RnBeads report

Option	Value
analyze.sites	yes
region.types	default
differential.permutations	0
differential.comparison.columns	lineage, karyotype, sex
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
ectoderm vs. non.ectoderm (based on lineage)	35094
ectoderm, mesoderm vs. non.ectoderm, mesoderm (based on lineage)	47551
endoderm vs. non.endoderm (based on lineage)	28524
epithelial vs. non.epithelial (based on lineage)	155229
extraembryonic mesoderm, trophectoderm vs. non.extraembryonic mesoderm, trophectoderm (based on lineage)	75671
inner cell mass vs. non.inner cell mass (based on lineage)	79546
mesoderm vs. non.mesoderm (based on lineage)	47347
cancer vs. normal (based on karyotype)	136749
B vs. non.B (based on sex)	58957
F vs. non.F (based on sex)	18041
M vs. non.M (based on sex)	30798

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
ectoderm vs. non.ectoderm (based on lineage)	2611	2306	2048	2338
ectoderm, mesoderm vs. non.ectoderm, mesoderm (based on lineage)	2727	389	340	299
endoderm vs. non.endoderm (based on lineage)	6969	891	664	972
epithelial vs. non.epithelial (based on lineage)	15569	2245	1484	785
extraembryonic mesoderm, trophectoderm vs. non.extraembryonic mesoderm, trophectoderm (based on lineage)	3240	800	600	723
inner cell mass vs. non.inner cell mass (based on lineage)	7348	1354	1667	2570
mesoderm vs. non.mesoderm (based on lineage)	4997	1935	3186	1492
cancer vs. normal (based on karyotype)	10160	5776	4309	5114
B vs. non.B (based on sex)	5272	688	487	261
F vs. non.F (based on sex)	3422	77	163	213
M vs. non.M (based on sex)	1837	41	0	139

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
ectoderm vs. non.ectoderm (based on lineage)	csv	csv	csv	csv
ectoderm, mesoderm vs. non.ectoderm, mesoderm (based on lineage)	csv	csv	csv	csv
endoderm vs. non.endoderm (based on lineage)	csv	csv	csv	csv
epithelial vs. non.epithelial (based on lineage)	csv	csv	csv	csv
extraembryonic mesoderm, trophectoderm vs. non.extraembryonic mesoderm, trophectoderm (based on lineage)	csv	csv	csv	csv
inner cell mass vs. non.inner cell mass (based on lineage)	csv	csv	csv	csv
mesoderm vs. non.mesoderm (based on lineage)	csv	csv	csv	csv
cancer vs. normal (based on karyotype)	csv	csv	csv	csv
B vs. non.B (based on sex)	csv	csv	csv	csv
F vs. non.F (based on sex)	csv	csv	csv	csv
M vs. non.M (based on sex)	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:0007205	3e-04	27.6757	0.1265	3	32	protein kinase C-activating G-protein coupled receptor signaling pathway
GO:0030001	5e-04	4.4379	2.3828	9	603	metal ion transport
GO:0034377	0.0012	47.697	0.0514	2	13	plasma lipoprotein particle assembly
GO:0034367	0.002	34.9667	0.0672	2	17	macromolecular complex remodeling
GO:0034369	0.002	34.9667	0.0672	2	17	plasma lipoprotein particle remodeling
GO:0003009	0.0034	26.2146	0.0869	2	22	skeletal muscle contraction
GO:0010625	0.004	Inf	0.004	1	1	positive regulation of Schwann cell proliferation
GO:0010730	0.004	Inf	0.004	1	1	negative regulation of hydrogen peroxide biosynthetic process
GO:0010903	0.004	Inf	0.004	1	1	negative regulation of very-low-density lipoprotein particle remodeling
GO:0042930	0.004	Inf	0.004	1	1	enterobactin transport
GO:0060345	0.004	Inf	0.004	1	1	spleen trabecula formation
GO:0060354	0.004	Inf	0.004	1	1	negative regulation of cell adhesion molecule production
GO:0071502	0.004	Inf	0.004	1	1	cellular response to temperature stimulus
GO:2000057	0.004	Inf	0.004	1	1	negative regulation of Wnt signaling pathway involved in digestive tract morphogenesis
GO:0006820	0.0041	4.3626	1.5332	6	388	anion transport
GO:0007218	0.0047	9.6283	0.3398	3	86	neuropeptide signaling pathway
GO:0031102	0.005	20.9633	0.1067	2	27	neuron projection regeneration
