RnBeads: Example 2

Option	Value
analyze.sites	yes
differential.report.sites	yes
region.types	tiling, genes, promoters, cpgislands
differential.permutations	0
differential.comparison.columns	tissue, blood_lineage, differentiation_level_blood, differentiation_level_skin, cmp_blood_CLP_CMP
differential.comparison.columns.all.pairwise	blood_lineage, differentiation_level_blood, differentiation_level_skin
columns.pairing	default
differential.site.test.method	limma
differential.variability	no
differential.variability.method	diffVar
covariate.adjustment.columns	default
differential.adjustment.sva	yes
differential.adjustment.celltype	yes
differential.enrichment.go	yes
differential.enrichment.lola	no
differential.enrichment.lola.dbs	${LOLACore}

	Rank Cutoff
blood vs. skin (based on tissue)	136763
lymphoid vs. multi (based on blood_lineage)	492830
lymphoid vs. myeloid (based on blood_lineage)	519017
multi vs. myeloid (based on blood_lineage)	528486
differentiated vs. progenitor (based on differentiation_level_blood)	457021
differentiated vs. stemCell (based on differentiation_level_blood)	594371
progenitor vs. stemCell (based on differentiation_level_blood)	540603
differentiated vs. progenitor (based on differentiation_level_skin)	4838
differentiated vs. stemCell (based on differentiation_level_skin)	549082
progenitor vs. stemCell (based on differentiation_level_skin)	507161
CLP vs. CMP (based on cmp_blood_CLP_CMP)	616010

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
blood vs. skin (based on tissue)	11848	2604	3178	722
lymphoid vs. multi (based on blood_lineage)	20549	924	1326	576
lymphoid vs. myeloid (based on blood_lineage)	3824	269	259	142
multi vs. myeloid (based on blood_lineage)	24432	1929	3492	1402
differentiated vs. progenitor (based on differentiation_level_blood)	1103	165	231	148
differentiated vs. stemCell (based on differentiation_level_blood)	34831	6192	5886	2720
progenitor vs. stemCell (based on differentiation_level_blood)	32326	3577	4475	1796
differentiated vs. progenitor (based on differentiation_level_skin)	17090	1585	1850	1200
differentiated vs. stemCell (based on differentiation_level_skin)	12389	1056	1228	668
progenitor vs. stemCell (based on differentiation_level_skin)	11766	1112	1225	687
CLP vs. CMP (based on cmp_blood_CLP_CMP)	22567	2511	2787	1771

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
blood vs. skin (based on tissue)	csv	csv	csv	csv
lymphoid vs. multi (based on blood_lineage)	csv	csv	csv	csv
lymphoid vs. myeloid (based on blood_lineage)	csv	csv	csv	csv
multi vs. myeloid (based on blood_lineage)	csv	csv	csv	csv
differentiated vs. progenitor (based on differentiation_level_blood)	csv	csv	csv	csv
differentiated vs. stemCell (based on differentiation_level_blood)	csv	csv	csv	csv
progenitor vs. stemCell (based on differentiation_level_blood)	csv	csv	csv	csv
differentiated vs. progenitor (based on differentiation_level_skin)	csv	csv	csv	csv
differentiated vs. stemCell (based on differentiation_level_skin)	csv	csv	csv	csv
progenitor vs. stemCell (based on differentiation_level_skin)	csv	csv	csv	csv
CLP vs. CMP (based on cmp_blood_CLP_CMP)	csv	csv	csv	csv

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 5

Wordclouds for GO enrichment terms.

