RnBeads report

Option	Value
analyze.sites	yes
differential.report.sites	yes
region.types	default
differential.permutations	0
differential.comparison.columns	6, 7
differential.comparison.columns.all.pairwise	6, 7
columns.pairing	default
differential.site.test.method	limma
differential.variability	no
differential.variability.method	diffVar
covariate.adjustment.columns	default
differential.adjustment.sva	no
differential.adjustment.celltype	no
differential.enrichment.go	yes
differential.enrichment.lola	no
differential.enrichment.lola.dbs	${LOLACore}

	Rank Cutoff
BrM_ERP vs. BrM_HER2P (based on Tiss_Subprim)	45
BrM_ERP vs. BrM_TNBC (based on Tiss_Subprim)	73153
BrM_ERP vs. Bx_ERP (based on Tiss_Subprim)	0
BrM_ERP vs. Bx_HER2P (based on Tiss_Subprim)	201
BrM_ERP vs. Bx_TNBC (based on Tiss_Subprim)	76661
BrM_HER2P vs. BrM_TNBC (based on Tiss_Subprim)	81041
BrM_HER2P vs. Bx_ERP (based on Tiss_Subprim)	95461
BrM_HER2P vs. Bx_HER2P (based on Tiss_Subprim)	87803
BrM_HER2P vs. Bx_TNBC (based on Tiss_Subprim)	79388
BrM_TNBC vs. Bx_ERP (based on Tiss_Subprim)	71052
BrM_TNBC vs. Bx_HER2P (based on Tiss_Subprim)	75153
BrM_TNBC vs. Bx_TNBC (based on Tiss_Subprim)	56404
Bx_ERP vs. Bx_HER2P (based on Tiss_Subprim)	4
Bx_ERP vs. Bx_TNBC (based on Tiss_Subprim)	67795
Bx_HER2P vs. Bx_TNBC (based on Tiss_Subprim)	61717
NT vs. YT (based on NT)	97803

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
BrM_ERP vs. BrM_HER2P (based on Tiss_Subprim)	0	10	40	0
BrM_ERP vs. BrM_TNBC (based on Tiss_Subprim)	6873	19	305	355
BrM_ERP vs. Bx_ERP (based on Tiss_Subprim)	46	11	0	12
BrM_ERP vs. Bx_HER2P (based on Tiss_Subprim)	6	0	0	1
BrM_ERP vs. Bx_TNBC (based on Tiss_Subprim)	77	0	60	177
BrM_HER2P vs. BrM_TNBC (based on Tiss_Subprim)	10318	1021	1185	1329
BrM_HER2P vs. Bx_ERP (based on Tiss_Subprim)	1958	45	13	0
BrM_HER2P vs. Bx_HER2P (based on Tiss_Subprim)	155	0	0	0
BrM_HER2P vs. Bx_TNBC (based on Tiss_Subprim)	5120	343	2972	1537
BrM_TNBC vs. Bx_ERP (based on Tiss_Subprim)	8917	220	1549	1316
BrM_TNBC vs. Bx_HER2P (based on Tiss_Subprim)	5505	1475	1249	2321
BrM_TNBC vs. Bx_TNBC (based on Tiss_Subprim)	94	0	71	39
Bx_ERP vs. Bx_HER2P (based on Tiss_Subprim)	93	0	25	2
Bx_ERP vs. Bx_TNBC (based on Tiss_Subprim)	4104	9	3	70
Bx_HER2P vs. Bx_TNBC (based on Tiss_Subprim)	3087	46	1351	872
NT vs. YT (based on NT)	6882	1380	2098	2799

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
BrM_ERP vs. BrM_HER2P (based on Tiss_Subprim)	csv	csv	csv	csv
BrM_ERP vs. BrM_TNBC (based on Tiss_Subprim)	csv	csv	csv	csv
BrM_ERP vs. Bx_ERP (based on Tiss_Subprim)	csv	csv	csv	csv
BrM_ERP vs. Bx_HER2P (based on Tiss_Subprim)	csv	csv	csv	csv
BrM_ERP vs. Bx_TNBC (based on Tiss_Subprim)	csv	csv	csv	csv
BrM_HER2P vs. BrM_TNBC (based on Tiss_Subprim)	csv	csv	csv	csv
BrM_HER2P vs. Bx_ERP (based on Tiss_Subprim)	csv	csv	csv	csv
BrM_HER2P vs. Bx_HER2P (based on Tiss_Subprim)	csv	csv	csv	csv
BrM_HER2P vs. Bx_TNBC (based on Tiss_Subprim)	csv	csv	csv	csv
BrM_TNBC vs. Bx_ERP (based on Tiss_Subprim)	csv	csv	csv	csv
BrM_TNBC vs. Bx_HER2P (based on Tiss_Subprim)	csv	csv	csv	csv
BrM_TNBC vs. Bx_TNBC (based on Tiss_Subprim)	csv	csv	csv	csv
Bx_ERP vs. Bx_HER2P (based on Tiss_Subprim)	csv	csv	csv	csv
Bx_ERP vs. Bx_TNBC (based on Tiss_Subprim)	csv	csv	csv	csv
Bx_HER2P vs. Bx_TNBC (based on Tiss_Subprim)	csv	csv	csv	csv
NT vs. YT (based on NT)	csv	csv	csv	csv