GO:0071825	0.005	20.9633	0.1067	2	27	protein-lipid complex subunit organization
GO:0048878	0.0052	3.3346	2.7227	8	689	chemical homeostasis
GO:0055085	0.0058	2.8726	4.0267	10	1019	transmembrane transport
GO:0034381	0.0058	19.4074	0.1146	2	29	plasma lipoprotein particle clearance
GO:0071312	0.0058	19.4074	0.1146	2	29	cellular response to alkaloid
GO:0051051	0.0065	4.6197	1.1894	5	301	negative regulation of transport
GO:0033344	0.007	17.4625	0.1265	2	32	cholesterol efflux
GO:0050879	0.0075	16.8978	0.1304	2	33	multicellular organismal movement
GO:0016125	0.0078	7.9806	0.407	3	103	sterol metabolic process
GO:0002740	0.0079	257.1837	0.0079	1	2	negative regulation of cytokine secretion involved in immune response
GO:0007198	0.0079	257.1837	0.0079	1	2	adenylate cyclase-inhibiting serotonin receptor signaling pathway
GO:0018916	0.0079	257.1837	0.0079	1	2	nitrobenzene metabolic process
GO:0034395	0.0079	257.1837	0.0079	1	2	regulation of transcription from RNA polymerase II promoter in response to iron
GO:0050713	0.0079	257.1837	0.0079	1	2	negative regulation of interleukin-1 beta secretion
GO:0050968	0.0079	257.1837	0.0079	1	2	detection of chemical stimulus involved in sensory perception of pain
GO:0060741	0.0079	257.1837	0.0079	1	2	prostate gland stromal morphogenesis
GO:0070458	0.0079	257.1837	0.0079	1	2	cellular detoxification of nitrogen compound
GO:1903426	0.0079	257.1837	0.0079	1	2	regulation of reactive oxygen species biosynthetic process
GO:2000382	0.0079	257.1837	0.0079	1	2	positive regulation of mesoderm development
GO:0006695	0.0079	16.3685	0.1344	2	34	cholesterol biosynthetic process
GO:0055081	0.0079	16.3685	0.1344	2	34	anion homeostasis
GO:0046165	0.0093	7.4544	0.4347	3	110	alcohol biosynthetic process
GO:0006694	0.0095	7.3848	0.4386	3	111	steroid biosynthetic process

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0006968	0.0034	25.9012	0.0871	2	38	cellular defense response
GO:0002249	0.0069	225.3929	0.0069	1	3	lymphocyte anergy
GO:0002667	0.0069	225.3929	0.0069	1	3	regulation of T cell anergy
GO:0006420	0.0069	225.3929	0.0069	1	3	arginyl-tRNA aminoacylation
GO:0070268	0.0069	225.3929	0.0069	1	3	cornification
GO:0006533	0.0091	150.25	0.0092	1	4	aspartate catabolic process
GO:0048539	0.0091	150.25	0.0092	1	4	bone marrow development

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0048568	0	9.7558	1.5875	12	379	embryonic organ development
GO:0048704	0	19.0213	0.377	6	90	embryonic skeletal system morphogenesis
GO:0043009	0	6.5114	2.3206	12	554	chordate embryonic development
GO:0001501	0	7.5399	1.621	10	387	skeletal system development
GO:0007389	0	7.3196	1.6671	10	398	pattern specification process
GO:0061029	0	94.44	0.0461	3	11	eyelid development in camera-type eye
GO:0009952	0	10.3254	0.7959	7	190	anterior/posterior pattern specification
GO:0048729	0	6.042	1.998	10	477	tissue morphogenesis
GO:0048485	1e-04	44.4106	0.0838	3	20	sympathetic nervous system development
GO:0002088	1e-04	18.966	0.2429	4	58	lens development in camera-type eye
GO:0009887	1e-04	4.9271	2.4535	10	627	organ morphogenesis
GO:0072175	1e-04	11.5109	0.4943	5	118	epithelial tube formation
GO:0003180	2e-04	164.6667	0.0209	2	5	aortic valve morphogenesis
GO:0001654	2e-04	6.7202	1.198	7	286	eye development
GO:0032501	3e-04	2.7417	20.9855	34	5010	multicellular organismal process
GO:0035108	3e-04	9.6906	0.5822	5	139	limb morphogenesis
GO:0035239	3e-04	6.0731	1.3194	7	315	tube morphogenesis
GO:0016331	3e-04	9.3383	0.6032	5	144	morphogenesis of embryonic epithelium
GO:2000679	5e-04	82.3137	0.0335	2	8	positive regulation of transcription regulatory region DNA binding
GO:0048736	5e-04	8.5307	0.6576	5	157	appendage development
