RnBeads: ZillerWGBS

Option	Value
analyze.sites	yes
region.types	tiling, genes, promoters, cpgislands
differential.permutations	0
differential.comparison.columns	cmp_ESC_vs_differentiated, cmp_colon_tumor_vs_normal, cmp_brain_AD_vs_normal, cmp_derGermLayer_meso_vs_ecto, cmp_derGermLayer_meso_vs_endo, cmp_derGermLayer_endo_vs_ecto
differential.comparison.columns.all.pairwise	default
columns.pairing	default
differential.site.test.method	limma
covariate.adjustment.columns	default
differential.adjustment.sva	yes
differential.adjustment.celltype	yes
differential.enrichment	yes

	Rank Cutoff
ESC vs. derived (based on cmp_ESC_vs_differentiated)	4320614
normal vs. tumor (based on cmp_colon_tumor_vs_normal)	0
AD vs. control (based on cmp_brain_AD_vs_normal)	4105800
ectoderm vs. mesoderm (based on cmp_derGermLayer_meso_vs_ecto)	3783408
endoderm vs. mesoderm (based on cmp_derGermLayer_meso_vs_endo)	3882234
ectoderm vs. endoderm (based on cmp_derGermLayer_endo_vs_ecto)	3636816

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 difference in means across all sites in a region of the two groups being compared and the mean of quotients in mean methylation as well as a combined p-value calculated from all site p-values in the region [1]. 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	genes	promoters	cpgislands
ESC vs. derived (based on cmp_ESC_vs_differentiated)	4931	2317	349	145
normal vs. tumor (based on cmp_colon_tumor_vs_normal)	0	0	0	0
AD vs. control (based on cmp_brain_AD_vs_normal)	165	1395	265	218
ectoderm vs. mesoderm (based on cmp_derGermLayer_meso_vs_ecto)	669	1062	74	225
endoderm vs. mesoderm (based on cmp_derGermLayer_meso_vs_endo)	1774	1399	162	328
ectoderm vs. endoderm (based on cmp_derGermLayer_endo_vs_ecto)	439	1056	91	143

comparison
regions
differential methylation measure

Figure 3

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 4

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
[symbol]: associated gene symbol to the given region [only valid for gene associated regions]
[entrezID]: Entrez ID of the gene associated with the region [only valid for gene associated regions]
mean.mean.g1,mean.mean.g2: (where g1 and g2 is replaced by the respective group names in the table) mean of mean methylation levels for group 1 and 2 across all sites in a region
mean.mean.diff: Mean difference in means across all sites in a region
mean.mean.quot.log2: log2 of the mean quotient in means across all sites in a region
comb.p.val: Combined p-value aggregating p-values of all sites in the region using a generalization of Fisher's method [1]
comb.p.adj.fdr: FDR adjusted combined p-value
combinedRank: mean.mean.diff, mean.mean.quot.log2 and comb.p.val are ranked for all regions. This column aggregates them using the maximum, i.e. worst rank of a site among the three measures
num.sites: number of sites associated with the region
mean.num.na.g1,mean.num.na.g2: Mean number of NA methylation values accross all sites in group 1 and group 2 respectively
mean.mean.covg.g1,mean.mean.covg.g2: Mean value of mean coverage values (across all samples in a group) across all sites in a region
mean.nsamples.covg.thresh.g1,mean.nsamples.covg.thresh.g2: mean number of samples (accross all considered sites) that have a coverage larger than 5 for the site in group 1 and group 2 respectively

The tables for the individual comparisons can be found here:

	tiling	genes	promoters	cpgislands
ESC vs. derived (based on cmp_ESC_vs_differentiated)	csv	csv	csv	csv
normal vs. tumor (based on cmp_colon_tumor_vs_normal)	csv	csv	csv	csv
AD vs. control (based on cmp_brain_AD_vs_normal)	csv	csv	csv	csv
ectoderm vs. mesoderm (based on cmp_derGermLayer_meso_vs_ecto)	csv	csv	csv	csv
endoderm vs. mesoderm (based on cmp_derGermLayer_meso_vs_endo)	csv	csv	csv	csv
ectoderm vs. endoderm (based on cmp_derGermLayer_endo_vs_ecto)	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 5

Wordclouds for GO enrichment terms.

comparison
Hypermethylation/hypomethylation
ontology
regions
differential methylation measure

