RnBeads: Johansson et al. & Reinius et al.

Option	Value
analyze.sites	yes
differential.report.sites	yes
region.types	promoters
differential.permutations	0
differential.comparison.columns	Age Group
differential.comparison.columns.all.pairwise	default
columns.pairing	default
differential.site.test.method	limma
differential.variability	yes
differential.variability.method	diffVar
covariate.adjustment.columns	Genome-wide methylation, Gender
differential.adjustment.sva	yes
differential.adjustment.celltype	yes
differential.enrichment.go	yes
differential.enrichment.lola	no
differential.enrichment.lola.dbs	${LOLACore}

	comparison	adjustment	covariateTable
1	young vs. senior (based on Age Group)	Genome-wide methylation,Gender,ct_1,ct_2,ct_3,ct_4,ct_5,ct_6	csv

	Rank Cutoff
young vs. senior (based on Age Group)	59023

	Rank Cutoff
young vs. senior (based on Age Group)	22582

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 [2]. 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:

	promoters
young vs. senior (based on Age Group)	996

comparison
regions
differential methylation measure

Figure 6

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 7

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 [2]
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
End: end coordinate of the regions
[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.var.g1, mean.var.g2: Average variances found in the regions for the twp groups. g1 and g2 is replaced by the group name
mean.var.diff: Average difference between the variances found in the two groups over the regions
mean.var.log.ratio: Region-wise average for the log2 ratio between the variances found in the two groups
comb.p.val.var: Combined p-value aggregating p-values of all sites in the region using a generalization of Fisher's method
comb.p.adj.var.fdr: FDR adjusted combined p-value
combinedRank.var: mean.var.diff, mean.var.log.ratio and comb.p.val.var are ranked for all regions and the higher (=worst) rank is selected.

The tables for the individual comparisons can be found here:

	promoters
young vs. senior (based on Age Group)	csv

Differential Variability

Differential variability on the region level was computed similar to differential methylation, but the mean of variances, the log-ratio of the quotient of variances as well as the p-values from the differentiality test were employed. Ranking was performed in line with the ranking of differential methylation.

The following rank cutoffs have been automatically selected for the analysis of differentially variable regions:

	promoters
young vs. senior (based on Age Group)	2340

comparison
regions
differential variability measure

Figure 8

Scatterplot for differential variable regions. 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).

comparison
regions
difference metric
significance metric

Figure 9

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

comparison
regions
rankCutoff

Figure 10

Scatterplot comparing differentially methylated (DMRs) and variable regions (DVRs), as well as regions that are both differentially methylated and variable. The dotted lines corrspond to the respective rank cutoffs used to call a region differentially methylated/variable.

GO Enrichment Analysis

GO 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 11

Wordclouds for GO enrichment terms.

comparison
Hypermethylation/hypomethylation
ontology
regions
differential methylation measure