comparison
Hypermethylation/hypomethylation
ontology
regions
differential methylation measure

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0032946	6e-04	11.6298	0.3818	4	117	positive regulation of mononuclear cell proliferation
GO:0051251	6e-04	8.096	0.6885	5	211	positive regulation of lymphocyte activation
GO:0022407	9e-04	5.8745	1.1454	6	351	regulation of cell-cell adhesion
GO:0050867	0.0016	6.4939	0.8517	5	261	positive regulation of cell activation
GO:0002376	0.0016	2.8717	5.9391	14	1820	immune system process
GO:0033599	0.0017	37.3318	0.062	2	19	regulation of mammary gland epithelial cell proliferation
GO:1903039	0.0018	8.4559	0.5189	4	159	positive regulation of leukocyte cell-cell adhesion
GO:0042110	0.002	5.023	1.3314	6	408	T cell activation
GO:0060749	0.0021	33.3979	0.0685	2	21	mammary gland alveolus development
GO:1903708	0.0021	8.0368	0.545	4	167	positive regulation of hemopoiesis
GO:0002694	0.0022	4.9348	1.3543	6	415	regulation of leukocyte activation
GO:0042102	0.0023	12.5677	0.2611	3	80	positive regulation of T cell proliferation
GO:0060216	0.0025	30.2133	0.0751	2	23	definitive hemopoiesis
GO:0006958	0.003	27.5826	0.0816	2	25	complement activation, classical pathway
GO:0030878	0.0032	26.4317	0.0848	2	26	thyroid gland development
GO:0035702	0.0033	Inf	0.0033	1	1	monocyte homeostasis
GO:0097052	0.0033	Inf	0.0033	1	1	L-kynurenine metabolic process
GO:1905221	0.0033	Inf	0.0033	1	1	positive regulation of platelet formation
GO:1990959	0.0033	Inf	0.0033	1	1	eosinophil homeostasis
GO:1990960	0.0033	Inf	0.0033	1	1	basophil homeostasis
GO:0050670	0.0035	6.9947	0.6233	4	191	regulation of lymphocyte proliferation
GO:0070663	0.0041	6.6696	0.6527	4	200	regulation of leukocyte proliferation
GO:0002460	0.0046	6.4368	0.6755	4	207	adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
GO:0043588	0.0059	5.9881	0.7244	4	222	skin development
GO:0001817	0.0064	3.9397	1.6806	6	515	regulation of cytokine production
GO:0001869	0.0065	311.4118	0.0065	1	2	negative regulation of complement activation, lectin pathway
GO:0060574	0.0065	311.4118	0.0065	1	2	intestinal epithelial cell maturation
GO:0060764	0.0065	311.4118	0.0065	1	2	cell-cell signaling involved in mammary gland development
GO:0090271	0.0065	311.4118	0.0065	1	2	positive regulation of fibroblast growth factor production
GO:0097535	0.0065	311.4118	0.0065	1	2	lymphoid lineage cell migration into thymus
GO:0097536	0.0065	311.4118	0.0065	1	2	thymus epithelium morphogenesis
GO:1902232	0.0065	311.4118	0.0065	1	2	regulation of positive thymic T cell selection
GO:1903860	0.0065	311.4118	0.0065	1	2	negative regulation of dendrite extension
GO:2000813	0.0065	311.4118	0.0065	1	2	negative regulation of barbed-end actin filament capping
GO:0045580	0.0066	8.4689	0.3818	3	117	regulation of T cell differentiation
GO:0051142	0.0098	155.6961	0.0098	1	3	positive regulation of NK T cell proliferation
GO:0060435	0.0098	155.6961	0.0098	1	3	bronchiole development

LOLA Enrichment Analysis

No LOLA Enrichment Analysis was conducted

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0060481	1e-04	168.9574	0.0184	2	6	lobar bronchus epithelium development
GO:0045346	5e-04	75.0686	0.0338	2	11	regulation of MHC class II biosynthetic process
GO:0060433	6e-04	67.5574	0.0369	2	12	bronchus development
GO:0048646	6e-04	3.9647	2.9981	10	975	anatomical structure formation involved in morphogenesis
GO:0060395	8e-04	18.111	0.1845	3	60	SMAD protein signal transduction
GO:0002227	9e-04	51.9574	0.0461	2	15	innate immune response in mucosa