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0050911	0	162.9451	0.1211	4	368	detection of chemical stimulus involved in sensory perception of smell
GO:0009593	0	134.7397	0.1454	4	442	detection of chemical stimulus
GO:0050906	0	132.2511	0.1481	4	450	detection of stimulus involved in sensory perception
GO:0007606	0	130.4425	0.15	4	456	sensory perception of chemical stimulus
GO:0007186	1e-04	50.5984	0.3675	4	1117	G-protein coupled receptor signaling pathway
GO:0050877	2e-04	48.0274	0.3856	4	1172	neurological system process
GO:0044707	0.0093	Inf	1.9639	5	5969	single-multicellular organism process

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0021937	4e-04	Inf	4e-04	1	6	cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation
GO:0021702	8e-04	Inf	8e-04	1	12	cerebellar Purkinje cell differentiation
GO:0021936	8e-04	Inf	8e-04	1	12	regulation of cerebellar granule cell precursor proliferation
GO:0021692	9e-04	Inf	9e-04	1	13	cerebellar Purkinje cell layer morphogenesis
GO:0021527	0.001	Inf	0.001	1	15	spinal cord association neuron differentiation
GO:0021697	0.0014	Inf	0.0014	1	22	cerebellar cortex formation
GO:0021846	0.0018	Inf	0.0018	1	27	cell proliferation in forebrain
GO:0021587	0.0024	Inf	0.0024	1	37	cerebellum morphogenesis
GO:2000179	0.0026	Inf	0.0026	1	39	positive regulation of neural precursor cell proliferation
GO:0021695	0.0031	Inf	0.0031	1	47	cerebellar cortex development
GO:0021879	0.0034	Inf	0.0034	1	51	forebrain neuron differentiation
GO:0021766	0.0034	Inf	0.0034	1	52	hippocampus development
GO:0021510	0.0059	Inf	0.0059	1	90	spinal cord development
GO:0022037	0.0061	Inf	0.0061	1	92	metencephalon development

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0002277	9e-04	2531.5	9e-04	1	2	myeloid dendritic cell activation involved in immune response
GO:0002588	9e-04	2531.5	9e-04	1	2	positive regulation of antigen processing and presentation of peptide antigen via MHC class II
GO:0060738	9e-04	2531.5	9e-04	1	2	epithelial-mesenchymal signaling involved in prostate gland development
GO:0060741	0.0014	1265.6667	0.0014	1	3	prostate gland stromal morphogenesis
GO:2001181	0.0014	1265.6667	0.0014	1	3	positive regulation of interleukin-10 secretion
GO:0060528	0.0018	843.7222	0.0018	1	4	secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development
GO:0060743	0.0018	843.7222	0.0018	1	4	epithelial cell maturation involved in prostate gland development
GO:0002580	0.0023	632.75	0.0023	1	5	regulation of antigen processing and presentation of peptide or polysaccharide antigen via MHC class II
GO:0044351	0.0023	632.75	0.0023	1	5	macropinocytosis
GO:0032688	0.0028	506.1667	0.0028	1	6	negative regulation of interferon-beta production
GO:0048852	0.0028	506.1667	0.0028	1	6	diencephalon morphogenesis
GO:2000049	0.0028	506.1667	0.0028	1	6	positive regulation of cell-cell adhesion mediated by cadherin
GO:2000778	0.0028	506.1667	0.0028	1	6	positive regulation of interleukin-6 secretion
GO:0002583	0.0032	421.7778	0.0032	1	7	regulation of antigen processing and presentation of peptide antigen
GO:0016584	0.0032	421.7778	0.0032	1	7	nucleosome positioning
GO:0033148	0.0032	421.7778	0.0032	1	7	positive regulation of intracellular estrogen receptor signaling pathway
GO:0051091	0.0035	29.98	0.093	2	202	positive regulation of sequence-specific DNA binding transcription factor activity
GO:0090197	0.0037	361.5	0.0037	1	8	positive regulation of chemokine secretion
GO:2000484	0.0046	281.1296	0.0046	1	10	positive regulation of interleukin-8 secretion
GO:0002579	0.0055	229.9848	0.0055	1	12	positive regulation of antigen processing and presentation
GO:0071294	0.0055	229.9848	0.0055	1	12	cellular response to zinc ion
GO:0030522	0.0059	22.8797	0.1211	2	263	intracellular receptor signaling pathway
GO:0010803	0.0064	194.5769	0.0064	1	14	regulation of tumor necrosis factor-mediated signaling pathway
GO:0071276	0.0064	194.5769	0.0064	1	14	cellular response to cadmium ion
GO:0050718	0.0083	148.7549	0.0083	1	18	positive regulation of interleukin-1 beta secretion
GO:2000406	0.0092	133.0789	0.0092	1	20	positive regulation of T cell migration
GO:0003002	0.0092	18.1244	0.152	2	330	regionalization