GO Enrichment Analysis

GO Enrichment Analysis was conducted using a hypergeometric test that addresses the hierarchical structure of the ontology (see [2] for details). The wordclouds and tables below contain significant GO terms according to these tests.

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:0006335	0	262.3377	0.075	10	32	DNA replication-dependent chromatin assembly
GO:0006334	0	70.4815	0.2436	11	104	nucleosome assembly
GO:0040029	0	46.6289	0.3116	10	133	regulation of gene expression, epigenetic
GO:0071824	0	32.7216	0.492	11	210	protein-DNA complex subunit organization
GO:0032200	0	39.227	0.3655	10	156	telomere organization
GO:0006338	0	28.7637	0.5552	11	237	chromatin remodeling
GO:0009593	0	15.2	0.6724	8	287	detection of chemical stimulus
GO:0007606	0	14.6648	0.6958	8	297	sensory perception of chemical stimulus
GO:0050906	0	13.8815	0.7333	8	313	detection of stimulus involved in sensory perception
GO:0050911	0	17.3415	0.5037	7	215	detection of chemical stimulus involved in sensory perception of smell
GO:0065003	0	5.5207	3.294	13	1406	protein-containing complex assembly
GO:0007186	1e-04	5.638	2.2819	10	974	G protein-coupled receptor signaling pathway
GO:0035195	1e-04	9.9941	0.7122	6	304	miRNA-mediated gene silencing
GO:0016441	1e-04	9.6	0.7403	6	316	post-transcriptional gene silencing
GO:0031047	1e-04	8.9514	0.7919	6	338	gene silencing by RNA
GO:0050877	4e-04	4.4231	2.8559	10	1219	nervous system process
GO:0050789	7e-04	4.508	24.8523	34	10608	regulation of biological process
GO:0010467	0.0038	2.5135	13.457	22	5744	gene expression
GO:0002032	0.0047	437.3243	0.0047	1	2	desensitization of G protein-coupled receptor signaling pathway by arrestin
GO:0061885	0.0047	437.3243	0.0047	1	2	positive regulation of mini excitatory postsynaptic potential
GO:0002025	0.007	218.6486	0.007	1	3	norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure
GO:0044245	0.007	218.6486	0.007	1	3	polysaccharide digestion
GO:0099601	0.0084	15.7164	0.1382	2	59	regulation of neurotransmitter receptor activity
GO:0014054	0.0093	145.7568	0.0094	1	4	positive regulation of gamma-aminobutyric acid secretion
GO:0044278	0.0093	145.7568	0.0094	1	4	cell wall disruption in another organism
GO:0051919	0.0093	145.7568	0.0094	1	4	positive regulation of fibrinolysis
GO:1990911	0.0093	145.7568	0.0094	1	4	response to psychosocial stress

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0050911	0	41.0424	0.3844	10	215	detection of chemical stimulus involved in sensory perception of smell
GO:0009593	0	30.2375	0.5131	10	287	detection of chemical stimulus
GO:0007606	0	29.1656	0.531	10	297	sensory perception of chemical stimulus
GO:0050906	0	27.5977	0.5596	10	313	detection of stimulus involved in sensory perception
GO:0007186	0	9.6636	1.7414	11	974	G protein-coupled receptor signaling pathway
GO:0048252	0	1199.2593	0.0054	2	3	lauric acid metabolic process
GO:0050877	0	6.5221	2.1795	10	1219	nervous system process
GO:0043651	5e-04	74.8843	0.0322	2	18	linoleic acid metabolic process
GO:1901625	0.0018	Inf	0.0018	1	1	cellular response to ergosterol
GO:1905608	0.0018	Inf	0.0018	1	1	positive regulation of presynapse assembly
GO:0032501	0.0025	3.1495	12.0112	20	6718	multicellular organismal process
GO:0003095	0.0036	578.2143	0.0036	1	2	pressure natriuresis
GO:0031408	0.0036	578.2143	0.0036	1	2	oxylipin biosynthetic process
GO:1905652	0.0036	578.2143	0.0036	1	2	negative regulation of artery morphogenesis
GO:0019369	0.0037	24.4021	0.0912	2	51	arachidonic acid metabolic process
GO:0046456	0.004	23.4423	0.0948	2	53	icosanoid biosynthetic process
GO:1901568	0.0062	18.6655	0.118	2	66	fatty acid derivative metabolic process
GO:0036101	0.0071	192.7143	0.0072	1	4	leukotriene B4 catabolic process
GO:0051919	0.0071	192.7143	0.0072	1	4	positive regulation of fibrinolysis
GO:0097211	0.0089	144.5268	0.0089	1	5	cellular response to gonadotropin-releasing hormone
GO:1905700	0.0089	144.5268	0.0089	1	5	negative regulation of xenobiotic detoxification by transmembrane export across the plasma membrane