GO:0001841	7e-04	10.8606	0.4105	4	98	neural tube formation
GO:0001709	8e-04	18.84	0.1801	3	43	cell fate determination
GO:0001649	8e-04	7.6621	0.7288	5	174	osteoblast differentiation
GO:0043518	9e-04	54.8627	0.0461	2	11	negative regulation of DNA damage response, signal transduction by p53 class mediator
GO:0060900	9e-04	54.8627	0.0461	2	11	embryonic camera-type eye formation
GO:0060429	9e-04	3.5138	3.707	11	885	epithelium development
GO:0001764	0.0016	8.815	0.5014	4	122	neuron migration
GO:0035113	0.0016	8.7096	0.5068	4	121	embryonic appendage morphogenesis
GO:0050789	0.0018	2.6901	32.647	43	7794	regulation of biological process
GO:0042733	0.0019	13.44	0.2471	3	59	embryonic digit morphogenesis
GO:0048812	0.0022	3.8729	2.3499	8	561	neuron projection morphogenesis
GO:0060231	0.0022	32.902	0.0712	2	17	mesenchymal to epithelial transition
GO:0060713	0.0022	32.902	0.0712	2	17	labyrinthine layer morphogenesis
GO:0042471	0.0023	32.5417	0.0716	2	18	ear morphogenesis
GO:0000902	0.0025	3.0714	4.1929	11	1001	cell morphogenesis
GO:2000027	0.0026	7.652	0.5739	4	137	regulation of organ morphogenesis
GO:0051101	0.0029	11.5708	0.2848	3	68	regulation of DNA binding
GO:0022008	0.0033	2.8273	5.0013	12	1194	neurogenesis
GO:0018345	0.0038	24.6667	0.0922	2	22	protein palmitoylation
GO:0045909	0.0038	24.6667	0.0922	2	22	positive regulation of vasodilation
GO:0046320	0.0038	24.6667	0.0922	2	22	regulation of fatty acid oxidation
GO:0009889	0.0038	2.2231	13.6301	23	3254	regulation of biosynthetic process
GO:0003294	0.0042	Inf	0.0042	1	1	atrial ventricular junction remodeling
GO:0010232	0.0042	Inf	0.0042	1	1	vascular transport
GO:0010652	0.0042	Inf	0.0042	1	1	positive regulation of cell communication by chemical coupling
GO:0018009	0.0042	Inf	0.0042	1	1	N-terminal peptidyl-L-cysteine N-palmitoylation
GO:0021852	0.0042	Inf	0.0042	1	1	pyramidal neuron migration
GO:0035332	0.0042	Inf	0.0042	1	1	positive regulation of hippo signaling
GO:0035732	0.0042	Inf	0.0042	1	1	nitric oxide storage
GO:0035898	0.0042	Inf	0.0042	1	1	parathyroid hormone secretion
GO:0048698	0.0042	Inf	0.0042	1	1	negative regulation of collateral sprouting in absence of injury
GO:0060156	0.0042	Inf	0.0042	1	1	milk ejection
GO:2000607	0.0042	Inf	0.0042	1	1	negative regulation of cell proliferation involved in mesonephros development
GO:2000703	0.0042	Inf	0.0042	1	1	negative regulation of fibroblast growth factor receptor signaling pathway involved in ureteric bud formation
GO:2000734	0.0042	Inf	0.0042	1	1	negative regulation of glial cell-derived neurotrophic factor receptor signaling pathway involved in ureteric bud formation
GO:2000802	0.0042	Inf	0.0042	1	1	positive regulation of endocardial cushion to mesenchymal transition involved in heart valve formation
GO:2001111	0.0042	Inf	0.0042	1	1	positive regulation of lens epithelial cell proliferation
GO:0045664	0.0043	4.3035	1.5456	6	369	regulation of neuron differentiation
GO:0010629	0.0045	2.9769	3.8662	10	923	negative regulation of gene expression
GO:0001843	0.0047	9.6323	0.3393	3	81	neural tube closure
GO:0032720	0.0049	21.4442	0.1047	2	25	negative regulation of tumor necrosis factor production
GO:0048589	0.0049	4.9439	1.11	5	265	developmental growth
GO:0035282	0.0052	9.2733	0.3519	3	84	segmentation
GO:0031111	0.0052	20.549	0.1089	2	26	negative regulation of microtubule polymerization or depolymerization
GO:0042127	0.0054	2.7518	4.6327	11	1106	regulation of cell proliferation
GO:0051960	0.0058	3.5782	2.1823	7	521	regulation of nervous system development
GO:0032502	0.0059	2.2122	14.3534	23	3774	developmental process
GO:0007507	0.0064	3.9445	1.6797	6	401	heart development
GO:0007140	0.0065	18.2614	0.1215	2	29	male meiosis
GO:0009954	0.0065	18.2614	0.1215	2	29	proximal/distal pattern formation