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0045321	0	5.1253	3.2746	13	1027	leukocyte activation
GO:0042102	2e-04	15.4112	0.2933	4	92	positive regulation of T cell proliferation
GO:0043312	4e-04	5.9004	1.3679	7	429	neutrophil degranulation
GO:0030834	4e-04	23.1984	0.1467	3	46	regulation of actin filament depolymerization
GO:0042119	4e-04	5.7598	1.3998	7	439	neutrophil activation
GO:1903039	5e-04	8.6963	0.6473	5	203	positive regulation of leukocyte cell-cell adhesion
GO:0002263	6e-04	4.8696	1.9131	8	600	cell activation involved in immune response
GO:0051798	6e-04	65.2	0.0383	2	12	positive regulation of hair follicle development
GO:0032946	7e-04	11.0909	0.4018	4	126	positive regulation of mononuclear cell proliferation
GO:0043242	7e-04	19.1718	0.1754	3	55	negative regulation of protein complex disassembly
GO:0002275	7e-04	5.292	1.5177	7	476	myeloid cell activation involved in immune response
GO:0002444	8e-04	5.2343	1.5337	7	481	myeloid leukocyte mediated immunity
GO:0046365	8e-04	18.1224	0.1849	3	58	monosaccharide catabolic process
GO:0044130	9e-04	54.3261	0.0446	2	14	negative regulation of growth of symbiont in host
GO:0034341	0.0012	9.5841	0.4623	4	145	response to interferon-gamma
GO:0044144	0.0012	46.559	0.051	2	16	modulation of growth of symbiont involved in interaction with host
GO:0044110	0.0015	40.7337	0.0574	2	18	growth involved in symbiotic interaction
GO:0055114	0.0015	3.7865	2.7772	9	871	oxidation-reduction process
GO:0050901	0.0016	38.335	0.0606	2	19	leukocyte tethering or rolling
GO:0032649	0.0018	13.6374	0.2423	3	76	regulation of interferon-gamma production
GO:0002544	0.0018	36.2029	0.0638	2	20	chronic inflammatory response
GO:0019430	0.0018	36.2029	0.0638	2	20	removal of superoxide radicals
GO:0071526	0.0018	36.2029	0.0638	2	20	semaphorin-plexin signaling pathway
GO:0060333	0.0021	12.9255	0.2551	3	80	interferon-gamma-mediated signaling pathway
GO:0009110	0.0022	32.5783	0.0701	2	22	vitamin biosynthetic process
GO:0071450	0.0022	32.5783	0.0701	2	22	cellular response to oxygen radical
GO:0051261	0.0023	12.4383	0.2646	3	83	protein depolymerization
GO:0006959	0.0024	7.7945	0.5644	4	177	humoral immune response
GO:0006779	0.0024	31.0248	0.0733	2	23	porphyrin-containing compound biosynthetic process
GO:0061621	0.0026	29.6126	0.0765	2	24	canonical glycolysis
GO:0000303	0.0029	28.3233	0.0797	2	25	response to superoxide
GO:0061615	0.0029	28.3233	0.0797	2	25	glycolytic process through fructose-6-phosphate
GO:0050670	0.0029	7.4046	0.5931	4	186	regulation of lymphocyte proliferation
GO:0042634	0.0031	27.1413	0.0829	2	26	regulation of hair cycle
GO:0002149	0.0032	Inf	0.0032	1	1	hypochlorous acid biosynthetic process
GO:0010722	0.0032	Inf	0.0032	1	1	regulation of ferrochelatase activity
GO:0019442	0.0032	Inf	0.0032	1	1	tryptophan catabolic process to acetyl-CoA
GO:0035238	0.0032	Inf	0.0032	1	1	vitamin A biosynthetic process
GO:0061048	0.0032	Inf	0.0032	1	1	negative regulation of branching involved in lung morphogenesis
GO:1901810	0.0032	Inf	0.0032	1	1	beta-carotene metabolic process
GO:1990268	0.0032	Inf	0.0032	1	1	response to gold nanoparticle
GO:1990539	0.0032	Inf	0.0032	1	1	fructose import across plasma membrane
GO:0070663	0.0035	6.9774	0.6281	4	197	regulation of leukocyte proliferation
GO:0006007	0.0038	24.1208	0.0925	2	29	glucose catabolic process
GO:0050832	0.0041	23.2578	0.0957	2	30	defense response to fungus
GO:0045055	0.0042	3.8199	2.0694	7	649	regulated exocytosis
GO:0016192	0.0044	2.7429	5.2228	12	1638	vesicle-mediated transport
GO:0019318	0.0045	6.4993	0.6728	4	211	hexose metabolic process
GO:0045926	0.0045	6.4993	0.6728	4	211	negative regulation of growth
GO:0051693	0.0049	21.0028	0.1052	2	33	actin filament capping
GO:0019731	0.0052	20.3451	0.1084	2	34	antibacterial humoral response
GO:0045601	0.0052	20.3451	0.1084	2	34	regulation of endothelial cell differentiation
GO:0045785	0.0053	4.8549	1.1351	5	356	positive regulation of cell adhesion
GO:0001937	0.0055	19.7273	0.1116	2	35	negative regulation of endothelial cell proliferation
GO:0006734	0.0059	19.1458	0.1148	2	36	NADH metabolic process
GO:0002876	0.0064	319.2553	0.0064	1	2	positive regulation of chronic inflammatory response to antigenic stimulus
GO:0010693	0.0064	319.2553	0.0064	1	2	negative regulation of alkaline phosphatase activity
GO:0015755	0.0064	319.2553	0.0064	1	2	fructose transport
GO:0018283	0.0064	319.2553	0.0064	1	2	iron incorporation into metallo-sulfur cluster
GO:0019478	0.0064	319.2553	0.0064	1	2	D-amino acid catabolic process
GO:0035606	0.0064	319.2553	0.0064	1	2	peptidyl-cysteine S-trans-nitrosylation
GO:0045994	0.0064	319.2553	0.0064	1	2	positive regulation of translational initiation by iron
GO:1901671	0.0064	319.2553	0.0064	1	2	positive regulation of superoxide dismutase activity
GO:1904231	0.0064	319.2553	0.0064	1	2	positive regulation of succinate dehydrogenase activity
GO:1904234	0.0064	319.2553	0.0064	1	2	positive regulation of aconitate hydratase activity
GO:1904999	0.0064	319.2553	0.0064	1	2	positive regulation of leukocyte adhesion to arterial endothelial cell
GO:2000334	0.0064	319.2553	0.0064	1	2	positive regulation of blood microparticle formation
GO:0051186	0.0066	4.5996	1.1957	5	375	cofactor metabolic process
GO:0022407	0.0067	4.5869	1.1989	5	376	regulation of cell-cell adhesion
GO:0010594	0.0074	8.1333	0.3986	3	125	regulation of endothelial cell migration
GO:0045087	0.0074	3.8543	1.7442	6	591	innate immune response
GO:0006775	0.0075	16.6856	0.1307	2	41	fat-soluble vitamin metabolic process
GO:0051251	0.0077	5.5462	0.7844	4	246	positive regulation of lymphocyte activation
GO:0035821	0.0079	7.9365	0.4081	3	128	modification of morphology or physiology of other organism
GO:0061844	0.0079	16.2674	0.1339	2	42	antimicrobial humoral immune response mediated by antimicrobial peptide
GO:0035094	0.0083	15.8696	0.1371	2	43	response to nicotine
GO:0090199	0.0086	15.4907	0.1403	2	44	regulation of release of cytochrome c from mitochondria
GO:0045071	0.0094	14.7846	0.1467	2	46	negative regulation of viral genome replication
GO:0042214	0.0095	159.617	0.0096	1	3	terpene metabolic process
GO:0046136	0.0095	159.617	0.0096	1	3	positive regulation of vitamin metabolic process
GO:0052330	0.0095	159.617	0.0096	1	3	positive regulation by organism of programmed cell death in other organism involved in symbiotic interaction
GO:0052501	0.0095	159.617	0.0096	1	3	positive regulation by organism of apoptotic process in other organism involved in symbiotic interaction
GO:0060559	0.0095	159.617	0.0096	1	3	positive regulation of calcidiol 1-monooxygenase activity
GO:1903347	0.0095	159.617	0.0096	1	3	negative regulation of bicellular tight junction assembly
GO:0042110	0.0097	4.1815	1.3105	5	411	T cell activation
GO:0034113	0.0098	14.4551	0.1499	2	47	heterotypic cell-cell adhesion

Differential Variability

GO enrichment analysis was also performed for differentially variable regions.

comparison
Hypermethylation/hypomethylation
ontology
regions
differential methylation measure