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0050911	0	47.5422	0.2784	8	215	detection of chemical stimulus involved in sensory perception of smell
GO:0009593	0	35.1144	0.3716	8	287	detection of chemical stimulus
GO:0007606	0	33.8781	0.3845	8	297	sensory perception of chemical stimulus
GO:0050906	0	32.0686	0.4052	8	313	detection of stimulus involved in sensory perception
GO:0007186	0	9.7041	1.261	8	974	G protein-coupled receptor signaling pathway
GO:0050877	1e-04	7.6163	1.5782	8	1219	nervous system process
GO:0044335	0.0026	809.9	0.0026	1	2	canonical Wnt signaling pathway involved in neural crest cell differentiation
GO:0009822	0.0039	404.925	0.0039	1	3	alkaloid catabolic process
GO:0036378	0.0052	269.9333	0.0052	1	4	calcitriol biosynthetic process from calciol
GO:0042369	0.0052	269.9333	0.0052	1	4	vitamin D catabolic process
GO:0044107	0.0052	269.9333	0.0052	1	4	cellular alcohol metabolic process
GO:0044278	0.0052	269.9333	0.0052	1	4	cell wall disruption in another organism
GO:0061317	0.0065	202.4375	0.0065	1	5	canonical Wnt signaling pathway involved in cardiac muscle cell fate commitment
GO:0035195	0.0068	8.8029	0.3936	3	304	miRNA-mediated gene silencing
GO:0016441	0.0075	8.459	0.4091	3	316	post-transcriptional gene silencing
GO:0014034	0.0077	161.94	0.0078	1	6	neural crest cell fate commitment
GO:0016098	0.0077	161.94	0.0078	1	6	monoterpenoid metabolic process
GO:0002933	0.009	134.9417	0.0091	1	7	lipid hydroxylation
GO:0045617	0.009	134.9417	0.0091	1	7	negative regulation of keratinocyte differentiation
GO:0046222	0.009	134.9417	0.0091	1	7	aflatoxin metabolic process
GO:0031047	0.009	7.8925	0.4376	3	338	gene silencing by RNA
GO:0055007	0.0093	15.2565	0.1463	2	113	cardiac muscle cell differentiation

