.9911	0.0087	1	8	positive regulation of RIG-I signaling pathway
GO:1904851	0.0086	139.9911	0.0087	1	8	positive regulation of establishment of protein localization to telomere
GO:1904871	0.0086	139.9911	0.0087	1	8	positive regulation of protein localization to Cajal body
GO:1903405	0.0097	122.4844	0.0097	1	9	protein localization to nuclear body
GO:0044271	0.01	3.4921	4.941	10	4564	cellular nitrogen compound biosynthetic process

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0032759	0.0015	1426.3636	0.0015	1	2	positive regulation of TRAIL production
GO:0071409	0.0023	713.1364	0.0023	1	3	cellular response to cycloheximide
GO:2000566	0.0023	713.1364	0.0023	1	3	positive regulation of CD8-positive, alpha-beta T cell proliferation
GO:0042270	0.0046	285.2	0.0046	1	6	protection from natural killer cell mediated cytotoxicity
GO:0002476	0.0053	237.6515	0.0053	1	7	antigen processing and presentation of endogenous peptide antigen via MHC class Ib
GO:0060509	0.0053	237.6515	0.0053	1	7	Type I pneumocyte differentiation
GO:0061179	0.0061	203.6883	0.0061	1	8	negative regulation of insulin secretion involved in cellular response to glucose stimulus
GO:0071499	0.0061	203.6883	0.0061	1	8	cellular response to laminar fluid shear stress
GO:2001185	0.0061	203.6883	0.0061	1	8	regulation of CD8-positive, alpha-beta T cell activation
GO:0002480	0.0069	178.2159	0.0069	1	9	antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent
GO:0043249	0.0076	158.404	0.0076	1	10	erythrocyte maturation
GO:0051024	0.0076	158.404	0.0076	1	10	positive regulation of immunoglobulin secretion
GO:0002716	0.0084	142.5545	0.0084	1	11	negative regulation of natural killer cell mediated immunity
GO:0097067	0.0091	129.5868	0.0092	1	12	cellular response to thyroid hormone stimulus
GO:0032736	0.0099	118.7803	0.0099	1	13	positive regulation of interleukin-13 production
GO:0042789	0.0099	118.7803	0.0099	1	13	mRNA transcription from RNA polymerase II promoter

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:1904431	0	1120.3571	0.0041	2	4	positive regulation of t-circle formation
GO:0010792	0	560.1071	0.0061	2	6	DNA double-strand break processing involved in repair via single-strand annealing
GO:2001252	3e-04	26.7847	0.1396	3	137	positive regulation of chromosome organization
GO:0036297	8e-04	55.8821	0.0428	2	42	interstrand cross-link repair
GO:0032846	0.001	18.1453	0.2038	3	200	positive regulation of homeostatic process
GO:0035921	0.001	Inf	0.001	1	1	desmosome disassembly
GO:1900387	0.001	Inf	0.001	1	1	negative regulation of cell-cell adhesion by negative regulation of transcription from RNA polymerase II promoter
GO:0050672	0.0018	36.5948	0.0642	2	63	negative regulation of lymphocyte proliferation
GO:0032204	0.0019	36.0023	0.0652	2	64	regulation of telomere maintenance
GO:0070563	0.002	1045.7333	0.002	1	2	negative regulation of vitamin D receptor signaling pathway
GO:0070664	0.0021	34.3341	0.0683	2	67	negative regulation of leukocyte proliferation
GO:0000726	0.0024	31.8714	0.0734	2	72	non-recombinational repair
GO:0003273	0.0041	348.5333	0.0041	1	4	cell migration involved in endocardial cushion formation
GO:0006933	0.0041	348.5333	0.0041	1	4	negative regulation of cell adhesion involved in substrate-bound cell migration
GO:0010957	0.0051	261.3833	0.0051	1	5	negative regulation of vitamin D biosynthetic process
GO:0006610	0.0081	149.3333	0.0082	1	8	ribosomal protein import into nucleus
GO:0030210	0.0081	149.3333	0.0082	1	8	heparin biosynthetic process
GO:1901419	0.0081	149.3333	0.0082	1	8	regulation of response to alcohol
GO:0002695	0.0087	16.0963	0.1426	2	140	negative regulation of leukocyte activation
GO:0032200	0.0087	16.0963	0.1426	2	140	telomere organization
GO:0033629	0.0091	130.6583	0.0092	1	9	negative regulation of cell adhesion mediated by integrin
GO:0035414	0.0091	130.6583	0.0092	1	9	negative regulation of catenin import into nucleus
GO:0071550	0.0091	130.6583	0.0092	1	9	death-inducing signaling complex assembly