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:2000381	5e-04	5064	5e-04	1	2	negative regulation of mesoderm development
GO:0035582	8e-04	2531.8333	8e-04	1	3	sequestering of BMP in extracellular matrix
GO:0003419	0.0011	1687.7778	0.0011	1	4	growth plate cartilage chondrocyte proliferation
GO:0071692	0.0013	1265.75	0.0013	1	5	protein localization to extracellular region
GO:0021937	0.0016	1012.5333	0.0016	1	6	cerebellar Purkinje cell-granule cell precursor cell signaling involved in regulation of granule cell precursor cell proliferation
GO:0048263	0.0024	632.7083	0.0024	1	9	determination of dorsal identity
GO:0032926	0.0026	562.3704	0.0026	1	10	negative regulation of activin receptor signaling pathway
GO:0021702	0.0032	460.0606	0.0032	1	12	cerebellar Purkinje cell differentiation
GO:0021936	0.0032	460.0606	0.0032	1	12	regulation of cerebellar granule cell precursor proliferation
GO:0050911	0.0034	40.5109	0.0969	2	368	detection of chemical stimulus involved in sensory perception of smell
GO:0021692	0.0034	421.6944	0.0034	1	13	cerebellar Purkinje cell layer morphogenesis
GO:0042074	0.0034	421.6944	0.0034	1	13	cell migration involved in gastrulation
GO:1900116	0.0034	421.6944	0.0034	1	13	extracellular negative regulation of signal transduction
GO:0021527	0.0039	361.4048	0.0039	1	15	spinal cord association neuron differentiation
GO:0009593	0.0049	33.5295	0.1163	2	442	detection of chemical stimulus
GO:0003416	0.005	281.0185	0.005	1	19	endochondral bone growth
GO:0050906	0.005	32.9129	0.1184	2	450	detection of stimulus involved in sensory perception
GO:0007606	0.0052	32.4648	0.12	2	456	sensory perception of chemical stimulus
GO:0071773	0.0055	252.8833	0.0055	1	21	cellular response to BMP stimulus
GO:0021697	0.0058	240.8254	0.0058	1	22	cerebellar cortex formation
GO:0023019	0.0058	240.8254	0.0058	1	22	signal transduction involved in regulation of gene expression
GO:0060351	0.0058	240.8254	0.0058	1	22	cartilage development involved in endochondral bone morphogenesis
GO:0021846	0.0071	194.4487	0.0071	1	27	cell proliferation in forebrain
GO:0021587	0.0097	140.3426	0.0097	1	37	cerebellum morphogenesis