GO:0042472	0.0065	8.5309	0.3812	3	91	inner ear morphogenesis
GO:0050905	0.0065	8.5309	0.3812	3	91	neuromuscular process
GO:0045597	0.0066	3.4792	2.241	7	535	positive regulation of cell differentiation
GO:0034113	0.0069	17.6078	0.1257	2	30	heterotypic cell-cell adhesion
GO:0048048	0.0074	16.9993	0.1299	2	31	embryonic eye morphogenesis
GO:2001141	0.0075	2.128	11.7829	20	2813	regulation of RNA biosynthetic process
GO:0048667	0.0077	3.3789	2.3038	7	550	cell morphogenesis involved in neuron differentiation
GO:0006357	0.0078	2.5032	5.5752	12	1331	regulation of transcription from RNA polymerase II promoter
GO:0031099	0.008	7.8979	0.4105	3	98	regeneration
GO:0002011	0.0081	16.2168	0.1356	2	33	morphogenesis of an epithelial sheet
GO:0021569	0.0082	247.0196	0.0082	1	2	rhombomere 3 development
GO:0051241	0.0082	4.345	1.2566	5	300	negative regulation of multicellular organismal process
GO:0042060	0.0083	3.3277	2.3373	7	558	wound healing
GO:0051093	0.0083	3.3277	2.3373	7	558	negative regulation of developmental process
GO:0003366	0.0084	242.2885	0.0084	1	2	cell-matrix adhesion involved in ameboidal cell migration
GO:0006601	0.0084	242.2885	0.0084	1	2	creatine biosynthetic process
GO:0021568	0.0084	242.2885	0.0084	1	2	rhombomere 2 development
GO:0021658	0.0084	242.2885	0.0084	1	2	rhombomere 3 morphogenesis
GO:0046618	0.0084	242.2885	0.0084	1	2	drug export
GO:0060995	0.0084	242.2885	0.0084	1	2	cell-cell signaling involved in kidney development
GO:0061290	0.0084	242.2885	0.0084	1	2	canonical Wnt signaling pathway involved in metanephric kidney development
GO:0061386	0.0084	242.2885	0.0084	1	2	closure of optic fissure
GO:0071639	0.0084	242.2885	0.0084	1	2	positive regulation of monocyte chemotactic protein-1 production
GO:1900625	0.0084	242.2885	0.0084	1	2	positive regulation of monocyte aggregation
GO:2000276	0.0084	242.2885	0.0084	1	2	negative regulation of oxidative phosphorylation uncoupler activity
GO:2000664	0.0084	242.2885	0.0084	1	2	positive regulation of interleukin-5 secretion
GO:2000667	0.0084	242.2885	0.0084	1	2	positive regulation of interleukin-13 secretion
GO:2000683	0.0084	242.2885	0.0084	1	2	regulation of cellular response to X-ray
GO:2000793	0.0084	242.2885	0.0084	1	2	cell proliferation involved in heart valve development
GO:0072676	0.0084	15.9001	0.1382	2	33	lymphocyte migration
GO:0080090	0.0087	2.0021	19.0503	28	4548	regulation of primary metabolic process
GO:0042180	0.0087	5.3319	0.8126	4	194	cellular ketone metabolic process
GO:0003008	0.0087	2.5586	4.9469	11	1181	system process
GO:0001738	0.0089	15.402	0.1424	2	34	morphogenesis of a polarized epithelium
GO:0009953	0.0091	7.5	0.4314	3	103	dorsal/ventral pattern formation
GO:0007159	0.0099	14.4937	0.1508	2	36	leukocyte cell-cell adhesion
GO:0043124	0.0099	14.4937	0.1508	2	36	negative regulation of I-kappaB kinase/NF-kappaB signaling
GO:1901796	0.0099	14.4937	0.1508	2	36	regulation of signal transduction by p53 class mediator

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0001501	2e-04	6.6272	1.254	7	387	skeletal system development
GO:0046330	4e-04	23.0765	0.1491	3	46	positive regulation of JNK cascade
GO:0007423	5e-04	5.7909	1.4257	7	440	sensory organ development
GO:0009887	6e-04	4.4546	2.4562	9	758	organ morphogenesis
GO:0007605	7e-04	11.3495	0.3986	4	123	sensory perception of sound
GO:0090263	7e-04	19.0688	0.1782	3	55	positive regulation of canonical Wnt signaling pathway
GO:0070304	8e-04	18.7075	0.1815	3	56	positive regulation of stress-activated protein kinase signaling cascade
GO:0032735	0.001	49.7002	0.0486	2	15	positive regulation of interleukin-12 production
GO:0042730	0.0012	46.1465	0.0518	2	16	fibrinolysis