GO:0071621	0.0017	13.9354	0.2368	3	77	granulocyte chemotaxis
GO:0045638	0.0021	12.8853	0.2552	3	83	negative regulation of myeloid cell differentiation
GO:0002688	0.0022	12.7254	0.2583	3	84	regulation of leukocyte chemotaxis
GO:0002251	0.0022	32.1479	0.0707	2	23	organ or tissue specific immune response
GO:0060143	0.0022	32.1479	0.0707	2	23	positive regulation of syncytium formation by plasma membrane fusion
GO:0000470	0.0024	30.6847	0.0738	2	24	maturation of LSU-rRNA
GO:0090022	0.0027	29.3488	0.0769	2	25	regulation of neutrophil chemotaxis
GO:0045937	0.0028	3.4372	3.0289	9	985	positive regulation of phosphate metabolic process
GO:0007275	0.0028	2.3415	13.4654	23	4379	multicellular organism development
GO:2001237	0.0028	11.5757	0.2829	3	92	negative regulation of extrinsic apoptotic signaling pathway
GO:0032733	0.0029	28.1241	0.0799	2	26	positive regulation of interleukin-10 production
GO:0002732	0.0031	Inf	0.0031	1	1	positive regulation of dendritic cell cytokine production
GO:0002807	0.0031	Inf	0.0031	1	1	positive regulation of antimicrobial peptide biosynthetic process
GO:0002808	0.0031	Inf	0.0031	1	1	regulation of antibacterial peptide biosynthetic process
GO:0006965	0.0031	Inf	0.0031	1	1	positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria
GO:0032498	0.0031	Inf	0.0031	1	1	detection of muramyl dipeptide
GO:0070351	0.0031	Inf	0.0031	1	1	negative regulation of white fat cell proliferation
GO:0042832	0.0031	26.9974	0.083	2	27	defense response to protozoan
GO:0061844	0.0033	25.9574	0.0861	2	28	antimicrobial humoral immune response mediated by antimicrobial peptide
GO:0000460	0.0038	24.1003	0.0922	2	30	maturation of 5.8S rRNA
GO:0002823	0.0038	24.1003	0.0922	2	30	negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
GO:0002714	0.0041	23.2678	0.0953	2	31	positive regulation of B cell mediated immunity
GO:0050864	0.0046	9.7088	0.3352	3	109	regulation of B cell activation
GO:0042092	0.0049	21.0824	0.1045	2	34	type 2 immune response
GO:0002683	0.0057	4.7654	1.1531	5	375	negative regulation of immune system process
GO:0007166	0.0059	2.542	6.1162	13	1989	cell surface receptor signaling pathway
GO:0006597	0.0061	330.9375	0.0061	1	2	spermine biosynthetic process
GO:0032701	0.0061	330.9375	0.0061	1	2	negative regulation of interleukin-18 production
GO:0035419	0.0061	330.9375	0.0061	1	2	activation of MAPK activity involved in innate immune response
GO:0060574	0.0061	330.9375	0.0061	1	2	intestinal epithelial cell maturation
GO:0060764	0.0061	330.9375	0.0061	1	2	cell-cell signaling involved in mammary gland development
GO:1902523	0.0061	330.9375	0.0061	1	2	positive regulation of protein K63-linked ubiquitination
GO:2000363	0.0061	330.9375	0.0061	1	2	positive regulation of prostaglandin-E synthase activity
GO:2000424	0.0061	330.9375	0.0061	1	2	positive regulation of eosinophil chemotaxis
GO:0042088	0.0064	18.2277	0.1199	2	39	T-helper 1 type immune response
GO:0002889	0.0074	16.8574	0.1291	2	42	regulation of immunoglobulin mediated immune response
GO:0042981	0.0075	2.7631	4.1789	10	1359	regulation of apoptotic process
GO:0048706	0.0078	7.9661	0.4059	3	132	embryonic skeletal system development
GO:0043954	0.0081	16.0527	0.1353	2	44	cellular component maintenance
GO:0097529	0.0088	7.6092	0.4243	3	138	myeloid leukocyte migration
GO:0002381	0.0088	15.3211	0.1414	2	46	immunoglobulin production involved in immunoglobulin mediated immune response
GO:0010862	0.0088	15.3211	0.1414	2	46	positive regulation of pathway-restricted SMAD protein phosphorylation