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0035574	1e-04	200.9744	0.0134	2	15	histone H4-K20 demethylation
GO:0045653	1e-04	163.2604	0.016	2	18	negative regulation of megakaryocyte differentiation
GO:0006335	4e-04	86.9944	0.0285	2	32	DNA replication-dependent nucleosome assembly
GO:0016577	4e-04	84.1828	0.0294	2	33	histone demethylation
GO:0008214	4e-04	79.0707	0.0312	2	35	protein dealkylation
GO:0032776	4e-04	79.0707	0.0312	2	35	DNA methylation on cytosine
GO:0051290	5e-04	72.4676	0.0339	2	38	protein heterotetramerization
GO:0034080	6e-04	68.6447	0.0357	2	40	CENP-A containing nucleosome assembly
GO:0000183	6e-04	66.8803	0.0366	2	41	chromatin silencing at rDNA
GO:1901532	7e-04	63.6098	0.0383	2	43	regulation of hematopoietic progenitor cell differentiation
GO:0034724	9e-04	54.309	0.0446	2	50	DNA replication-independent nucleosome organization
GO:0043048	9e-04	Inf	9e-04	1	1	dolichyl monophosphate biosynthetic process
GO:0070988	0.0014	43.4139	0.0553	2	62	demethylation
GO:0006303	0.0015	41.3386	0.058	2	65	double-strand break repair via nonhomologous end joining
GO:0043044	0.0018	37.7295	0.0633	2	71	ATP-dependent chromatin remodeling
GO:0045815	0.0021	34.6978	0.0686	2	77	positive regulation of gene expression, epigenetic
GO:0006305	0.0026	30.5961	0.0776	2	87	DNA alkylation
GO:0044728	0.0035	26.5153	0.0892	2	100	DNA methylation or demethylation
GO:0042989	0.0045	301.6346	0.0045	1	5	sequestering of actin monomers
GO:1990592	0.0045	301.6346	0.0045	1	5	protein K69-linked ufmylation
GO:0006489	0.0053	241.2923	0.0053	1	6	dolichyl diphosphate biosynthetic process
GO:0071569	0.0053	241.2923	0.0053	1	6	protein ufmylation
GO:0000723	0.0055	20.752	0.1132	2	127	telomere maintenance
GO:1903707	0.0058	20.2617	0.1159	2	130	negative regulation of hemopoiesis
GO:0031497	0.0066	18.9197	0.1239	2	139	chromatin assembly
GO:0031047	0.0076	17.6213	0.1328	2	149	gene silencing by RNA
GO:0000724	0.0077	17.3826	0.1346	2	151	double-strand break repair via homologous recombination
GO:0045814	0.0077	17.3826	0.1346	2	151	negative regulation of gene expression, epigenetic
GO:0048552	0.0089	134.0171	0.0089	1	10	regulation of metalloenzyme activity
GO:0065004	0.0096	15.491	0.1507	2	169	protein-DNA complex assembly

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0006818	2e-04	31.4222	0.123	3	138	hydrogen transport
GO:0015876	0.0018	1206.7692	0.0018	1	2	acetyl-CoA transport
GO:0070901	0.0018	1206.7692	0.0018	1	2	mitochondrial tRNA methylation
GO:1901337	0.0018	1206.7692	0.0018	1	2	thioester transport
GO:1902600	0.0033	27.0712	0.0874	2	98	hydrogen ion transmembrane transport
GO:0090261	0.0036	402.2051	0.0036	1	4	positive regulation of inclusion body assembly
GO:0022900	0.0052	21.4435	0.1097	2	123	electron transport chain
GO:0035814	0.0053	241.2923	0.0053	1	6	negative regulation of renal sodium excretion
GO:0044539	0.0062	201.0641	0.0062	1	7	long-chain fatty acid import
GO:0051256	0.0062	201.0641	0.0062	1	7	mitotic spindle midzone assembly
GO:0006123	0.0071	172.3297	0.0071	1	8	mitochondrial electron transport, cytochrome c to oxygen
GO:1900864	0.0071	172.3297	0.0071	1	8	mitochondrial RNA modification
GO:0010459	0.008	150.7788	0.008	1	9	negative regulation of heart rate
GO:0051231	0.008	150.7788	0.008	1	9	spindle elongation
GO:0042407	0.0089	134.0171	0.0089	1	10	cristae formation