GO:0048568	0.0013	5.625	1.2281	6	379	embryonic organ development
GO:0001502	0.0017	37.994	0.0616	2	19	cartilage condensation
GO:0048839	0.0018	8.5214	0.5249	4	162	inner ear development
GO:0070328	0.0021	33.9892	0.068	2	21	triglyceride homeostasis
GO:0008344	0.0021	13.0222	0.256	3	79	adult locomotory behavior
GO:0055088	0.0023	12.6862	0.2625	3	81	lipid homeostasis
GO:0051130	0.0026	4.2691	1.9096	7	604	positive regulation of cellular component organization
GO:0032355	0.0028	11.7744	0.2819	3	87	response to estradiol
GO:0050794	0.0028	2.9015	24.0984	33	7437	regulation of cellular process
GO:0032964	0.0029	28.0691	0.081	2	25	collagen biosynthetic process
GO:0048704	0.0031	11.3657	0.2916	3	90	embryonic skeletal system morphogenesis
GO:0001958	0.0032	26.8974	0.0842	2	26	endochondral ossification
GO:0002920	0.0032	26.8974	0.0842	2	26	regulation of humoral immune response
GO:0002408	0.0032	Inf	0.0032	1	1	myeloid dendritic cell chemotaxis
GO:0007634	0.0032	Inf	0.0032	1	1	optokinetic behavior
GO:0010902	0.0032	Inf	0.0032	1	1	positive regulation of very-low-density lipoprotein particle remodeling
GO:0019836	0.0032	Inf	0.0032	1	1	hemolysis by symbiont of host erythrocytes
GO:0021560	0.0032	Inf	0.0032	1	1	abducens nerve development
GO:0021599	0.0032	Inf	0.0032	1	1	abducens nerve formation
GO:0030844	0.0032	Inf	0.0032	1	1	positive regulation of intermediate filament depolymerization
GO:0035659	0.0032	Inf	0.0032	1	1	Wnt signaling pathway involved in wound healing, spreading of epidermal cells
GO:0038115	0.0032	Inf	0.0032	1	1	chemokine (C-C motif) ligand 19 signaling pathway
GO:0038116	0.0032	Inf	0.0032	1	1	chemokine (C-C motif) ligand 21 signaling pathway
GO:0044179	0.0032	Inf	0.0032	1	1	hemolysis in other organism
GO:0045108	0.0032	Inf	0.0032	1	1	regulation of intermediate filament polymerization or depolymerization
GO:0051801	0.0032	Inf	0.0032	1	1	cytolysis in other organism involved in symbiotic interaction
GO:0097022	0.0032	Inf	0.0032	1	1	lymphocyte migration into lymph node
GO:2000522	0.0032	Inf	0.0032	1	1	positive regulation of immunological synapse formation
GO:2000525	0.0032	Inf	0.0032	1	1	positive regulation of T cell costimulation
GO:2000526	0.0032	Inf	0.0032	1	1	positive regulation of glycoprotein biosynthetic process involved in immunological synapse formation
GO:2000547	0.0032	Inf	0.0032	1	1	regulation of dendritic cell dendrite assembly
GO:1900047	0.0034	25.8195	0.0875	2	27	negative regulation of hemostasis
GO:0030111	0.0034	7.106	0.6254	4	193	regulation of Wnt signaling pathway
GO:0010557	0.0035	3.1726	3.8042	10	1174	positive regulation of macromolecule biosynthetic process
GO:0051239	0.0035	2.7961	5.8618	13	1809	regulation of multicellular organismal process
GO:0050819	0.0039	23.9031	0.094	2	29	negative regulation of coagulation
GO:0035115	0.0045	22.2511	0.1005	2	31	embryonic forelimb morphogenesis
GO:0009628	0.0046	3.4771	2.6895	8	830	response to abiotic stimulus
GO:0040011	0.0046	3.0425	3.95	10	1219	locomotion
GO:0007166	0.0047	2.5566	7.5727	15	2337	cell surface receptor signaling pathway
GO:0060325	0.0048	21.5077	0.1037	2	32	face morphogenesis
GO:0031960	0.0051	9.4038	0.35	3	108	response to corticosteroid
GO:0042471	0.0052	9.3143	0.3532	3	109	ear morphogenesis
GO:0031328	0.0054	2.9663	4.0407	10	1247	positive regulation of cellular biosynthetic process
GO:0050789	0.0062	11.2015	0.4108	3	263	regulation of biological process
GO:0035137	0.0064	18.4278	0.1199	2	37	hindlimb morphogenesis
GO:2000179	0.0064	18.4278	0.1199	2	37	positive regulation of neural precursor cell proliferation
GO:0010260	0.0065	315.275	0.0065	1	2	organ senescence
GO:0014834	0.0065	315.275	0.0065	1	2	skeletal muscle satellite cell maintenance involved in skeletal muscle regeneration