GO:0000448	0.0092	165.4583	0.0092	1	3	cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0002296	0.0092	165.4583	0.0092	1	3	T-helper 1 cell lineage commitment
GO:0002784	0.0092	165.4583	0.0092	1	3	regulation of antimicrobial peptide production
GO:0002803	0.0092	165.4583	0.0092	1	3	positive regulation of antibacterial peptide production
GO:0002925	0.0092	165.4583	0.0092	1	3	positive regulation of humoral immune response mediated by circulating immunoglobulin
GO:0035993	0.0092	165.4583	0.0092	1	3	deltoid tuberosity development
GO:0051835	0.0092	165.4583	0.0092	1	3	positive regulation of synapse structural plasticity
GO:0060435	0.0092	165.4583	0.0092	1	3	bronchiole development
GO:0060585	0.0092	165.4583	0.0092	1	3	positive regulation of prostaglandin-endoperoxide synthase activity
GO:1903660	0.0092	165.4583	0.0092	1	3	negative regulation of complement-dependent cytotoxicity
GO:0048598	0.0099	3.5859	1.8481	6	601	embryonic morphogenesis
GO:0032722	0.0099	14.3404	0.1507	2	49	positive regulation of chemokine production

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0002823	0	51.9083	0.096	4	30	negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
GO:0032722	0	29.9556	0.1568	4	49	positive regulation of chemokine production
GO:0002251	1e-04	49.575	0.0736	3	23	organ or tissue specific immune response
GO:0032760	1e-04	21.3725	0.2144	4	67	positive regulation of tumor necrosis factor production
GO:0031348	1e-04	11.557	0.4897	5	153	negative regulation of defense response
GO:0002707	2e-04	33.0292	0.1056	3	33	negative regulation of lymphocyte mediated immunity
GO:0042088	3e-04	27.5139	0.1248	3	39	T-helper 1 type immune response
GO:0050715	4e-04	13.0395	0.3425	4	107	positive regulation of cytokine secretion
GO:0043950	4e-04	81	0.032	2	10	positive regulation of cAMP-mediated signaling
GO:1903555	5e-04	11.9848	0.3713	4	116	regulation of tumor necrosis factor superfamily cytokine production
GO:0002862	5e-04	71.9955	0.0352	2	11	negative regulation of inflammatory response to antigenic stimulus
GO:0045346	5e-04	71.9955	0.0352	2	11	regulation of MHC class II biosynthetic process
GO:0002674	6e-04	64.7918	0.0384	2	12	negative regulation of acute inflammatory response
GO:0002819	7e-04	10.8167	0.4097	4	128	regulation of adaptive immune response
GO:0032103	9e-04	7.4638	0.7457	5	233	positive regulation of response to external stimulus
GO:0097529	0.001	10.0032	0.4417	4	138	myeloid leukocyte migration
GO:0002227	0.001	49.8305	0.048	2	15	innate immune response in mucosa
GO:0050727	0.0011	7.0257	0.7905	5	247	regulation of inflammatory response
GO:1900424	0.0012	46.2682	0.0512	2	16	regulation of defense response to bacterium
GO:0032102	0.0012	6.9383	0.8001	5	250	negative regulation of response to external stimulus
GO:0042742	0.0014	9.0713	0.4863	4	158	defense response to bacterium
GO:0050867	0.0014	6.6355	0.8353	5	261	positive regulation of cell activation
GO:0002703	0.0015	8.8085	0.4993	4	156	regulation of leukocyte mediated immunity
GO:0022603	0.0016	3.7389	2.7844	9	870	regulation of anatomical structure morphogenesis
GO:0032703	0.0017	38.096	0.0608	2	19	negative regulation of interleukin-2 production
GO:0035025	0.0017	38.096	0.0608	2	19	positive regulation of Rho protein signal transduction
GO:0002702	0.0017	13.9199	0.2368	3	74	positive regulation of production of molecular mediator of immune response
GO:0009607	0.0018	4.4906	1.7697	7	574	response to biotic stimulus
GO:0043032	0.0018	35.9773	0.064	2	20	positive regulation of macrophage activation