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0050848	6e-04	65.5758	0.0368	2	35	regulation of calcium-mediated signaling
GO:0051296	0.0011	Inf	0.0011	1	1	establishment of meiotic spindle orientation
GO:1902103	0.0011	Inf	0.0011	1	1	negative regulation of metaphase/anaphase transition of meiotic cell cycle
GO:0007308	0.0021	1012	0.0021	1	2	oocyte construction
GO:0007314	0.0021	1012	0.0021	1	2	oocyte anterior/posterior axis specification
GO:0008355	0.0021	1012	0.0021	1	2	olfactory learning
GO:0030719	0.0021	1012	0.0021	1	2	P granule organization
GO:0060965	0.0021	1012	0.0021	1	2	negative regulation of gene silencing by miRNA
GO:0042307	0.0025	31.2878	0.0748	2	71	positive regulation of protein import into nucleus
GO:0003130	0.0032	505.9667	0.0032	1	3	BMP signaling pathway involved in heart induction
GO:0003133	0.0032	505.9667	0.0032	1	3	endodermal-mesodermal cell signaling
GO:0009786	0.0032	505.9667	0.0032	1	3	regulation of asymmetric cell division
GO:0090081	0.0032	505.9667	0.0032	1	3	regulation of heart induction by regulation of canonical Wnt signaling pathway
GO:1901993	0.0032	505.9667	0.0032	1	3	regulation of meiotic cell cycle phase transition
GO:0007292	0.0042	23.6892	0.0979	2	93	female gamete generation
GO:0007195	0.0042	337.2889	0.0042	1	4	adenylate cyclase-inhibiting dopamine receptor signaling pathway
GO:0032417	0.0042	337.2889	0.0042	1	4	positive regulation of sodium:proton antiporter activity
GO:0051582	0.0042	337.2889	0.0042	1	4	positive regulation of neurotransmitter uptake
GO:0051586	0.0042	337.2889	0.0042	1	4	positive regulation of dopamine uptake involved in synaptic transmission
GO:0060913	0.0042	337.2889	0.0042	1	4	cardiac cell fate determination
GO:0090308	0.0042	337.2889	0.0042	1	4	regulation of methylation-dependent chromatin silencing
GO:0070886	0.0053	252.95	0.0053	1	5	positive regulation of calcineurin-NFAT signaling cascade
GO:1901386	0.0053	252.95	0.0053	1	5	negative regulation of voltage-gated calcium channel activity
GO:0007612	0.0056	20.3167	0.1137	2	108	learning
GO:0051223	0.0059	9.555	0.3801	3	361	regulation of protein transport
GO:0051241	0.006	9.5006	0.3822	3	363	negative regulation of multicellular organismal process
GO:0000212	0.0063	202.3467	0.0063	1	6	meiotic spindle organization
GO:0003376	0.0063	202.3467	0.0063	1	6	sphingosine-1-phosphate signaling pathway
GO:0032020	0.0063	202.3467	0.0063	1	6	ISG15-protein conjugation
GO:0035860	0.0063	202.3467	0.0063	1	6	glial cell-derived neurotrophic factor receptor signaling pathway
GO:0060406	0.0063	202.3467	0.0063	1	6	positive regulation of penile erection
GO:0019827	0.0065	18.881	0.1221	2	116	stem cell maintenance
GO:0007166	0.0073	3.9692	3.2248	8	3063	cell surface receptor signaling pathway
GO:0007028	0.0073	168.6111	0.0074	1	7	cytoplasm organization
GO:0000187	0.0078	17.0692	0.1348	2	128	activation of MAPK activity
GO:0003129	0.0084	144.5143	0.0084	1	8	heart induction
GO:0007614	0.0084	144.5143	0.0084	1	8	short-term memory
GO:0060969	0.0084	144.5143	0.0084	1	8	negative regulation of gene silencing
GO:0001714	0.0094	126.4417	0.0095	1	9	endodermal cell fate specification
GO:0051940	0.0094	126.4417	0.0095	1	9	regulation of catecholamine uptake involved in synaptic transmission
GO:0060147	0.0094	126.4417	0.0095	1	9	regulation of posttranscriptional gene silencing
GO:0060966	0.0094	126.4417	0.0095	1	9	regulation of gene silencing by RNA