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0006335	0	2020.5	0.0947	24	32	DNA replication-dependent chromatin assembly
GO:0006334	0	243.8485	0.3078	26	104	nucleosome assembly
GO:0071824	0	102.6897	0.6215	26	210	protein-DNA complex subunit organization
GO:0032200	0	121.5152	0.4617	24	156	telomere organization
GO:0006338	0	89.3981	0.7014	26	237	chromatin remodeling
GO:0045653	0	1664.3529	0.0533	14	18	negative regulation of megakaryocyte differentiation
GO:0006336	0	369.5359	0.0947	14	32	DNA replication-independent chromatin assembly
GO:0006352	0	60.1251	0.367	14	124	DNA-templated transcription, initiation
GO:0065003	0	13.7923	4.1608	27	1406	protein-containing complex assembly
GO:0045637	0	35.7788	0.5859	14	198	regulation of myeloid cell differentiation
GO:0040029	0	34.3368	0.3936	10	133	regulation of gene expression, epigenetic
GO:0045596	0	11.5176	1.8614	15	629	negative regulation of cell differentiation
GO:0044085	0	6.3643	8.7122	28	2944	cellular component biogenesis
GO:0006996	0	5.8918	10.6417	30	3596	organelle organization
GO:0002520	0	7.7222	2.7048	15	914	immune system development
GO:0030097	0	7.8913	2.4148	14	816	hemopoiesis
GO:2000026	0	5.2884	3.8323	15	1295	regulation of multicellular organismal development
GO:0097659	0	3.7794	9.4372	23	3189	nucleic acid-templated transcription
GO:0002682	0	4.9197	3.7376	14	1263	regulation of immune system process
GO:0034654	1e-04	3.2841	10.5411	23	3562	nucleobase-containing compound biosynthetic process
GO:0048513	5e-04	2.8477	9.6562	20	3263	animal organ development
GO:0065007	9e-04	3.7846	33.3603	43	11273	biological regulation
GO:0009059	0.0011	2.5824	12.6392	23	4271	macromolecule biosynthetic process
GO:0016070	0.0012	2.5603	12.7191	23	4298	RNA metabolic process
GO:0010467	0.0013	3.7979	4.9018	12	2555	gene expression
GO:0048485	0.0019	35.113	0.0651	2	22	sympathetic nervous system development
GO:0008152	0.0022	3.0211	31.6942	41	10710	metabolic process
GO:0046483	0.0023	2.3766	15.9714	26	5397	heterocycle metabolic process
GO:0044249	0.0027	2.3436	15.2375	25	5149	cellular biosynthetic process
GO:0097275	0.003	Inf	0.003	1	1	cellular ammonium homeostasis
GO:0097276	0.003	Inf	0.003	1	1	cellular creatinine homeostasis
GO:0097277	0.003	Inf	0.003	1	1	cellular urea homeostasis
GO:2000763	0.003	Inf	0.003	1	1	positive regulation of transcription from RNA polymerase II promoter involved in norepinephrine biosynthetic process
GO:2000764	0.003	Inf	0.003	1	1	positive regulation of semaphorin-plexin signaling pathway involved in outflow tract morphogenesis
GO:0007631	0.0032	11.0481	0.2959	3	100	feeding behavior
GO:1901360	0.005	2.1997	16.803	26	5678	organic cyclic compound metabolic process
GO:0002032	0.0059	344.0638	0.0059	1	2	desensitization of G protein-coupled receptor signaling pathway by arrestin
GO:0042412	0.0059	344.0638	0.0059	1	2	taurine biosynthetic process
GO:0061032	0.0059	344.0638	0.0059	1	2	visceral serous pericardium development
GO:0061885	0.0059	344.0638	0.0059	1	2	positive regulation of mini excitatory postsynaptic potential
GO:0090663	0.0059	344.0638	0.0059	1	2	galanin-activated signaling pathway
GO:1903929	0.0059	344.0638	0.0059	1	2	primary palate development
GO:0002025	0.0089	172.0213	0.0089	1	3	norepinephrine-epinephrine-mediated vasodilation involved in regulation of systemic arterial blood pressure
GO:0009822	0.0089	172.0213	0.0089	1	3	alkaloid catabolic process
GO:2001260	0.0089	172.0213	0.0089	1	3	regulation of semaphorin-plexin signaling pathway
GO:0021515	0.0096	14.6051	0.148	2	50	cell differentiation in spinal cord

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:1905700	0	372.092	0.0096	2	5	negative regulation of xenobiotic detoxification by transmembrane export across the plasma membrane
GO:2001023	1e-04	279.0517	0.0115	2	6	regulation of response to drug
GO:0098754	1e-04	18.0213	0.2599	4	136	detoxification
GO:0010273	2e-04	111.5793	0.0229	2	12	detoxification of copper ion
GO:0097501	4e-04	85.8143	0.0287	2	15	stress response to metal ion
GO:0046618	6e-04	65.6065	0.0363	2	19	xenobiotic export
GO:0071294	7e-04	58.6933	0.0401	2	21	cellular response to zinc ion
GO:0071280	0.001	50.6803	0.0459	2	24	cellular response to copper ion
GO:1903671	0.001	48.4738	0.0478	2	25	negative regulation of sprouting angiogenesis
GO:0071276	0.0018	35.9466	0.0631	2	33	cellular response to cadmium ion
GO:0021767	0.0019	Inf	0.0019	1	1	mammillary body development
GO:0042668	0.0019	Inf	0.0019	1	1	auditory receptor cell fate determination
GO:0045609	0.0019	Inf	0.0019	1	1	positive regulation of inner ear auditory receptor cell differentiation
GO:0045633	0.0019	Inf	0.0019	1	1	positive regulation of mechanoreceptor differentiation
GO:0061374	0.0019	Inf	0.0019	1	1	mammillothalamic axonal tract development
GO:0061381	0.0019	Inf	0.0019	1	1	cell migration in diencephalon
GO:0043524	0.0022	12.8372	0.2618	3	137	negative regulation of neuron apoptotic process
GO:0006882	0.0023	31.8305	0.0707	2	37	cellular zinc ion homeostasis
GO:0032501	0.0027	2.9764	12.8396	21	6718	multicellular organismal process
GO:0042667	0.0038	539.6	0.0038	1	2	auditory receptor cell fate specification
GO:0061379	0.0038	539.6	0.0038	1	2	inferior colliculus development
GO:0097214	0.0038	539.6	0.0038	1	2	positive regulation of lysosomal membrane permeability
GO:1905652	0.0038	539.6	0.0038	1	2	negative regulation of artery morphogenesis
GO:2000296	0.0038	539.6	0.0038	1	2	negative regulation of hydrogen peroxide catabolic process
GO:2000376	0.0038	539.6	0.0038	1	2	positive regulation of oxygen metabolic process
GO:0001661	0.0057	269.7833	0.0057	1	3	conditioned taste aversion
GO:0007412	0.0057	269.7833	0.0057	1	3	axon target recognition
GO:0010840	0.0057	269.7833	0.0057	1	3	regulation of circadian sleep/wake cycle, wakefulness
GO:0046952	0.0057	269.7833	0.0057	1	3	ketone body catabolic process
GO:0055073	0.0057	269.7833	0.0057	1	3	cadmium ion homeostasis
GO:0009653	0.0064	2.9011	4.952	11	2591	anatomical structure morphogenesis
GO:0043491	0.007	8.4374	0.3937	3	206	protein kinase B signaling
GO:0140115	0.0072	17.1077	0.1281	2	67	export across plasma membrane
GO:0051919	0.0076	179.8444	0.0076	1	4	positive regulation of fibrinolysis
GO:0061030	0.0076	179.8444	0.0076	1	4	epithelial cell differentiation involved in mammary gland alveolus development
GO:0006357	0.0092	2.841	4.4608	10	2334	regulation of transcription by RNA polymerase II
GO:0021764	0.0095	134.875	0.0096	1	5	amygdala development
GO:0021855	0.0095	134.875	0.0096	1	5	hypothalamus cell migration
GO:0036091	0.0095	134.875	0.0096	1	5	positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress
GO:0060120	0.0095	134.875	0.0096	1	5	inner ear receptor cell fate commitment
GO:0097211	0.0095	134.875	0.0096	1	5	cellular response to gonadotropin-releasing hormone