GO:1990266	0.0018	13.5368	0.2432	3	76	neutrophil migration
GO:0002367	0.0019	13.353	0.2464	3	77	cytokine production involved in immune response
GO:0071621	0.0019	13.353	0.2464	3	77	granulocyte chemotaxis
GO:0007596	0.0019	8.2595	0.5313	4	166	blood coagulation
GO:0002456	0.0021	13	0.2528	3	79	T cell mediated immunity
GO:0002286	0.0021	12.8304	0.256	3	80	T cell activation involved in immune response
GO:0042102	0.0021	12.8304	0.256	3	80	positive regulation of T cell proliferation
GO:0044259	0.0021	12.8304	0.256	3	80	multicellular organismal macromolecule metabolic process
GO:0045638	0.0024	12.3469	0.2656	3	83	negative regulation of myeloid cell differentiation
GO:0031294	0.0024	30.8319	0.0736	2	23	lymphocyte costimulation
GO:0060143	0.0024	30.8319	0.0736	2	23	positive regulation of syncytium formation by plasma membrane fusion
GO:0002688	0.0025	12.1937	0.2688	3	84	regulation of leukocyte chemotaxis
GO:2000026	0.0025	2.8338	5.5177	13	1724	regulation of multicellular organismal development
GO:0051149	0.0027	11.756	0.2784	3	87	positive regulation of muscle cell differentiation
GO:0061061	0.0027	4.1312	1.9075	7	596	muscle structure development
GO:0050878	0.0028	5.685	0.9698	5	303	regulation of body fluid levels
GO:0048869	0.0028	2.3588	11.701	21	3656	cellular developmental process
GO:0090022	0.0029	28.1473	0.08	2	25	regulation of neutrophil chemotaxis
GO:0042089	0.0031	11.2188	0.2912	3	91	cytokine biosynthetic process
GO:0032733	0.0031	26.9728	0.0832	2	26	positive regulation of interleukin-10 production
GO:2001237	0.0032	11.092	0.2944	3	92	negative regulation of extrinsic apoptotic signaling pathway
GO:0002519	0.0032	Inf	0.0032	1	1	natural killer cell tolerance induction
GO:0002652	0.0032	Inf	0.0032	1	1	regulation of tolerance induction dependent upon immune response
GO:0002732	0.0032	Inf	0.0032	1	1	positive regulation of dendritic cell cytokine production
GO:0002807	0.0032	Inf	0.0032	1	1	positive regulation of antimicrobial peptide biosynthetic process
GO:0002808	0.0032	Inf	0.0032	1	1	regulation of antibacterial peptide biosynthetic process
GO:0006965	0.0032	Inf	0.0032	1	1	positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria
GO:0016108	0.0032	Inf	0.0032	1	1	tetraterpenoid metabolic process
GO:0016121	0.0032	Inf	0.0032	1	1	carotene catabolic process
GO:0016122	0.0032	Inf	0.0032	1	1	xanthophyll metabolic process
GO:0032498	0.0032	Inf	0.0032	1	1	detection of muramyl dipeptide
GO:0032712	0.0032	Inf	0.0032	1	1	negative regulation of interleukin-3 production
GO:0034760	0.0032	Inf	0.0032	1	1	negative regulation of iron ion transmembrane transport
GO:0042694	0.0032	Inf	0.0032	1	1	muscle cell fate specification
GO:0046005	0.0032	Inf	0.0032	1	1	positive regulation of circadian sleep/wake cycle, REM sleep
GO:0070351	0.0032	Inf	0.0032	1	1	negative regulation of white fat cell proliferation
GO:0071656	0.0032	Inf	0.0032	1	1	negative regulation of granulocyte colony-stimulating factor production
GO:0032967	0.0033	25.8922	0.0864	2	27	positive regulation of collagen biosynthetic process
GO:0042832	0.0033	25.8922	0.0864	2	27	defense response to protozoan
GO:0044253	0.0033	25.8922	0.0864	2	27	positive regulation of multicellular organismal metabolic process
GO:0002521	0.0034	4.5213	1.4754	6	461	leukocyte differentiation
GO:0001894	0.0035	6.9925	0.6241	4	195	tissue homeostasis
GO:0001773	0.0036	24.8948	0.0896	2	28	myeloid dendritic cell activation
GO:0032689	0.0036	24.8948	0.0896	2	28	negative regulation of interferon-gamma production