Differential Methylation

Parameter Overview

Introduction: Differential Methylation of Sample Groups

Comparisons

P-values

Region Level

Differential Methylation Tables

Enrichment Analysis

References

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0043249	1e-04	170.3261	0.0159	2	10	erythrocyte maturation
GO:0009399	0.0016	Inf	0.0016	1	1	nitrogen fixation
GO:1904057	0.0016	Inf	0.0016	1	1	negative regulation of sensory perception of pain
GO:0046676	0.0019	34.8696	0.0653	2	41	negative regulation of insulin secretion
GO:0002792	0.0026	29.5501	0.0764	2	48	negative regulation of peptide secretion
GO:0061515	0.0026	29.5501	0.0764	2	48	myeloid cell development
GO:0006668	0.0032	653.2083	0.0032	1	2	sphinganine-1-phosphate metabolic process
GO:0019264	0.0032	653.2083	0.0032	1	2	glycine biosynthetic process from serine
GO:0044571	0.0032	653.2083	0.0032	1	2	[2Fe-2S] cluster assembly
GO:1990523	0.0032	653.2083	0.0032	1	2	bone regeneration
GO:0015820	0.0048	326.5833	0.0048	1	3	leucine transport
GO:0035928	0.0048	326.5833	0.0048	1	3	rRNA import into mitochondrion
GO:0060392	0.0048	326.5833	0.0048	1	3	negative regulation of SMAD protein import into nucleus
GO:0071409	0.0048	326.5833	0.0048	1	3	cellular response to cycloheximide
GO:0097428	0.0048	326.5833	0.0048	1	3	protein maturation by iron-sulfur cluster transfer
GO:1902731	0.0048	326.5833	0.0048	1	3	negative regulation of chondrocyte proliferation
GO:0046888	0.006	19.1145	0.1162	2	73	negative regulation of hormone secretion
GO:0006564	0.0064	217.7083	0.0064	1	4	L-serine biosynthetic process
GO:0071603	0.0064	217.7083	0.0064	1	4	endothelial cell-cell adhesion
GO:0090027	0.0064	217.7083	0.0064	1	4	negative regulation of monocyte chemotaxis
GO:0040029	0.0066	8.7346	0.3885	3	244	regulation of gene expression, epigenetic
GO:0070124	0.0078	16.5387	0.1337	2	84	mitochondrial translational initiation
GO:0070125	0.0078	16.5387	0.1337	2	84	mitochondrial translational elongation
GO:0061484	0.0079	163.2708	0.008	1	5	hematopoietic stem cell homeostasis
GO:0070126	0.0082	16.1429	0.1369	2	86	mitochondrial translational termination
GO:0043624	0.0089	7.8113	0.433	3	272	cellular protein complex disassembly
GO:0030218	0.0095	14.8944	0.1481	2	93	erythrocyte differentiation

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0051260	0.0017	15.0703	0.2474	3	259	protein homooligomerization
GO:0019264	0.0019	1120.5	0.0019	1	2	glycine biosynthetic process from serine
GO:0006564	0.0038	373.4524	0.0038	1	4	L-serine biosynthetic process
GO:0050911	0.0048	10.4366	0.3534	3	370	detection of chemical stimulus involved in sensory perception of smell
GO:0009593	0.0083	8.5045	0.4308	3	451	detection of chemical stimulus
GO:0007606	0.0089	8.2576	0.4432	3	464	sensory perception of chemical stimulus
GO:0050906	0.0089	8.2576	0.4432	3	464	detection of stimulus involved in sensory perception
GO:0035999	0.0095	124.4365	0.0096	1	10	tetrahydrofolate interconversion