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0048252	0	3601.7778	0.002	2	3	lauric acid metabolic process
GO:0043651	1e-04	224.9028	0.0122	2	18	linoleic acid metabolic process
GO:0046456	6e-04	70.4052	0.0359	2	53	icosanoid biosynthetic process
GO:1901625	7e-04	Inf	7e-04	1	1	cellular response to ergosterol
GO:1905608	7e-04	Inf	7e-04	1	1	positive regulation of presynapse assembly
GO:0003095	0.0014	1620.8	0.0014	1	2	pressure natriuresis
GO:0031408	0.0014	1620.8	0.0014	1	2	oxylipin biosynthetic process
GO:0015908	0.0018	38.93	0.0637	2	94	fatty acid transport
GO:0036101	0.0027	540.2	0.0027	1	4	leukotriene B4 catabolic process
GO:0002933	0.0047	270.05	0.0047	1	7	lipid hydroxylation
GO:0048680	0.0061	202.5125	0.0061	1	9	positive regulation of axon regeneration
GO:0097267	0.0061	202.5125	0.0061	1	9	omega-hydroxylase P450 pathway
GO:0050911	0.0089	16.6886	0.1458	2	215	detection of chemical stimulus involved in sensory perception of smell

Differential Methylation

Parameter Overview

Introduction: Differential Methylation of Sample Groups

Comparisons

P-values

Site Level

Differential Methylation Tables

Region Level

Differential Methylation Tables

GO Enrichment Analysis

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0008210	0	111.788	0.0356	3	34	estrogen metabolic process
GO:0035195	2e-04	16.3108	0.3186	4	304	miRNA-mediated gene silencing
GO:0016441	3e-04	15.6716	0.3312	4	316	post-transcriptional gene silencing
GO:0031047	4e-04	14.6191	0.3543	4	338	gene silencing by RNA
GO:0008209	4e-04	86.2827	0.0283	2	27	androgen metabolic process
GO:1904639	0.001	Inf	0.001	1	1	cellular response to resveratrol
GO:1904728	0.001	Inf	0.001	1	1	positive regulation of replicative senescence
GO:1904827	0.001	Inf	0.001	1	1	negative regulation of hydrogen sulfide biosynthetic process
GO:1904830	0.001	Inf	0.001	1	1	negative regulation of aortic smooth muscle cell differentiation
GO:1905955	0.001	Inf	0.001	1	1	negative regulation of endothelial tube morphogenesis
GO:0042445	0.0013	16.241	0.2243	3	214	hormone metabolic process
GO:0032705	0.0021	1012.625	0.0021	1	2	negative regulation of interleukin-21 production
GO:0033241	0.0021	1012.625	0.0021	1	2	regulation of cellular amine catabolic process
GO:0097323	0.0021	1012.625	0.0021	1	2	B cell adhesion
GO:1900082	0.0021	1012.625	0.0021	1	2	negative regulation of arginine catabolic process
GO:1901846	0.0021	1012.625	0.0021	1	2	positive regulation of cell communication by electrical coupling involved in cardiac conduction
GO:1904695	0.0021	1012.625	0.0021	1	2	positive regulation of vascular associated smooth muscle contraction
GO:1904762	0.0021	1012.625	0.0021	1	2	positive regulation of myofibroblast differentiation
GO:0009822	0.0031	506.2812	0.0031	1	3	alkaloid catabolic process
GO:0031048	0.0031	506.2812	0.0031	1	3	heterochromatin assembly by small RNA
GO:0060940	0.0031	506.2812	0.0031	1	3	epithelial to mesenchymal transition involved in cardiac fibroblast development
GO:0106016	0.0031	506.2812	0.0031	1	3	positive regulation of inflammatory response to wounding
GO:1900039	0.0031	506.2812	0.0031	1	3	positive regulation of cellular response to hypoxia
GO:1901670	0.0031	506.2812	0.0031	1	3	negative regulation of superoxide dismutase activity
GO:0042102	0.0042	23.6073	0.0975	2	93	positive regulation of T cell proliferation
GO:0000821	0.0042	337.5	0.0042	1	4	regulation of arginine metabolic process
GO:0036378	0.0042	337.5	0.0042	1	4	calcitriol biosynthetic process from calciol
GO:0042369	0.0042	337.5	0.0042	1	4	vitamin D catabolic process
GO:0044107	0.0042	337.5	0.0042	1	4	cellular alcohol metabolic process
GO:0060936	0.0042	337.5	0.0042	1	4	cardiac fibroblast cell development
GO:0060938	0.0042	337.5	0.0042	1	4	epicardium-derived cardiac fibroblast cell differentiation
GO:1903766	0.0042	337.5	0.0042	1	4	positive regulation of potassium ion export across plasma membrane