GO:0019086	0.0065	315.275	0.0065	1	2	late viral transcription
GO:0034059	0.0065	315.275	0.0065	1	2	response to anoxia
GO:0034371	0.0065	315.275	0.0065	1	2	chylomicron remodeling
GO:0060697	0.0065	315.275	0.0065	1	2	positive regulation of phospholipid catabolic process
GO:0060876	0.0065	315.275	0.0065	1	2	semicircular canal formation
GO:0070172	0.0065	315.275	0.0065	1	2	positive regulation of tooth mineralization
GO:0072610	0.0065	315.275	0.0065	1	2	interleukin-12 secretion
GO:2000253	0.0065	315.275	0.0065	1	2	positive regulation of feeding behavior
GO:0035113	0.007	8.3591	0.3921	3	121	embryonic appendage morphogenesis
GO:0009605	0.0071	2.7204	4.8897	11	1509	response to external stimulus
GO:0070542	0.0074	16.969	0.1296	2	40	response to fatty acid
GO:0050795	0.0076	8.0824	0.405	3	125	regulation of behavior
GO:0002673	0.0078	16.5325	0.1329	2	41	regulation of acute inflammatory response
GO:0010628	0.0079	2.9463	3.5903	9	1108	positive regulation of gene expression
GO:0030902	0.0087	7.6998	0.4245	3	131	hindbrain development
GO:0071229	0.0087	7.6998	0.4245	3	131	cellular response to acid chemical
GO:1903034	0.0088	5.3676	0.8198	4	253	regulation of response to wounding
GO:0007389	0.0089	4.3183	1.2897	5	398	pattern specification process
GO:0010171	0.0093	14.9899	0.1458	2	45	body morphogenesis
GO:0000432	0.0097	157.625	0.0097	1	3	positive regulation of transcription from RNA polymerase II promoter by glucose
GO:0001768	0.0097	157.625	0.0097	1	3	establishment of T cell polarity
GO:0001907	0.0097	157.625	0.0097	1	3	killing by symbiont of host cells
GO:0002885	0.0097	157.625	0.0097	1	3	positive regulation of hypersensitivity
GO:0010898	0.0097	157.625	0.0097	1	3	positive regulation of triglyceride catabolic process
GO:0010916	0.0097	157.625	0.0097	1	3	negative regulation of very-low-density lipoprotein particle clearance
GO:0021570	0.0097	157.625	0.0097	1	3	rhombomere 4 development
GO:0021754	0.0097	157.625	0.0097	1	3	facial nucleus development
GO:0031133	0.0097	157.625	0.0097	1	3	regulation of axon diameter
GO:0060066	0.0097	157.625	0.0097	1	3	oviduct development
GO:0060166	0.0097	157.625	0.0097	1	3	olfactory pit development
GO:0060279	0.0097	157.625	0.0097	1	3	positive regulation of ovulation
GO:0071464	0.0097	157.625	0.0097	1	3	cellular response to hydrostatic pressure
GO:0097029	0.0097	157.625	0.0097	1	3	mature dendritic cell differentiation
GO:2000507	0.0097	157.625	0.0097	1	3	positive regulation of energy homeostasis
GO:0006928	0.0098	2.6978	4.3971	10	1357	cellular component movement

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0006750	0.0014	44.014	0.0555	2	13	glutathione biosynthetic process
GO:0019370	0.0016	40.3429	0.0597	2	14	leukotriene biosynthetic process
GO:1901687	0.0029	28.4661	0.0811	2	19	glutathione derivative biosynthetic process
GO:1901071	0.0032	26.8825	0.0854	2	20	glucosamine-containing compound metabolic process
GO:0043043	0.0036	25.4656	0.0896	2	21	peptide biosynthetic process
GO:0001913	0.0039	24.1904	0.0939	2	22	T cell mediated cytotoxicity
GO:0006751	0.0043	Inf	0.0043	1	1	glutathione catabolic process
GO:0042489	0.0043	Inf	0.0043	1	1	negative regulation of odontogenesis of dentin-containing tooth
GO:1990166	0.0043	Inf	0.0043	1	1	protein localization to site of double-strand break
GO:2000568	0.0043	Inf	0.0043	1	1	positive regulation of memory T cell activation
GO:0006045	0.0085	237.6981	0.0085	1	2	N-acetylglucosamine biosynthetic process
GO:0035552	0.0085	237.6981	0.0085	1	2	oxidative single-stranded DNA demethylation
GO:0071799	0.0085	237.6981	0.0085	1	2	cellular response to prostaglandin D stimulus
GO:0042267	0.0087	15.5931	0.1408	2	33	natural killer cell mediated cytotoxicity