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0006351	0	6.8612	6.5215	20	3197	transcription, DNA-templated
GO:0034654	0	6.7444	7.3884	21	3622	nucleobase-containing compound biosynthetic process
GO:0016070	0	5.2305	8.0208	20	3932	RNA metabolic process
GO:0021530	0	1045.8621	0.0061	2	3	spinal cord oligodendrocyte cell fate specification
GO:0045666	0	30.2142	0.1591	4	78	positive regulation of neuron differentiation
GO:0010629	0	6.8113	2.0419	10	1001	negative regulation of gene expression
GO:0045934	0	6.653	2.0868	10	1023	negative regulation of nucleobase-containing compound metabolic process
GO:0009059	0	4.5871	8.8225	20	4325	macromolecule biosynthetic process
GO:0021510	0	25.9776	0.1836	4	90	spinal cord development
GO:0048665	0	57.926	0.0632	3	31	neuron fate specification
GO:0021779	0	348.5747	0.0102	2	5	oligodendrocyte cell fate commitment
GO:0021780	0	348.5747	0.0102	2	5	glial cell fate specification
GO:0007423	0	9.0208	0.9832	7	482	sensory organ development
GO:0009890	0	6.1192	2.2541	10	1105	negative regulation of biosynthetic process
GO:1902679	1e-04	6.562	1.8338	9	899	negative regulation of RNA biosynthetic process
GO:0032502	1e-04	4.3878	10.0566	21	4930	developmental process
GO:1902680	1e-04	5.8367	2.354	10	1154	positive regulation of RNA biosynthetic process
GO:0046483	1e-04	4.5177	12.0781	23	5921	heterocycle metabolic process
GO:0006725	1e-04	4.5002	12.1067	23	5935	cellular aromatic compound metabolic process
GO:0010628	1e-04	5.5121	2.4805	10	1216	positive regulation of gene expression
GO:0044249	1e-04	4.146	10.4442	21	5120	cellular biosynthetic process
GO:2000113	1e-04	5.9025	2.0236	9	992	negative regulation of cellular macromolecule biosynthetic process
GO:0034641	1e-04	4.2635	12.5065	23	6131	cellular nitrogen compound metabolic process
GO:1901360	1e-04	4.2624	12.5085	23	6132	organic cyclic compound metabolic process
GO:0000122	1e-04	7.3879	1.1892	7	583	negative regulation of transcription from RNA polymerase II promoter
GO:0021892	1e-04	149.3498	0.0184	2	9	cerebral cortex GABAergic interneuron differentiation
GO:0055123	2e-04	16.8732	0.2774	4	136	digestive system development
GO:0007399	2e-04	4.5404	3.8023	12	1864	nervous system development
GO:0007420	2e-04	8.6992	0.8607	6	463	brain development
GO:0031018	2e-04	31.7542	0.1102	3	54	endocrine pancreas development
GO:0006335	2e-04	130.6724	0.0204	2	10	DNA replication-dependent nucleosome assembly
GO:0065007	2e-04	8.0245	19.9745	29	9792	biological regulation
GO:0045944	2e-04	6.0931	1.687	8	827	positive regulation of transcription from RNA polymerase II promoter
GO:0045935	2e-04	5.0033	2.709	10	1328	positive regulation of nucleobase-containing compound metabolic process
GO:0050794	3e-04	9.0274	8.4683	16	5630	regulation of cellular process
GO:0021954	3e-04	25.2824	0.1367	3	67	central nervous system neuron development
GO:2000112	3e-04	4.9542	3.7062	11	2393	regulation of cellular macromolecule biosynthetic process
GO:0009891	3e-04	4.6457	2.8966	10	1420	positive regulation of biosynthetic process
GO:0060581	4e-04	80.3873	0.0306	2	15	cell fate commitment involved in pattern specification
GO:0016577	5e-04	69.6598	0.0347	2	17	histone demethylation
GO:0021514	5e-04	69.6598	0.0347	2	17	ventral spinal cord interneuron differentiation
GO:0008214	7e-04	61.4564	0.0388	2	19	protein dealkylation
GO:0021513	0.0012	45.4063	0.051	2	25	spinal cord dorsal/ventral patterning
GO:0021871	0.0012	45.4063	0.051	2	25	forebrain regionalization
GO:0044707	0.0012	3.2545	12.176	21	5969	single-multicellular organism process
GO:2001141	0.0019	5.2603	1.9493	7	1465	regulation of RNA biosynthetic process
GO:0014003	0.0019	34.7954	0.0653	2	32	oligodendrocyte development
GO:0021543	0.0019	13.5477	0.2489	3	122	pallium development
GO:0003327	0.002	Inf	0.002	1	1	type B pancreatic cell fate commitment
GO:0003359	0.002	Inf	0.002	1	1	noradrenergic neuron fate commitment
GO:0007400	0.002	Inf	0.002	1	1	neuroblast fate determination