GO:0006805	0.0045	22.6077	0.1017	2	97	xenobiotic metabolic process
GO:0035634	0.0052	253.1094	0.0052	1	5	response to stilbenoid
GO:1902731	0.0052	253.1094	0.0052	1	5	negative regulation of chondrocyte proliferation
GO:0016098	0.0063	202.475	0.0063	1	6	monoterpenoid metabolic process
GO:0033239	0.0063	202.475	0.0063	1	6	negative regulation of cellular amine metabolic process
GO:0045590	0.0063	202.475	0.0063	1	6	negative regulation of regulatory T cell differentiation
GO:1900408	0.0063	202.475	0.0063	1	6	negative regulation of cellular response to oxidative stress

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0002819	0	25.1065	0.256	5	173	regulation of adaptive immune response
GO:2000316	0	115.5429	0.034	3	23	regulation of T-helper 17 type immune response
GO:0043207	0	8.5927	1.854	10	1253	response to external biotic stimulus
GO:0044419	0	7.6084	2.0715	10	1400	biological process involved in interspecies interaction between organisms
GO:0009617	0	10.9687	0.8774	7	593	response to bacterium
GO:0045622	0	72.1607	0.0518	3	35	regulation of T-helper cell differentiation
GO:2000514	1e-04	41.9247	0.0858	3	58	regulation of CD4-positive, alpha-beta T cell activation
GO:0032819	1e-04	183.9545	0.0148	2	10	positive regulation of natural killer cell proliferation
GO:0046635	1e-04	39.0726	0.0917	3	62	positive regulation of alpha-beta T cell activation
GO:0046637	1e-04	39.0726	0.0917	3	62	regulation of alpha-beta T cell differentiation
GO:0002294	1e-04	38.419	0.0932	3	63	CD4-positive, alpha-beta T cell differentiation involved in immune response
GO:0002287	1e-04	37.7869	0.0947	3	64	alpha-beta T cell activation involved in immune response
GO:0050865	1e-04	9.2388	0.8434	6	570	regulation of cell activation
GO:0002292	2e-04	33.8824	0.1051	3	71	T cell differentiation involved in immune response
GO:0098586	2e-04	31.5519	0.1125	3	76	cellular response to virus
GO:1903131	3e-04	10.4726	0.5948	5	402	mononuclear cell differentiation
GO:0032103	3e-04	10.3921	0.5993	5	405	positive regulation of response to external stimulus
GO:0070663	4e-04	13.7621	0.3492	4	236	regulation of leukocyte proliferation
GO:0002824	4e-04	23.9583	0.1465	3	99	positive regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
GO:0140546	6e-04	12.2585	0.3906	4	264	defense response to symbiont
GO:0050868	6e-04	21.2804	0.1642	3	111	negative regulation of T cell activation
GO:0050778	6e-04	8.7859	0.7043	5	476	positive regulation of immune response
GO:0031349	6e-04	12.2107	0.3921	4	265	positive regulation of defense response
GO:1902105	6e-04	12.1634	0.3936	4	266	regulation of leukocyte differentiation
GO:0042104	6e-04	63.9249	0.037	2	25	positive regulation of activated T cell proliferation
GO:0001916	7e-04	61.2576	0.0385	2	26	positive regulation of T cell mediated cytotoxicity
GO:0043372	8e-04	54.4411	0.0429	2	29	positive regulation of CD4-positive, alpha-beta T cell differentiation
GO:1901223	8e-04	54.4411	0.0429	2	29	negative regulation of NIK/NF-kappaB signaling
GO:0002230	9e-04	52.4935	0.0444	2	30	positive regulation of defense response to virus by host
GO:0035195	0.001	10.5973	0.4498	4	304	miRNA-mediated gene silencing
GO:0032946	0.001	17.6549	0.1968	3	133	positive regulation of mononuclear cell proliferation
GO:0046640	0.001	48.9879	0.0473	2	32	regulation of alpha-beta T cell proliferation
GO:0016441	0.0011	10.1821	0.4676	4	316	post-transcriptional gene silencing
GO:0032814	0.0013	43.2139	0.0533	2	36	regulation of natural killer cell activation
GO:0031047	0.0014	9.4982	0.5001	4	338	gene silencing by RNA
GO:0001815	0.0015	Inf	0.0015	1	1	positive regulation of antibody-dependent cellular cytotoxicity
GO:0002737	0.0015	Inf	0.0015	1	1	negative regulation of plasmacytoid dendritic cell cytokine production
GO:1904639	0.0015	Inf	0.0015	1	1	cellular response to resveratrol
GO:1904728	0.0015	Inf	0.0015	1	1	positive regulation of replicative senescence