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0032514	0.0034	Inf	0.0034	1	1	positive regulation of protein phosphatase type 2B activity
GO:0042697	0.0034	Inf	0.0034	1	1	menopause
GO:1990166	0.0034	Inf	0.0034	1	1	protein localization to site of double-strand break
GO:0007308	0.0068	300.2143	0.0068	1	2	oocyte construction
GO:0007314	0.0068	300.2143	0.0068	1	2	oocyte anterior/posterior axis specification
GO:0030719	0.0068	300.2143	0.0068	1	2	P granule organization
GO:0034970	0.0068	300.2143	0.0068	1	2	histone H3-R2 methylation
GO:0051533	0.0068	300.2143	0.0068	1	2	positive regulation of NFAT protein import into nucleus
GO:0061051	0.0068	300.2143	0.0068	1	2	positive regulation of cell growth involved in cardiac muscle cell development
GO:1902261	0.0068	300.2143	0.0068	1	2	positive regulation of delayed rectifier potassium channel activity
GO:0006584	0.0085	15.7236	0.1393	2	41	catecholamine metabolic process

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

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0007617	1e-04	41.8868	0.0885	3	20	mating behavior
GO:0002125	1e-04	233.2407	0.0177	2	4	maternal aggressive behavior
GO:0042713	2e-04	155.4815	0.0221	2	5	sperm ejaculation
GO:0019098	2e-04	28.4649	0.1239	3	28	reproductive behavior
GO:0045924	4e-04	93.2741	0.031	2	7	regulation of female receptivity
GO:0001101	6e-04	6.51	1.0356	6	234	response to acid chemical
GO:0033993	7e-04	4.2427	2.4475	9	553	response to lipid
GO:0035815	8e-04	58.2824	0.0443	2	10	positive regulation of renal sodium excretion
GO:0043084	8e-04	58.2824	0.0443	2	10	penile erection
GO:0042711	0.001	51.8025	0.0487	2	11	maternal behavior
GO:0031960	0.0013	9.2404	0.478	4	108	response to corticosteroid
GO:0007625	0.0017	38.8426	0.062	2	14	grooming behavior
GO:0006590	0.0019	35.8519	0.0664	2	15	thyroid hormone generation
GO:0034694	0.0022	33.2884	0.0708	2	16	response to prostaglandin
GO:0032892	0.0028	29.1227	0.0797	2	18	positive regulation of organic acid transport
GO:0044062	0.0028	29.1227	0.0797	2	18	regulation of excretion
GO:0051412	0.0028	29.1227	0.0797	2	18	response to corticosterone
GO:0007275	0.0028	2.1973	16.7119	27	3776	multicellular organismal development
GO:0033057	0.0031	27.4074	0.0841	2	19	multicellular organismal reproductive behavior
GO:0042445	0.0033	7.1009	0.6152	4	139	hormone metabolic process
GO:0051954	0.0035	25.8827	0.0885	2	20	positive regulation of amine transport
GO:0046717	0.0036	10.5858	0.3098	3	70	acid secretion
GO:0018958	0.0041	10.1296	0.3231	3	73	phenol-containing compound metabolic process
GO:0009651	0.0042	23.2907	0.0974	2	22	response to salt stress
GO:0060450	0.0044	Inf	0.0044	1	1	positive regulation of hindgut contraction
GO:0030431	0.0046	22.1799	0.1018	2	23	sleep
GO:0051591	0.0048	9.579	0.3408	3	77	response to cAMP
GO:0001975	0.005	21.17	0.1062	2	24	response to amphetamine
GO:0021513	0.0054	20.248	0.1106	2	25	spinal cord dorsal/ventral patterning
GO:0031069	0.0054	20.248	0.1106	2	25	hair follicle morphogenesis
GO:0007204	0.0055	6.0951	0.7126	4	161	positive regulation of cytosolic calcium ion concentration
GO:0021510	0.0067	8.4319	0.385	3	87	spinal cord development
GO:0006820	0.0071	3.8372	1.7172	6	388	anion transport
GO:0006775	0.0072	17.2428	0.1283	2	29	fat-soluble vitamin metabolic process
GO:0045777	0.0072	17.2428	0.1283	2	29	positive regulation of blood pressure
GO:0048665	0.0077	16.6257	0.1328	2	30	neuron fate specification
GO:0055078	0.0082	16.0511	0.1372	2	31	sodium ion homeostasis
GO:0001992	0.0088	229.0182	0.0089	1	2	regulation of systemic arterial blood pressure by vasopressin
GO:0010701	0.0088	229.0182	0.0089	1	2	positive regulation of norepinephrine secretion

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0045132	0	60.2775	0.0626	3	22	meiotic chromosome segregation