Figure 12

Workclouds for GO enrichment terms (Differential Variability)

comparison
Hypermethylation/hypomethylation
ontology
regions
differential methylation measure

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0002305	0.0024	Inf	0.0024	1	1	CD8-positive, gamma-delta intraepithelial T cell differentiation
GO:0018979	0.0024	Inf	0.0024	1	1	trichloroethylene metabolic process
GO:0007181	0.0048	429.0571	0.0048	1	2	transforming growth factor beta receptor complex assembly
GO:0018931	0.0048	429.0571	0.0048	1	2	naphthalene metabolic process
GO:0042197	0.0048	429.0571	0.0048	1	2	halogenated hydrocarbon metabolic process
GO:0031338	0.0076	16.6093	0.1315	2	55	regulation of vesicle fusion
GO:0006432	0.0095	143	0.0096	1	4	phenylalanyl-tRNA aminoacylation
GO:0006682	0.0095	143	0.0096	1	4	galactosylceramide biosynthetic process
GO:0044537	0.0095	143	0.0096	1	4	regulation of circulating fibrinogen levels
GO:0097039	0.0095	143	0.0096	1	4	protein linear polyubiquitination
GO:0099590	0.0095	143	0.0096	1	4	neurotransmitter receptor internalization
GO:0032088	0.0096	14.6647	0.1483	2	62	negative regulation of NF-kappaB transcription factor activity

LOLA Enrichment Analysis

No LOLA Enrichment Analysis was conducted

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0021520	0	81.7418	0.0501	3	13	spinal cord motor neuron cell fate specification
GO:0060913	0	535.5357	0.0116	2	3	cardiac cell fate determination
GO:0001708	3e-04	14.5419	0.3082	4	80	cell fate specification
GO:0021953	3e-04	9.1522	0.6087	5	158	central nervous system neuron differentiation
GO:0021517	6e-04	20.9189	0.1618	3	42	ventral spinal cord development
GO:0021903	6e-04	66.9107	0.0385	2	10	rostrocaudal neural tube patterning
GO:0007389	8e-04	5.1676	1.5219	7	395	pattern specification process
GO:0048699	9e-04	3.1439	4.9123	13	1275	generation of neurons
GO:0021515	9e-04	17.3489	0.1926	3	50	cell differentiation in spinal cord
GO:0010454	9e-04	53.5214	0.0462	2	12	negative regulation of cell fate commitment
GO:0048935	9e-04	53.5214	0.0462	2	12	peripheral nervous system neuron development
GO:0007411	0.0013	6.8067	0.8091	5	210	axon guidance
GO:0060850	0.0017	38.2194	0.0616	2	16	regulation of transcription involved in cell fate commitment
GO:0014031	0.0017	13.8092	0.2389	3	62	mesenchymal cell development
GO:0048864	0.0017	13.8092	0.2389	3	62	stem cell development
GO:0014033	0.002	13.1384	0.2504	3	65	neural crest cell differentiation
GO:0007130	0.0021	33.4375	0.0694	2	18	synaptonemal complex assembly
GO:0048663	0.0023	12.5295	0.262	3	68	neuron fate commitment
GO:0007420	0.0023	3.8059	2.3618	8	613	brain development
GO:0051961	0.0025	5.7759	0.9478	5	246	negative regulation of nervous system development
GO:0003151	0.0027	11.8	0.2774	3	72	outflow tract morphogenesis
GO:0008344	0.0029	11.4661	0.2851	3	74	adult locomotory behavior
GO:0007141	0.0029	28.1523	0.0809	2	21	male meiosis I
GO:0035640	0.0032	26.7429	0.0848	2	22	exploration behavior
GO:0010721	0.0034	5.3891	1.0133	5	263	negative regulation of cell development
GO:0060914	0.0035	25.4677	0.0886	2	23	heart formation
GO:0048562	0.0038	5.2442	1.0403	5	270	embryonic organ morphogenesis
GO:0003142	0.0039	Inf	0.0039	1	1	cardiogenic plate morphogenesis
GO:0021568	0.0039	Inf	0.0039	1	1	rhombomere 2 development
GO:0042404	0.0039	Inf	0.0039	1	1	thyroid hormone catabolic process
GO:0060807	0.0039	Inf	0.0039	1	1	regulation of transcription from RNA polymerase II promoter involved in definitive endodermal cell fate specification
GO:0071329	0.0039	Inf	0.0039	1	1	cellular response to sucrose stimulus
GO:1904425	0.0039	Inf	0.0039	1	1	negative regulation of GTP binding
GO:1904530	0.0039	Inf	0.0039	1	1	negative regulation of actin filament binding
GO:1904708	0.0039	Inf	0.0039	1	1	regulation of granulosa cell apoptotic process
GO:0021884	0.0041	23.25	0.0963	2	25	forebrain neuron development
GO:0035295	0.0043	3.761	2.0612	7	535	tube development
GO:0009653	0.0043	2.4027	8.0507	16	2193	anatomical structure morphogenesis
GO:0000902	0.0045	3.1388	3.2286	9	838	cell morphogenesis
GO:0009954	0.0055	19.8003	0.1117	2	29	proximal/distal pattern formation
GO:0030154	0.0056	2.1383	13.1048	22	3575	cell differentiation
GO:0007399	0.0066	2.4851	6.1741	13	1755	nervous system development
GO:1900026	0.0067	17.8167	0.1233	2	32	positive regulation of substrate adhesion-dependent cell spreading
GO:0014003	0.0076	16.7009	0.131	2	34	oligodendrocyte development
GO:0001828	0.0077	263.0702	0.0077	1	2	inner cell mass cellular morphogenesis
GO:0007493	0.0077	263.0702	0.0077	1	2	endodermal cell fate determination
GO:0008050	0.0077	263.0702	0.0077	1	2	female courtship behavior
GO:0035332	0.0077	263.0702	0.0077	1	2	positive regulation of hippo signaling
GO:0051729	0.0077	263.0702	0.0077	1	2	germline cell cycle switching, mitotic to meiotic cell cycle
GO:0060184	0.0077	263.0702	0.0077	1	2	cell cycle switching
GO:0061010	0.0077	263.0702	0.0077	1	2	gall bladder development
GO:0061386	0.0077	263.0702	0.0077	1	2	closure of optic fissure
GO:0071657	0.0077	263.0702	0.0077	1	2	positive regulation of granulocyte colony-stimulating factor production
GO:0072272	0.0077	263.0702	0.0077	1	2	proximal/distal pattern formation involved in metanephric nephron development
GO:1903899	0.0077	263.0702	0.0077	1	2	positive regulation of PERK-mediated unfolded protein response
GO:1904616	0.0077	263.0702	0.0077	1	2	regulation of actin binding
GO:2000043	0.0077	263.0702	0.0077	1	2	regulation of cardiac cell fate specification
GO:2001111	0.0077	263.0702	0.0077	1	2	positive regulation of lens epithelial cell proliferation
GO:0001755	0.008	16.1937	0.1348	2	35	neural crest cell migration
GO:0031103	0.008	16.1937	0.1348	2	35	axon regeneration
GO:0014014	0.0094	14.8413	0.1464	2	38	negative regulation of gliogenesis
GO:0048483	0.0094	14.8413	0.1464	2	38	autonomic nervous system development
GO:0048667	0.0098	3.5661	1.8339	6	476	cell morphogenesis involved in neuron differentiation
GO:0021510	0.0099	14.4238	0.1503	2	41	spinal cord development