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0032103	0	11.3097	0.6742	6	405	positive regulation of response to external stimulus
GO:0071357	1e-04	38.8005	0.0916	3	55	cellular response to type I interferon
GO:0001959	1e-04	18.9837	0.2514	4	151	regulation of cytokine-mediated signaling pathway
GO:2000318	2e-04	117.6873	0.0216	2	13	positive regulation of T-helper 17 type immune response
GO:0045088	4e-04	13.4308	0.3512	4	211	regulation of innate immune response
GO:0032479	5e-04	22.8764	0.1515	3	91	regulation of type I interferon production
GO:0060339	5e-04	71.8889	0.0333	2	20	negative regulation of type I interferon-mediated signaling pathway
GO:0043207	7e-04	5.0553	2.0858	8	1253	response to external biotic stimulus
GO:1900017	8e-04	53.8967	0.0433	2	26	positive regulation of cytokine production involved in inflammatory response
GO:0031349	9e-04	10.616	0.4411	4	265	positive regulation of defense response
GO:0034391	0.001	49.7446	0.0466	2	28	regulation of smooth muscle cell apoptotic process
GO:0071480	0.001	49.7446	0.0466	2	28	cellular response to gamma radiation
GO:0002460	0.001	10.3736	0.4511	4	271	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
GO:0090322	0.0013	43.1013	0.0533	2	32	regulation of superoxide metabolic process
GO:0070588	0.0013	9.537	0.4894	4	294	calcium ion transmembrane transport
GO:0010837	0.0014	41.7084	0.0549	2	33	regulation of keratinocyte proliferation
GO:0044419	0.0015	4.477	2.3305	8	1400	biological process involved in interspecies interaction between organisms
GO:0035195	0.0015	9.2133	0.506	4	304	miRNA-mediated gene silencing
GO:0010212	0.0015	14.8685	0.2297	3	138	response to ionizing radiation
GO:0010613	0.0016	38.0212	0.0599	2	36	positive regulation of cardiac muscle hypertrophy
GO:0001879	0.0017	Inf	0.0017	1	1	detection of yeast
GO:0002383	0.0017	Inf	0.0017	1	1	immune response in brain or nervous system
GO:0031583	0.0017	Inf	0.0017	1	1	phospholipase D-activating G protein-coupled receptor signaling pathway
GO:0032491	0.0017	Inf	0.0017	1	1	detection of molecule of fungal origin
GO:0042313	0.0017	Inf	0.0017	1	1	protein kinase C deactivation
GO:0043179	0.0017	Inf	0.0017	1	1	rhythmic excitation
GO:0097281	0.0017	Inf	0.0017	1	1	immune complex formation
GO:1904639	0.0017	Inf	0.0017	1	1	cellular response to resveratrol
GO:1904728	0.0017	Inf	0.0017	1	1	positive regulation of replicative senescence
GO:1904827	0.0017	Inf	0.0017	1	1	negative regulation of hydrogen sulfide biosynthetic process
GO:1904830	0.0017	Inf	0.0017	1	1	negative regulation of aortic smooth muscle cell differentiation
GO:1905955	0.0017	Inf	0.0017	1	1	negative regulation of endothelial tube morphogenesis
GO:0016441	0.0017	8.8523	0.526	4	316	post-transcriptional gene silencing
GO:0042554	0.0019	34.9319	0.0649	2	39	superoxide anion generation
GO:0045429	0.0019	34.9319	0.0649	2	39	positive regulation of nitric oxide biosynthetic process
GO:0034767	0.0019	13.6446	0.2497	3	150	positive regulation of ion transmembrane transport
GO:1904707	0.002	34.0105	0.0666	2	40	positive regulation of vascular associated smooth muscle cell proliferation
GO:0031047	0.0022	8.2577	0.5626	4	338	gene silencing by RNA
GO:0045933	0.0023	31.5161	0.0716	2	43	positive regulation of muscle contraction