GO:0061844	0.0036	24.8948	0.0896	2	28	antimicrobial humoral immune response mediated by antimicrobial peptide
GO:1904019	0.0037	10.4987	0.3104	3	97	epithelial cell apoptotic process
GO:0002698	0.0037	10.4967	0.3107	3	99	negative regulation of immune effector process
GO:0008284	0.0039	3.5079	2.586	8	808	positive regulation of cell proliferation
GO:0060326	0.0041	6.674	0.6529	4	204	cell chemotaxis
GO:0001906	0.0042	9.9653	0.3265	3	102	cell killing
GO:0051240	0.0043	2.8677	4.5128	11	1465	positive regulation of multicellular organismal process
GO:0002714	0.0044	22.3153	0.0992	2	31	positive regulation of B cell mediated immunity
GO:0032496	0.0046	6.4455	0.6753	4	211	response to lipopolysaccharide
GO:0032732	0.0047	21.5701	0.1024	2	32	positive regulation of interleukin-1 production
GO:1903038	0.0047	9.5758	0.3393	3	106	negative regulation of leukocyte cell-cell adhesion
GO:0002520	0.0049	3.3658	2.6884	8	840	immune system development
GO:0019835	0.005	20.8729	0.1056	2	33	cytolysis
GO:0042092	0.0053	20.2194	0.1088	2	34	type 2 immune response
GO:0030225	0.0056	19.6054	0.112	2	35	macrophage differentiation
GO:0051241	0.0057	3.046	3.3701	9	1053	negative regulation of multicellular organismal process
GO:0002684	0.0058	3.5791	2.1859	7	683	positive regulation of immune system process
GO:0051707	0.0059	4.0289	1.6568	6	549	response to other organism
GO:0032757	0.0059	19.0276	0.1152	2	36	positive regulation of interleukin-8 production
GO:0032946	0.0062	8.6458	0.3745	3	117	positive regulation of mononuclear cell proliferation
GO:0001808	0.0064	317.66	0.0064	1	2	negative regulation of type IV hypersensitivity
GO:0002752	0.0064	317.66	0.0064	1	2	cell surface pattern recognition receptor signaling pathway
GO:0002859	0.0064	317.66	0.0064	1	2	negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target
GO:0002879	0.0064	317.66	0.0064	1	2	positive regulation of acute inflammatory response to non-antigenic stimulus
GO:0010841	0.0064	317.66	0.0064	1	2	positive regulation of circadian sleep/wake cycle, wakefulness
GO:0032701	0.0064	317.66	0.0064	1	2	negative regulation of interleukin-18 production
GO:0035419	0.0064	317.66	0.0064	1	2	activation of MAPK activity involved in innate immune response
GO:0042214	0.0064	317.66	0.0064	1	2	terpene metabolic process
GO:0050428	0.0064	317.66	0.0064	1	2	3'-phosphoadenosine 5'-phosphosulfate biosynthetic process
GO:0071594	0.0064	317.66	0.0064	1	2	thymocyte aggregation
GO:1902173	0.0064	317.66	0.0064	1	2	negative regulation of keratinocyte apoptotic process
GO:1902523	0.0064	317.66	0.0064	1	2	positive regulation of protein K63-linked ubiquitination
GO:2000363	0.0064	317.66	0.0064	1	2	positive regulation of prostaglandin-E synthase activity
GO:2000424	0.0064	317.66	0.0064	1	2	positive regulation of eosinophil chemotaxis
GO:2000521	0.0064	317.66	0.0064	1	2	negative regulation of immunological synapse formation
GO:2001189	0.0064	317.66	0.0064	1	2	negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell
GO:0009891	0.0064	2.5843	5.4473	12	1702	positive regulation of biosynthetic process
GO:0002764	0.0066	5.7924	0.7489	4	234	immune response-regulating signaling pathway
GO:1901224	0.0069	17.4815	0.1248	2	39	positive regulation of NIK/NF-kappaB signaling
GO:1903532	0.0069	4.5325	1.2066	5	377	positive regulation of secretion by cell
GO:0002218	0.007	8.2799	0.3905	3	122	activation of innate immune response
GO:0050708	0.0076	4.4348	1.2322	5	385	regulation of protein secretion
GO:0002833	0.008	16.1673	0.1344	2	42	positive regulation of response to biotic stimulus