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0016638	0.0011	48.7045	0.0489	2	16	oxidoreductase activity, acting on the CH-NH2 group of donors
GO:0005549	0.0014	15.1122	0.2199	3	72	odorant binding
GO:0042605	0.0015	40.1016	0.058	2	19	peptide antigen binding
GO:0016701	0.002	34.0795	0.0672	2	22	oxidoreductase activity, acting on single donors with incorporation of molecular oxygen
GO:0003834	0.0031	Inf	0.0031	1	1	beta-carotene 15,15'-monooxygenase activity
GO:0003975	0.0031	Inf	0.0031	1	1	UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity
GO:0005353	0.0031	Inf	0.0031	1	1	fructose transmembrane transporter activity
GO:0008445	0.0031	Inf	0.0031	1	1	D-aspartate oxidase activity
GO:0008887	0.0031	Inf	0.0031	1	1	glycerate kinase activity
GO:0008963	0.0031	Inf	0.0031	1	1	phospho-N-acetylmuramoyl-pentapeptide-transferase activity
GO:0034986	0.0031	Inf	0.0031	1	1	iron chaperone activity
GO:0035605	0.0031	Inf	0.0031	1	1	peptidyl-cysteine S-nitrosylase activity
GO:0004365	0.0061	333.6444	0.0061	1	2	glyceraldehyde-3-phosphate dehydrogenase (NAD+) (phosphorylating) activity
GO:0004458	0.0061	333.6444	0.0061	1	2	D-lactate dehydrogenase (cytochrome) activity
GO:0004833	0.0061	333.6444	0.0061	1	2	tryptophan 2,3-dioxygenase activity
GO:0008147	0.0061	333.6444	0.0061	1	2	structural constituent of bone
GO:0003976	0.0091	166.8111	0.0092	1	3	UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity
GO:0004117	0.0091	166.8111	0.0092	1	3	calmodulin-dependent cyclic-nucleotide phosphodiesterase activity
GO:0008131	0.0091	166.8111	0.0092	1	3	primary amine oxidase activity

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0140110	3e-04	3.5312	4.9442	14	1432	transcription regulator activity
GO:0001228	3e-04	6.1716	1.2982	7	376	transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0043565	0.0014	6.7166	0.8352	5	267	sequence-specific DNA binding
GO:0000977	0.0031	4.0436	1.9438	7	563	RNA polymerase II regulatory region sequence-specific DNA binding
GO:0000981	0.0033	7.1264	0.6191	4	205	RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0001605	0.0035	Inf	0.0035	1	1	adrenomedullin receptor activity
GO:0033798	0.0035	Inf	0.0035	1	1	thyroxine 5-deiodinase activity
GO:0044212	0.0049	3.3576	2.6896	8	779	transcription regulatory region DNA binding
GO:0001067	0.005	3.3485	2.6965	8	781	regulatory region nucleic acid binding
GO:0015077	0.0054	4.8217	1.1359	5	329	monovalent inorganic cation transmembrane transporter activity
GO:0001635	0.0069	294.2745	0.0069	1	2	calcitonin gene-related peptide receptor activity
GO:0036461	0.0069	294.2745	0.0069	1	2	BLOC-2 complex binding
GO:0022853	0.0077	7.9995	0.404	3	117	active ion transmembrane transporter activity
GO:0001105	0.008	16.1859	0.1347	2	39	RNA polymerase II transcription coactivator activity
GO:1990837	0.0082	3.3343	2.334	7	676	sequence-specific double-stranded DNA binding
GO:0005215	0.0083	2.7031	4.2295	10	1225	transporter activity
GO:0000982	0.0088	4.2681	1.2775	5	370	transcription factor activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0008146	0.0096	14.6029	0.1485	2	43	sulfotransferase activity