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0048245	1e-04	239.9111	0.0115	2	17	eosinophil chemotaxis
GO:0050850	2e-04	119.8444	0.0217	2	32	positive regulation of calcium-mediated signaling
GO:0032733	3e-04	99.8333	0.0258	2	38	positive regulation of interleukin-10 production
GO:0051345	4e-04	16.4236	0.3723	4	549	positive regulation of hydrolase activity
GO:0048247	6e-04	67.74	0.0373	2	55	lymphocyte chemotaxis
GO:0001879	7e-04	Inf	7e-04	1	1	detection of yeast
GO:0032491	7e-04	Inf	7e-04	1	1	detection of molecule of fungal origin
GO:1905183	7e-04	Inf	7e-04	1	1	negative regulation of protein serine/threonine phosphatase activity
GO:0032731	7e-04	61.8812	0.0407	2	60	positive regulation of interleukin-1 beta production
GO:0002548	8e-04	58.827	0.0427	2	63	monocyte chemotaxis
GO:0043207	8e-04	9.99	0.8498	5	1253	response to external biotic stimulus
GO:0050795	9e-04	54.3535	0.0461	2	68	regulation of behavior
GO:0032729	0.001	51.9807	0.0482	2	71	positive regulation of interferon-gamma production
GO:0030500	0.0012	47.8044	0.0522	2	77	regulation of bone mineralization
GO:0070098	0.0013	45.3727	0.0549	2	81	chemokine-mediated signaling pathway
GO:0032461	0.0014	1620.8	0.0014	1	2	positive regulation of protein oligomerization
GO:1905184	0.0014	1620.8	0.0014	1	2	positive regulation of protein serine/threonine phosphatase activity
GO:0044419	0.0014	8.8495	0.9494	5	1400	biological process involved in interspecies interaction between organisms
GO:1990868	0.0016	41.1801	0.0604	2	89	response to chemokine
GO:0030593	0.0018	38.0969	0.0651	2	96	neutrophil chemotaxis
GO:0110149	0.0018	38.0969	0.0651	2	96	regulation of biomineralization
GO:0032760	0.0019	37.2986	0.0665	2	98	positive regulation of tumor necrosis factor production
GO:0006952	0.0019	8.2078	1.0166	5	1499	defense response
GO:0060763	0.002	810.35	0.002	1	3	mammary duct terminal end bud growth
GO:0071226	0.002	810.35	0.002	1	3	cellular response to molecule of fungal origin
GO:2000503	0.002	810.35	0.002	1	3	positive regulation of natural killer cell chemotaxis
GO:0071347	0.002	36.1616	0.0685	2	101	cellular response to interleukin-1
GO:0045087	0.0023	15.4046	0.2845	3	506	innate immune response
GO:0071346	0.0024	33.4413	0.0739	2	109	cellular response to interferon-gamma
GO:0032652	0.0027	31.3743	0.0787	2	116	regulation of interleukin-1 production
GO:0002752	0.0027	540.2	0.0027	1	4	cell surface pattern recognition receptor signaling pathway
GO:0007186	0.003	8.9773	0.6605	4	974	G protein-coupled receptor signaling pathway
GO:0043308	0.0034	405.125	0.0034	1	5	eosinophil degranulation
GO:0097530	0.0039	25.8792	0.0949	2	140	granulocyte migration
GO:0032020	0.0041	324.08	0.0041	1	6	ISG15-protein conjugation
GO:0043307	0.0041	324.08	0.0041	1	6	eosinophil activation
GO:0051712	0.0041	324.08	0.0041	1	6	positive regulation of killing of cells of another organism
GO:0008360	0.0041	24.9666	0.0983	2	145	regulation of cell shape
GO:0030335	0.0044	11.4506	0.3506	3	517	positive regulation of cell migration