GO:0002889	0.008	16.1673	0.1344	2	42	regulation of immunoglobulin mediated immune response
GO:0010712	0.008	16.1673	0.1344	2	42	regulation of collagen metabolic process
GO:2000351	0.0083	15.772	0.1376	2	43	regulation of endothelial cell apoptotic process
GO:0043954	0.0087	15.3955	0.1408	2	44	cellular component maintenance
GO:0002793	0.0088	5.3222	0.8129	4	254	positive regulation of peptide secretion
GO:0001525	0.0089	4.2512	1.2834	5	401	angiogenesis
GO:0001562	0.0092	165.1771	0.0092	1	3	response to protozoan
GO:0072359	0.0092	2.9984	2.9957	8	936	circulatory system development
GO:0002381	0.0095	14.6939	0.1472	2	46	immunoglobulin production involved in immunoglobulin mediated immune response
GO:0032720	0.0095	14.6939	0.1472	2	46	negative regulation of tumor necrosis factor production
GO:0000103	0.0096	158.82	0.0096	1	3	sulfate assimilation
GO:0002296	0.0096	158.82	0.0096	1	3	T-helper 1 cell lineage commitment
GO:0002784	0.0096	158.82	0.0096	1	3	regulation of antimicrobial peptide production
GO:0002803	0.0096	158.82	0.0096	1	3	positive regulation of antibacterial peptide production
GO:0002838	0.0096	158.82	0.0096	1	3	negative regulation of immune response to tumor cell
GO:0002925	0.0096	158.82	0.0096	1	3	positive regulation of humoral immune response mediated by circulating immunoglobulin
GO:0034756	0.0096	158.82	0.0096	1	3	regulation of iron ion transport
GO:0035993	0.0096	158.82	0.0096	1	3	deltoid tuberosity development
GO:0051835	0.0096	158.82	0.0096	1	3	positive regulation of synapse structural plasticity
GO:0060585	0.0096	158.82	0.0096	1	3	positive regulation of prostaglandin-endoperoxide synthase activity
GO:0060988	0.0096	158.82	0.0096	1	3	lipid tube assembly
GO:0097029	0.0096	158.82	0.0096	1	3	mature conventional dendritic cell differentiation
GO:1901256	0.0096	158.82	0.0096	1	3	regulation of macrophage colony-stimulating factor production
GO:1903660	0.0096	158.82	0.0096	1	3	negative regulation of complement-dependent cytotoxicity
GO:0051050	0.0098	2.9644	3.0277	8	946	positive regulation of transport
GO:0045058	0.0099	14.3664	0.1504	2	47	T cell selection

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0071593	1e-04	278.4912	0.0148	2	4	lymphocyte aggregation
GO:0050776	1e-04	5.2945	1.966	9	531	regulation of immune response
GO:0070257	6e-04	69.5965	0.037	2	10	positive regulation of mucus secretion
GO:0032941	7e-04	19.7255	0.1703	3	46	secretion by tissue
GO:0008284	7e-04	3.8561	2.9917	10	808	positive regulation of cell proliferation
GO:0003093	7e-04	61.8596	0.0407	2	11	regulation of glomerular filtration
GO:1903555	9e-04	10.2364	0.4295	4	116	regulation of tumor necrosis factor superfamily cytokine production
GO:0032418	0.0014	14.8675	0.2222	3	60	lysosome localization
GO:0002521	0.0015	4.5728	1.7069	7	461	leukocyte differentiation
GO:0042534	0.0016	39.7544	0.0592	2	16	regulation of tumor necrosis factor biosynthetic process
GO:0032103	0.0017	6.3548	0.8627	5	233	positive regulation of response to external stimulus
GO:0032760	0.002	13.2355	0.2481	3	67	positive regulation of tumor necrosis factor production
GO:0007204	0.002	6.1099	0.896	5	242	positive regulation of cytosolic calcium ion concentration
GO:0002274	0.0023	7.8356	0.5554	4	150	myeloid leukocyte activation
GO:0002703	0.0026	7.5234	0.5776	4	156	regulation of leukocyte mediated immunity
GO:0044273	0.0027	29.2835	0.0778	2	21	sulfur compound catabolic process
GO:1990266	0.0028	11.5971	0.2814	3	76	neutrophil migration
GO:0003071	0.003	27.8175	0.0815	2	22	renal system process involved in regulation of systemic arterial blood pressure