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0002275	0	3.8654	6.7033	23	476	myeloid cell activation involved in immune response
GO:0002263	0	3.4747	8.4496	26	600	cell activation involved in immune response
GO:0043312	0	3.8897	6.0415	21	429	neutrophil degranulation
GO:0042119	0	3.794	6.1823	21	439	neutrophil activation
GO:0045321	0	3.2887	8.1869	24	605	leukocyte activation
GO:0002444	0	3.5281	6.6153	21	474	myeloid leukocyte mediated immunity
GO:0002544	0	26.1748	0.2093	4	15	chronic inflammatory response
GO:0045055	0	2.7636	9.1396	23	649	regulated exocytosis
GO:0016192	1e-04	2.0505	23.0674	42	1638	vesicle-mediated transport
GO:0032094	1e-04	11.9259	0.4929	5	35	response to food
GO:0045730	3e-04	15.003	0.3239	4	23	respiratory burst
GO:0009991	3e-04	2.9398	5.8725	16	417	response to extracellular stimulus
GO:0006968	3e-04	9.4101	0.6056	5	43	cellular defense response
GO:0070098	5e-04	6.5207	1.0139	6	72	chemokine-mediated signaling pathway
GO:1903039	6e-04	3.7575	2.8588	10	203	positive regulation of leukocyte cell-cell adhesion
GO:0019730	8e-04	5.9749	1.0984	6	78	antimicrobial humoral response
GO:0007186	9e-04	2.0193	15.6176	29	1109	G-protein coupled receptor signaling pathway
GO:0048870	0.001	2.4407	7.9436	18	593	cell motility
GO:0050911	0.0011	3.0537	4.1966	12	298	detection of chemical stimulus involved in sensory perception of smell
GO:0033013	0.0011	7.0053	0.7886	5	56	tetrapyrrole metabolic process
GO:0055114	0.0013	2.1093	12.266	24	871	oxidation-reduction process
GO:0050896	0.0013	1.7205	44.8271	62	3716	response to stimulus
GO:0045785	0.0016	2.7614	5.0134	13	356	positive regulation of cell adhesion
GO:0031295	0.0017	6.3777	0.859	5	61	T cell costimulation
GO:0042113	0.0017	3.5319	2.7179	9	193	B cell activation
GO:0045087	0.0017	2.1724	10.3648	21	736	innate immune response
GO:0034097	0.0017	2.0552	12.5617	24	892	response to cytokine
GO:0007584	0.0018	3.841	2.2251	8	158	response to nutrient
GO:0032940	0.0018	1.8787	17.899	31	1271	secretion by cell
GO:0042102	0.0019	4.9975	1.2956	6	92	positive regulation of T cell proliferation
GO:0002677	0.0019	47.1079	0.0704	2	5	negative regulation of chronic inflammatory response
GO:0002730	0.0019	47.1079	0.0704	2	5	regulation of dendritic cell cytokine production
GO:0043903	0.0021	3.4189	2.8024	9	199	regulation of symbiosis, encompassing mutualism through parasitism
GO:0006909	0.0022	3.3829	2.8306	9	201	phagocytosis
GO:0032496	0.0022	2.9425	3.9713	11	282	response to lipopolysaccharide
GO:0002374	0.0023	13.3008	0.2676	3	19	cytokine secretion involved in immune response
GO:0009593	0.0024	2.643	5.2247	13	371	detection of chemical stimulus
GO:0070887	0.0026	1.6047	37.4598	54	2660	cellular response to chemical stimulus
GO:0002694	0.0027	2.5014	5.9429	14	422	regulation of leukocyte activation
GO:0015942	0.0029	35.3286	0.0845	2	6	formate metabolic process
GO:0097527	0.0029	35.3286	0.0845	2	6	necroptotic signaling pathway
GO:0043207	0.0029	2.1045	10.1395	20	720	response to external biotic stimulus
GO:2000145	0.003	2.1013	10.1536	20	721	regulation of cell motility
GO:0071677	0.0035	11.1984	0.3098	3	22	positive regulation of mononuclear cell migration
GO:0002480	0.004	28.261	0.0986	2	7	antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-independent
GO:0002887	0.004	28.261	0.0986	2	7	negative regulation of myeloid leukocyte mediated immunity
GO:0043301	0.004	28.261	0.0986	2	7	negative regulation of leukocyte degranulation
GO:0006779	0.004	10.6378	0.3239	3	23	porphyrin-containing compound biosynthetic process
GO:0045662	0.004	10.6378	0.3239	3	23	negative regulation of myoblast differentiation
GO:0060142	0.0045	10.1306	0.338	3	24	regulation of syncytium formation by plasma membrane fusion
GO:0006955	0.0045	2.4433	5.6626	13	459	immune response
GO:0003008	0.0046	1.6672	24.7432	38	1757	system process
GO:0048247	0.0049	6.3235	0.69	4	49	lymphocyte chemotaxis
GO:0002685	0.0054	3.5099	2.1124	7	150	regulation of leukocyte migration
GO:0009617	0.0054	2.2982	6.4358	14	457	response to bacterium
GO:0042110	0.0056	2.3708	5.788	13	411	T cell activation
GO:0006766	0.0057	3.9368	1.6195	6	115	vitamin metabolic process
GO:0001886	0.0067	20.1837	0.1267	2	9	endothelial cell morphogenesis
GO:0010819	0.0067	20.1837	0.1267	2	9	regulation of T cell chemotaxis
GO:0046007	0.0067	20.1837	0.1267	2	9	negative regulation of activated T cell proliferation
GO:0042168	0.007	8.5074	0.3943	3	28	heme metabolic process
GO:1900271	0.007	8.5074	0.3943	3	28	regulation of long-term synaptic potentiation
GO:0097529	0.0073	3.3001	2.2391	7	159	myeloid leukocyte migration
GO:0002521	0.0074	2.2823	5.9992	13	426	leukocyte differentiation
GO:0007154	0.0077	1.4158	79.3979	97	5638	cell communication
GO:0050906	0.0079	2.3533	5.3655	12	381	detection of stimulus involved in sensory perception
GO:0051251	0.0082	2.7321	3.4643	9	246	positive regulation of lymphocyte activation
GO:0040015	0.0082	17.6595	0.1408	2	10	negative regulation of multicellular organism growth
GO:0072672	0.0082	17.6595	0.1408	2	10	neutrophil extravasation
GO:0005996	0.0084	2.7205	3.4784	9	247	monosaccharide metabolic process
GO:0050832	0.0084	7.8761	0.4225	3	30	defense response to fungus
GO:0044419	0.0086	1.8933	11.1816	20	794	interspecies interaction between organisms
GO:0006950	0.0088	1.465	46.867	62	3328	response to stress
GO:0032946	0.0088	3.5733	1.7744	6	126	positive regulation of mononuclear cell proliferation
GO:0030595	0.0088	3.5729	1.7743	6	128	leukocyte chemotaxis
GO:0050900	0.0091	3.5472	1.7863	6	133	leukocyte migration
GO:0071346	0.0092	3.5435	1.7885	6	127	cellular response to interferon-gamma
GO:0007606	0.0092	2.3021	5.4781	12	389	sensory perception of chemical stimulus
GO:0002684	0.0092	1.849	12.0266	21	854	positive regulation of immune system process
GO:0018119	0.01	15.6963	0.1549	2	11	peptidyl-cysteine S-nitrosylation
GO:0051873	0.01	15.6963	0.1549	2	11	killing by host of symbiont cells