GO:0021858	0.002	Inf	0.002	1	1	GABAergic neuron differentiation in basal ganglia
GO:0060165	0.002	Inf	0.002	1	1	regulation of timing of subpallium neuron differentiation
GO:0060580	0.002	Inf	0.002	1	1	ventral spinal cord interneuron fate determination
GO:0061100	0.002	Inf	0.002	1	1	lung neuroendocrine cell differentiation
GO:0061103	0.002	Inf	0.002	1	1	carotid body glomus cell differentiation
GO:0071259	0.002	Inf	0.002	1	1	cellular response to magnetism
GO:0021522	0.0022	32.6164	0.0694	2	34	spinal cord motor neuron differentiation
GO:0048663	0.0022	32.2692	0.0702	2	38	neuron fate commitment
GO:0043010	0.0022	8.1427	0.561	4	275	camera-type eye development
GO:0001764	0.0023	12.7891	0.2631	3	129	neuron migration
GO:0030154	0.0023	3.5579	4.4548	11	2493	cell differentiation
GO:0009889	0.0025	5.0618	2.0717	7	1599	regulation of biosynthetic process
GO:0030902	0.0026	12.2029	0.2754	3	135	hindbrain development
GO:0008544	0.0028	7.6533	0.5956	4	292	epidermis development
GO:0001709	0.0035	25.4415	0.0877	2	43	cell fate determination
GO:0070988	0.0038	24.255	0.0918	2	45	demethylation
GO:0010001	0.0039	10.4443	0.3203	3	157	glial cell differentiation
GO:0060042	0.0039	23.7022	0.0938	2	46	retina morphogenesis in camera-type eye
GO:0003326	0.0041	505.5	0.0041	1	2	pancreatic A cell fate commitment
GO:0003329	0.0041	505.5	0.0041	1	2	pancreatic PP cell fate commitment
GO:0008355	0.0041	505.5	0.0041	1	2	olfactory learning
GO:0014016	0.0041	505.5	0.0041	1	2	neuroblast differentiation
GO:0021750	0.0041	505.5	0.0041	1	2	vestibular nucleus development
GO:0035574	0.0041	505.5	0.0041	1	2	histone H4-K20 demethylation
GO:0060163	0.0041	505.5	0.0041	1	2	subpallium neuron fate commitment
GO:0060465	0.0041	505.5	0.0041	1	2	pharynx development
GO:0061074	0.0041	505.5	0.0041	1	2	regulation of neural retina development
GO:0061102	0.0041	505.5	0.0041	1	2	stomach neuroendocrine cell differentiation
GO:0061104	0.0041	505.5	0.0041	1	2	adrenal chromaffin cell differentiation
GO:0030855	0.0042	5.3106	1.0913	5	535	epithelial cell differentiation
GO:0045665	0.0054	20.0451	0.1102	2	54	negative regulation of neuron differentiation
GO:0006357	0.006	9.2931	0.3793	3	280	regulation of transcription from RNA polymerase II promoter
GO:0003358	0.0061	252.7333	0.0061	1	3	noradrenergic neuron development
GO:0014707	0.0061	252.7333	0.0061	1	3	branchiomeric skeletal muscle development
GO:0021902	0.0061	252.7333	0.0061	1	3	commitment of neuronal cell to specific neuron type in forebrain
GO:0050883	0.0061	252.7333	0.0061	1	3	musculoskeletal movement, spinal reflex action
GO:0060166	0.0061	252.7333	0.0061	1	3	olfactory pit development
GO:0048731	0.0061	4.1521	2.3984	7	1764	system development
GO:0021872	0.0068	17.6587	0.1244	2	61	forebrain generation of neurons
GO:0010468	0.007	4.1165	2.4764	7	1951	regulation of gene expression
GO:0009888	0.0071	3.6711	2.3585	7	1302	tissue development
GO:0048523	0.0075	2.6826	6.5888	13	3230	negative regulation of cellular process
GO:0007195	0.0081	168.4778	0.0082	1	4	adenylate cyclase-inhibiting dopamine receptor signaling pathway
GO:0032417	0.0081	168.4778	0.0082	1	4	positive regulation of sodium:proton antiporter activity
GO:0051582	0.0081	168.4778	0.0082	1	4	positive regulation of neurotransmitter uptake
GO:0051586	0.0081	168.4778	0.0082	1	4	positive regulation of dopamine uptake involved in synaptic transmission
GO:0097476	0.0081	168.4778	0.0082	1	4	spinal cord motor neuron migration
GO:0035270	0.0089	15.4256	0.1424	2	77	endocrine system development
GO:0019219	0.009	3.9007	2.5922	7	2023	regulation of nucleobase-containing compound metabolic process
GO:0051705	0.0092	15.0895	0.1448	2	71	multi-organism behavior
GO:0048699	0.0098	3.7801	1.8919	6	1015	generation of neurons

Differential Methylation

Parameter Overview

Introduction: Differential Methylation of Sample Groups

Comparisons

P-values

Site Level

Differential Methylation Tables

Region Level

Differential Methylation Tables

Enrichment Analysis

References