GO:0007135	1e-04	185.4853	0.0171	2	6	meiosis II
GO:0045880	0.0023	32.2097	0.0711	2	25	positive regulation of smoothened signaling pathway
GO:0007129	0.0026	29.6282	0.0768	2	27	synapsis
GO:0007131	0.0027	29.3473	0.0775	2	28	reciprocal meiotic recombination
GO:0032526	0.0028	11.7338	0.2845	3	100	response to retinoic acid
GO:0002879	0.0028	Inf	0.0028	1	1	positive regulation of acute inflammatory response to non-antigenic stimulus
GO:0033315	0.0028	Inf	0.0028	1	1	meiotic DNA replication checkpoint
GO:0042843	0.0028	Inf	0.0028	1	1	D-xylose catabolic process
GO:0070947	0.0028	Inf	0.0028	1	1	neutrophil mediated killing of fungus
GO:2000266	0.0028	Inf	0.0028	1	1	regulation of blood coagulation, intrinsic pathway
GO:0061458	0.0032	5.6364	1.0129	5	356	reproductive system development
GO:0032677	0.0047	21.7699	0.1024	2	36	regulation of interleukin-8 production
GO:0044707	0.0048	2.5225	13.8418	22	4865	single-multicellular organism process
GO:0006954	0.0052	4.9906	1.1381	5	400	inflammatory response
GO:0006968	0.0052	20.5572	0.1081	2	38	cellular defense response
GO:0002232	0.0057	360.4571	0.0057	1	2	leukocyte chemotaxis involved in inflammatory response
GO:0002752	0.0057	360.4571	0.0057	1	2	cell surface pattern recognition receptor signaling pathway
GO:0007066	0.0057	360.4571	0.0057	1	2	female meiosis sister chromatid cohesion
GO:0010845	0.0057	360.4571	0.0057	1	2	positive regulation of reciprocal meiotic recombination
GO:0018879	0.0057	360.4571	0.0057	1	2	biphenyl metabolic process
GO:0018894	0.0057	360.4571	0.0057	1	2	dibenzo-p-dioxin metabolic process
GO:0030150	0.0057	360.4571	0.0057	1	2	protein import into mitochondrial matrix
GO:0033595	0.0057	360.4571	0.0057	1	2	response to genistein
GO:0042138	0.0057	360.4571	0.0057	1	2	meiotic DNA double-strand break formation
GO:0045079	0.0057	360.4571	0.0057	1	2	negative regulation of chemokine biosynthetic process
GO:0045416	0.0057	360.4571	0.0057	1	2	positive regulation of interleukin-8 biosynthetic process
GO:0045918	0.0057	360.4571	0.0057	1	2	negative regulation of cytolysis
GO:0050756	0.0057	360.4571	0.0057	1	2	fractalkine metabolic process
GO:0060014	0.0057	360.4571	0.0057	1	2	granulosa cell differentiation
GO:0060992	0.0057	360.4571	0.0057	1	2	response to fungicide
GO:1901993	0.0057	360.4571	0.0057	1	2	regulation of meiotic cell cycle phase transition
GO:0032642	0.006	18.9713	0.1167	2	41	regulation of chemokine production
GO:0001541	0.0069	17.612	0.1252	2	44	ovarian follicle development
GO:0000280	0.0078	4.4955	1.2576	5	442	nuclear division
GO:0051321	0.0081	7.9515	0.415	3	150	meiotic cell cycle
GO:0051177	0.0083	185.5	0.0083	1	3	meiotic sister chromatid cohesion
GO:0001878	0.0085	180.2143	0.0085	1	3	response to yeast
GO:0006311	0.0085	180.2143	0.0085	1	3	meiotic gene conversion

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0019807	0.0021	Inf	0.0021	1	1	aspartoacylase activity
GO:0008138	0.003	27.6982	0.082	2	39	protein tyrosine/serine/threonine phosphatase activity
GO:0016314	0.0042	493.36	0.0042	1	2	phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity
GO:0030109	0.0042	493.36	0.0042	1	2	HLA-B specific inhibitory MHC class I receptor activity
GO:0004814	0.0063	246.66	0.0063	1	3	arginine-tRNA ligase activity
GO:0031849	0.0063	246.66	0.0063	1	3	olfactory receptor binding
GO:0033743	0.0063	246.66	0.0063	1	3	peptide-methionine (R)-S-oxide reductase activity
GO:0004197	0.0072	17.339	0.1283	2	61	cysteine-type endopeptidase activity
GO:0016874	0.0075	5.8309	0.793	4	377	ligase activity
GO:0004872	0.0077	4.0382	1.8068	6	859	receptor activity
GO:0034618	0.0084	164.4267	0.0084	1	4	arginine binding
GO:0047760	0.0084	164.4267	0.0084	1	4	butyrate-CoA ligase activity