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0005549	1e-04	7.9232	0.9944	7	72	odorant binding
GO:0008147	2e-04	Inf	0.0276	2	2	structural constituent of bone
GO:0004930	5e-04	2.4265	9.3635	21	678	G-protein coupled receptor activity
GO:0004984	9e-04	3.1184	4.1155	12	298	olfactory receptor activity
GO:0015238	0.001	18.0988	0.2072	3	15	drug transmembrane transporter activity
GO:0016638	0.0013	16.7054	0.221	3	16	oxidoreductase activity, acting on the CH-NH2 group of donors
GO:0019825	0.0018	8.5461	0.5248	4	38	oxygen binding
GO:0042605	0.0021	13.5704	0.2624	3	19	peptide antigen binding
GO:0004465	0.0027	36.0413	0.0829	2	6	lipoprotein lipase activity
GO:0004866	0.0032	3.8839	1.9197	7	139	endopeptidase inhibitor activity
GO:0016176	0.0038	28.8311	0.0967	2	7	superoxide-generating NADPH oxidase activator activity
GO:0004950	0.0042	10.3359	0.3315	3	24	chemokine receptor activity
GO:0020037	0.0044	4.172	1.533	6	111	heme binding
GO:0005164	0.0053	9.4358	0.3591	3	26	tumor necrosis factor receptor binding
GO:0019957	0.0064	20.5908	0.1243	2	9	C-C chemokine binding
GO:0060089	0.0067	1.7179	18.7409	30	1357	molecular transducer activity
GO:0099600	0.007	1.7996	14.8187	25	1073	transmembrane receptor activity
GO:0038023	0.0071	1.7774	15.6197	26	1131	signaling receptor activity
GO:0019955	0.0085	4.2293	1.2568	5	91	cytokine binding

Differential Methylation

Parameter Overview

Introduction: Differential Methylation of Sample Groups

Comparisons

P-values

Site Level

Differential Methylation Tables

Differential Variability

Region Level

Differential Methylation Tables

Differential Variability

GO Enrichment Analysis

Differential Variability

LOLA Enrichment Analysis

References

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0021879	0	15.8973	1.0155	12	49	forebrain neuron differentiation
GO:0022008	0	3.0521	19.1647	50	976	neurogenesis
GO:0048663	0	11.6103	1.4093	13	68	neuron fate commitment
GO:0001708	0	9.092	1.5859	12	77	cell fate specification
GO:0007399	0	3.4725	9.8597	30	573	nervous system development
GO:0001764	0	6.5384	2.6528	15	128	neuron migration
GO:0032989	0	2.6421	19.2539	45	929	cellular component morphogenesis
GO:0007275	0	1.8664	83.133	123	4261	multicellular organism development
GO:0048812	0	3.0115	11.0466	30	533	neuron projection morphogenesis
GO:0048667	0	3.1457	9.8653	28	476	cell morphogenesis involved in neuron differentiation
GO:0035107	0	5.6299	2.8187	14	136	appendage morphogenesis
GO:0048858	0	2.9096	11.399	30	550	cell projection morphogenesis
GO:0061564	0	3.1792	8.303	24	404	axon development
GO:0021513	0	18.0466	0.456	6	22	spinal cord dorsal/ventral patterning
GO:0060173	0	4.6967	3.3161	14	160	limb development
GO:0061364	0	Inf	0.0622	3	3	apoptotic process involved in luteolysis
GO:0007411	0	4.242	3.9051	15	190	axon guidance
GO:0003002	0	3.3659	6.5078	20	314	regionalization
GO:0007156	0	4.8493	2.9845	13	144	homophilic cell adhesion via plasma membrane adhesion molecules
GO:0060581	0	23.9935	0.3109	5	15	cell fate commitment involved in pattern specification
GO:0006935	0	2.7672	10.6736	27	515	chemotaxis
GO:0021983	0	10.5502	0.8083	7	39	pituitary gland development
GO:0021514	0	19.9919	0.3523	5	17	ventral spinal cord interneuron differentiation
GO:0050808	0	3.6871	4.7461	16	229	synapse organization
GO:0019098	0	12.5482	0.601	6	29	reproductive behavior
GO:0007267	0	2.1361	21.1299	41	1047	cell-cell signaling
GO:0021953	0	7.3517	1.2508	8	63	central nervous system neuron differentiation
GO:0048870	0	1.9849	27.2332	49	1314	cell motility
GO:0072001	0	4.1799	3.4141	13	167	renal system development
GO:0014031	0	7.1579	1.285	8	62	mesenchymal cell development
GO:0072132	0	8.6525	0.9534	7	46	mesenchyme morphogenesis
GO:0003205	1e-04	4.2642	3.0881	12	149	cardiac chamber development
GO:0014706	1e-04	2.9508	6.9637	19	336	striated muscle tissue development
GO:0003208	1e-04	6.4395	1.4093	8	68	cardiac ventricle morphogenesis
GO:0048934	1e-04	23.9188	0.2487	4	12	peripheral nervous system neuron differentiation
GO:0051962	1e-04	2.6992	8.8083	22	425	positive regulation of nervous system development
GO:0001709	1e-04	9.6783	0.7415	6	36	cell fate determination
GO:0001964	1e-04	13.3225	0.4767	5	23	startle response
GO:0030182	1e-04	2.4675	10.9859	25	585	neuron differentiation