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0045932	2e-04	118.6818	0.0215	2	26	negative regulation of muscle contraction
GO:0042666	8e-04	Inf	8e-04	1	1	negative regulation of ectodermal cell fate specification
GO:0071881	8e-04	Inf	8e-04	1	1	adenylate cyclase-inhibiting adrenergic receptor signaling pathway
GO:0071882	8e-04	Inf	8e-04	1	1	phospholipase C-activating adrenergic receptor signaling pathway
GO:2000383	8e-04	Inf	8e-04	1	1	regulation of ectoderm development
GO:0006940	0.0012	46.5842	0.0522	2	63	regulation of smooth muscle contraction
GO:0048866	0.0017	1307.4167	0.0017	1	2	stem cell fate specification
GO:0070473	0.0017	1307.4167	0.0017	1	2	negative regulation of uterine smooth muscle contraction
GO:1903524	0.0023	33.3797	0.072	2	87	positive regulation of blood circulation
GO:0071877	0.0023	713	0.0023	1	3	regulation of adrenergic receptor signaling pathway
GO:0001712	0.0025	653.6667	0.0025	1	3	ectodermal cell fate commitment
GO:0071878	0.0025	653.6667	0.0025	1	3	negative regulation of adrenergic receptor signaling pathway
GO:0071883	0.0025	653.6667	0.0025	1	3	activation of MAPK activity by adrenergic receptor signaling pathway
GO:0014834	0.0033	435.75	0.0033	1	4	skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration
GO:0035625	0.0033	435.75	0.0033	1	4	epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway
GO:0050955	0.0033	435.75	0.0033	1	4	thermoception
GO:0060214	0.0033	435.75	0.0033	1	4	endocardium formation
GO:0003012	0.0034	12.1524	0.3154	3	381	muscle system process
GO:0043456	0.0041	326.7917	0.0041	1	5	regulation of pentose-phosphate shunt
GO:0038031	0.005	261.4167	0.005	1	6	non-canonical Wnt signaling pathway via JNK cascade
GO:0060836	0.005	261.4167	0.005	1	6	lymphatic endothelial cell differentiation
GO:0060956	0.005	261.4167	0.005	1	6	endocardial cell differentiation
GO:0043603	0.0053	7.2186	0.7567	4	914	cellular amide metabolic process
GO:0010519	0.0058	217.8333	0.0058	1	7	negative regulation of phospholipase activity
GO:0060054	0.0058	217.8333	0.0058	1	7	positive regulation of epithelial cell proliferation involved in wound healing
GO:0070131	0.0058	217.8333	0.0058	1	7	positive regulation of mitochondrial translation
GO:0050880	0.0059	20.3414	0.1167	2	141	regulation of blood vessel size
GO:0006941	0.0059	20.1948	0.1176	2	142	striated muscle contraction
GO:0032811	0.0066	186.7024	0.0066	1	8	negative regulation of epinephrine secretion
GO:0043951	0.0066	186.7024	0.0066	1	8	negative regulation of cAMP-mediated signaling
GO:0060087	0.0066	186.7024	0.0066	1	8	relaxation of vascular smooth muscle
GO:0060452	0.0066	186.7024	0.0066	1	8	positive regulation of cardiac muscle contraction
GO:0061179	0.0066	186.7024	0.0066	1	8	negative regulation of insulin secretion involved in cellular response to glucose stimulus
GO:0051171	0.0068	4.6262	3.3446	8	4040	regulation of nitrogen compound metabolic process
GO:0010700	0.0074	163.3542	0.0075	1	9	negative regulation of norepinephrine secretion
GO:0033617	0.0074	163.3542	0.0075	1	9	mitochondrial respiratory chain complex IV assembly
GO:0045955	0.0083	145.1944	0.0083	1	10	negative regulation of calcium ion-dependent exocytosis
GO:0007186	0.009	6.3086	0.8836	4	1156	G-protein coupled receptor signaling pathway
GO:0048241	0.0091	130.6667	0.0091	1	11	epinephrine transport

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0006261	0.0011	16.4809	0.208	3	121	DNA-dependent DNA replication
GO:0008039	0.0017	Inf	0.0017	1	1	synaptic target recognition
GO:0038158	0.0017	Inf	0.0017	1	1	granulocyte colony-stimulating factor signaling pathway
GO:1903839	0.0017	Inf	0.0017	1	1	positive regulation of mRNA 3'-UTR binding
GO:0031508	0.0034	602.8846	0.0034	1	2	pericentric heterochromatin assembly
GO:1902527	0.0034	602.8846	0.0034	1	2	positive regulation of protein monoubiquitination
GO:0021879	0.0044	22.3143	0.0997	2	58	forebrain neuron differentiation
GO:0007179	0.0046	9.9237	0.3404	3	198	transforming growth factor beta receptor signaling pathway
GO:0021888	0.0051	301.4231	0.0052	1	3	hypothalamus gonadotrophin-releasing hormone neuron development
GO:0033489	0.0051	301.4231	0.0052	1	3	cholesterol biosynthetic process via desmosterol
GO:0033490	0.0051	301.4231	0.0052	1	3	cholesterol biosynthetic process via lathosterol
GO:0071586	0.0051	301.4231	0.0052	1	3	CAAX-box protein processing
GO:1902255	0.0051	301.4231	0.0052	1	3	positive regulation of intrinsic apoptotic signaling pathway by p53 class mediator
GO:1902415	0.0051	301.4231	0.0052	1	3	regulation of mRNA binding
GO:0021954	0.006	18.9212	0.1169	2	68	central nervous system neuron development
GO:0010992	0.0069	200.9359	0.0069	1	4	ubiquitin homeostasis
GO:2001168	0.0069	200.9359	0.0069	1	4	positive regulation of histone H2B ubiquitination
GO:0006282	0.0071	17.3378	0.1272	2	74	regulation of DNA repair
GO:0045787	0.0073	17.2334	0.1288	2	83	positive regulation of cell cycle
GO:0000082	0.0076	8.2489	0.4075	3	237	G1/S transition of mitotic cell cycle
GO:0090068	0.0081	8.0396	0.4178	3	243	positive regulation of cell cycle process
GO:0071559	0.0082	8.0057	0.4195	3	244	response to transforming growth factor beta
GO:0030223	0.0086	150.6923	0.0086	1	5	neutrophil differentiation
GO:0000079	0.01	14.5023	0.1513	2	88	regulation of cyclin-dependent protein serine/threonine kinase activity