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0007156	0	6.4325	5.8924	30	144	homophilic cell adhesion via plasma membrane adhesion molecules
GO:0060173	0	5.8779	6.5471	31	160	limb development
GO:0035107	0	6.3183	5.565	28	136	appendage morphogenesis
GO:0007275	0	2.1056	78.9377	136	2224	multicellular organism development
GO:0009790	0	2.6041	31.0781	71	774	embryo development
GO:0048663	0	9.7727	2.4039	17	59	neuron fate commitment
GO:0007399	0	2.6938	24.9712	59	718	nervous system development
GO:0010720	0	2.9366	18.0864	47	442	positive regulation of cell development
GO:0045944	0	2.2151	41.6559	82	1018	positive regulation of transcription from RNA polymerase II promoter
GO:0090596	0	3.8043	9.6979	32	237	sensory organ morphogenesis
GO:0007267	0	2.7857	20.261	50	533	cell-cell signaling
GO:0001708	0	7.1949	3.0145	17	74	cell fate specification
GO:0048729	0	2.5879	23.8151	55	582	tissue morphogenesis
GO:0048699	0	2.6698	21.901	52	578	generation of neurons
GO:0051962	0	3.0664	15.1022	41	372	positive regulation of nervous system development
GO:0099537	0	2.6026	22.7921	53	557	trans-synaptic signaling
GO:0001655	0	3.6241	9.7787	31	241	urogenital system development
GO:0050767	0	2.5935	21.9625	51	543	regulation of neurogenesis
GO:0007218	0	5.8427	3.7646	18	92	neuropeptide signaling pathway
GO:0045666	0	6.2737	3.1497	16	78	positive regulation of neuron differentiation
GO:0006355	0	1.6195	132.947	187	3249	regulation of transcription, DNA-templated
GO:2001141	0	1.6158	133.97	188	3274	regulation of RNA biosynthetic process
GO:0061138	0	3.9048	6.7517	23	165	morphogenesis of a branching epithelium
GO:0009952	0	5.5407	3.4735	16	87	anterior/posterior pattern specification
GO:0021983	0	9.3571	1.5959	11	39	pituitary gland development
GO:0060562	0	2.9997	11.9075	32	291	epithelial tube morphogenesis
GO:0019219	0	1.5586	154.9616	209	3787	regulation of nucleobase-containing compound metabolic process
GO:0032989	0	2.0267	38.0141	70	929	cellular component morphogenesis
GO:0048812	0	2.3713	21.81	47	533	neuron projection morphogenesis
GO:0048858	0	2.346	22.5056	48	550	cell projection morphogenesis
GO:0009887	0	3.3343	8.7467	26	231	animal organ morphogenesis
GO:0060485	0	3.3154	8.8122	26	216	mesenchyme development
GO:0030900	0	4.4835	4.6615	18	118	forebrain development
GO:0060581	0	20.7328	0.6138	7	15	cell fate commitment involved in pattern specification
GO:0051961	0	3.1062	10.0662	28	246	negative regulation of nervous system development
GO:0014031	0	6.3308	2.537	13	62	mesenchymal cell development
GO:0007268	0	2.3498	21.013	45	519	chemical synaptic transmission
GO:0021513	0	13.5564	0.9002	8	22	spinal cord dorsal/ventral patterning
GO:0001764	0	4.2504	4.889	18	120	neuron migration

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0043565	0	4.298	9.8373	36	267	sequence-specific DNA binding
GO:1990837	0	2.7338	26.6612	64	676	sequence-specific double-stranded DNA binding
GO:0001067	0	2.5846	30.8023	70	781	regulatory region nucleic acid binding
GO:0005509	0	2.5802	24.3342	56	617	calcium ion binding
GO:0001077	0	3.4767	9.781	30	248	transcriptional activator activity, RNA polymerase II core promoter proximal region sequence-specific binding
GO:0001653	0	4.8952	4.575	19	116	peptide receptor activity
GO:0005261	0	3.0373	11.0037	30	279	cation channel activity
GO:0071837	0	21.553	0.5916	7	15	HMG box domain binding
GO:0000978	0	2.8162	12.9756	33	329	RNA polymerase II core promoter proximal region sequence-specific DNA binding
GO:0004872	0	1.8467	51.942	87	1317	receptor activity
GO:0022838	0	2.6409	15.0265	36	381	substrate-specific channel activity
GO:0004871	0	1.8087	56.1226	92	1423	signal transducer activity
GO:0001228	0	4.2375	4.8736	18	128	transcriptional activator activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0001159	0	2.6775	13.5672	33	344	core promoter proximal region DNA binding
GO:0022803	0	2.5031	16.2097	37	411	passive transmembrane transporter activity
GO:0043169	0	1.4909	147.7013	194	3745	cation binding
GO:0022890	0	2.2698	19.1677	40	486	inorganic cation transmembrane transporter activity
GO:0015081	0	3.6443	5.561	18	141	sodium ion transmembrane transporter activity
GO:0022834	0	3.8985	4.6539	16	118	ligand-gated channel activity
GO:0000977	0	3.1319	7.4164	21	196	RNA polymerase II regulatory region sequence-specific DNA binding
GO:0003700	0	2.379	15.0741	33	418	DNA binding transcription factor activity
GO:0044212	0	2.5296	12.4891	29	330	transcription regulatory region DNA binding
GO:0015079	1e-04	3.1996	5.8765	17	149	potassium ion transmembrane transporter activity
GO:0008013	1e-04	4.5305	2.8002	11	71	beta-catenin binding
GO:0015075	1e-04	1.9284	25.0459	45	642	ion transmembrane transporter activity
GO:0022836	3e-04	2.8525	6.4983	17	168	gated channel activity
GO:0030594	4e-04	3.7723	3.2735	11	83	neurotransmitter receptor activity
GO:0022892	5e-04	1.6432	39.5579	61	1003	substrate-specific transporter activity
GO:0015277	6e-04	36.7132	0.1972	3	5	kainate selective glutamate receptor activity
GO:0008188	0.0011	5.9538	1.2111	6	31	neuropeptide receptor activity
GO:0016492	0.0016	Inf	0.0789	2	2	G-protein coupled neurotensin receptor activity
GO:0036461	0.0016	Inf	0.0789	2	2	BLOC-2 complex binding
GO:0015294	0.0016	3.1186	3.8651	11	98	solute:cation symporter activity
GO:0000981	0.0017	2.7799	5.053	13	138	RNA polymerase II transcription factor activity, sequence-specific DNA binding
GO:0042562	0.0017	4.017	2.2481	8	57	hormone binding
GO:0005244	0.0017	2.4597	6.9808	16	177	voltage-gated ion channel activity
GO:0008083	0.0018	2.6415	5.7187	14	145	growth factor activity
GO:0001227	0.0021	2.2754	8.4401	18	214	transcriptional repressor activity, RNA polymerase II transcription regulatory region sequence-specific binding
GO:0004930	0.0022	1.6688	26.5374	42	675	G-protein coupled receptor activity

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0007420	0	4.018	8.0626	28	613	brain development
GO:0048663	0	13.5712	0.8944	10	68	neuron fate commitment
GO:0001764	0	8.9022	1.5632	12	120	neuron migration
GO:0060284	0	3.201	9.9303	28	755	regulation of cell development
GO:0001708	0	10.4658	1.0027	9	77	cell fate specification
GO:0051960	0	3.2269	9.4699	27	720	regulation of nervous system development
GO:0022008	0	3.1691	10.1286	28	831	neurogenesis
GO:0019098	0	20.1535	0.3814	6	29	reproductive behavior
GO:0021953	0	6.803	1.8191	11	141	central nervous system neuron differentiation
GO:0032989	0	2.7723	12.2188	30	929	cellular component morphogenesis
GO:0048812	0	3.3239	7.0104	21	533	neuron projection morphogenesis
GO:0021513	0	22.6135	0.2894	5	22	spinal cord dorsal/ventral patterning
GO:0021872	0	10.6391	0.7629	7	58	forebrain generation of neurons
GO:0048858	0	3.2133	7.234	21	550	cell projection morphogenesis
GO:0032502	0	2.0814	38.1491	62	3250	developmental process
GO:0048667	0	3.3444	6.2607	19	476	cell morphogenesis involved in neuron differentiation
GO:0045665	0	5.2374	2.3149	11	176	negative regulation of neuron differentiation
GO:0003002	0	4.1554	3.6988	14	285	regionalization
GO:0007411	0	4.7761	2.7621	12	210	axon guidance
GO:0060581	0	27.8257	0.1973	4	15	cell fate commitment involved in pattern specification
GO:0045596	0	2.952	7.8258	21	595	negative regulation of cell differentiation
GO:0048870	0	2.2794	17.2826	35	1314	cell motility
GO:0061564	0	3.3428	5.5636	17	423	axon development
GO:0021514	1e-04	23.5416	0.2236	4	17	ventral spinal cord interneuron differentiation
GO:0007399	1e-04	3.0922	6.4668	18	591	nervous system development
GO:0035295	1e-04	2.9499	7.0367	19	535	tube development
GO:0007189	1e-04	9.0717	0.7497	6	57	adenylate cyclase-activating G-protein coupled receptor signaling pathway
GO:0007618	1e-04	12.0013	0.4866	5	37	mating
GO:0072091	1e-04	8.7282	0.776	6	59	regulation of stem cell proliferation
GO:0014706	1e-04	3.4343	4.4193	14	336	striated muscle tissue development
GO:0021537	2e-04	4.1224	2.8936	11	220	telencephalon development
GO:0021842	2e-04	Inf	0.0263	2	2	chemorepulsion involved in interneuron migration from the subpallium to the cortex
GO:0043503	2e-04	Inf	0.0263	2	2	skeletal muscle fiber adaptation
GO:0060180	2e-04	38.0769	0.1184	3	9	female mating behavior
GO:0051241	2e-04	2.2983	12.9159	27	982	negative regulation of multicellular organismal process
GO:0021903	3e-04	32.6352	0.1315	3	10	rostrocaudal neural tube patterning
GO:0048468	3e-04	2.3156	12.4596	26	1048	cell development
GO:0021517	3e-04	14.8591	0.3225	4	25	ventral spinal cord development
GO:0003148	3e-04	14.5655	0.3288	4	25	outflow tract septum morphogenesis