GO:0035929	0.003	27.8175	0.0815	2	22	steroid hormone secretion
GO:0045730	0.003	27.8175	0.0815	2	22	respiratory burst
GO:0051969	0.003	27.8175	0.0815	2	22	regulation of transmission of nerve impulse
GO:0007589	0.0032	10.9919	0.2962	3	80	body fluid secretion
GO:0002684	0.0035	3.5325	2.5288	8	683	positive regulation of immune system process
GO:0045061	0.0035	25.2855	0.0889	2	24	thymic T cell selection
GO:0044057	0.0036	4.427	1.4918	6	416	regulation of system process
GO:0003106	0.0037	Inf	0.0037	1	1	negative regulation of glomerular filtration by angiotensin
GO:0014895	0.0037	Inf	0.0037	1	1	smooth muscle hypertrophy
GO:0015993	0.0037	Inf	0.0037	1	1	molecular hydrogen transport
GO:0036275	0.0037	Inf	0.0037	1	1	response to 5-fluorouracil
GO:0046005	0.0037	Inf	0.0037	1	1	positive regulation of circadian sleep/wake cycle, REM sleep
GO:0070453	0.0037	Inf	0.0037	1	1	regulation of heme biosynthetic process
GO:1901401	0.0037	Inf	0.0037	1	1	regulation of tetrapyrrole metabolic process
GO:1901805	0.0037	Inf	0.0037	1	1	beta-glucoside catabolic process
GO:0014821	0.0038	24.1846	0.0926	2	25	phasic smooth muscle contraction
GO:0045187	0.0038	24.1846	0.0926	2	25	regulation of circadian sleep/wake cycle, sleep
GO:0050886	0.0038	10.3184	0.3147	3	85	endocrine process
GO:0051046	0.0039	3.4681	2.5733	8	695	regulation of secretion
GO:0022410	0.0045	22.247	0.1	2	27	circadian sleep/wake cycle process
GO:0043304	0.0051	20.5965	0.1074	2	29	regulation of mast cell degranulation
GO:0046329	0.0055	19.8596	0.1111	2	30	negative regulation of JNK cascade
GO:0031347	0.0063	3.9256	1.6698	6	451	regulation of defense response
GO:0050865	0.0065	3.8986	1.681	6	454	regulation of cell activation
GO:0002707	0.0066	17.9344	0.1222	2	33	negative regulation of lymphocyte mediated immunity
GO:0001555	0.0074	273.7069	0.0074	1	2	oocyte growth
GO:0001581	0.0074	273.7069	0.0074	1	2	detection of chemical stimulus involved in sensory perception of sour taste
GO:0001808	0.0074	273.7069	0.0074	1	2	negative regulation of type IV hypersensitivity
GO:0010841	0.0074	273.7069	0.0074	1	2	positive regulation of circadian sleep/wake cycle, wakefulness
GO:0036228	0.0074	273.7069	0.0074	1	2	protein localization to nuclear inner membrane
GO:0046967	0.0074	273.7069	0.0074	1	2	cytosol to ER transport
GO:0071594	0.0074	273.7069	0.0074	1	2	thymocyte aggregation
GO:0071626	0.0074	273.7069	0.0074	1	2	mastication
GO:0090290	0.0074	273.7069	0.0074	1	2	positive regulation of osteoclast proliferation
GO:0098583	0.0074	273.7069	0.0074	1	2	learned vocalization behavior
GO:0120054	0.0074	273.7069	0.0074	1	2	intestinal motility
GO:0120058	0.0074	273.7069	0.0074	1	2	positive regulation of small intestinal transit
GO:1901750	0.0074	273.7069	0.0074	1	2	leukotriene D4 biosynthetic process
GO:1902173	0.0074	273.7069	0.0074	1	2	negative regulation of keratinocyte apoptotic process
GO:1904346	0.0074	273.7069	0.0074	1	2	positive regulation of gastric mucosal blood circulation
GO:1905747	0.0074	273.7069	0.0074	1	2	negative regulation of saliva secretion
GO:1905748	0.0074	273.7069	0.0074	1	2	hard palate morphogenesis
GO:2000506	0.0074	273.7069	0.0074	1	2	negative regulation of energy homeostasis
GO:2000870	0.0074	273.7069	0.0074	1	2	regulation of progesterone secretion
GO:0030431	0.0074	16.8453	0.1296	2	35	sleep
GO:0070303	0.0074	16.8453	0.1296	2	35	negative regulation of stress-activated protein kinase signaling cascade
GO:0045987	0.0078	16.3488	0.1333	2	36	positive regulation of smooth muscle contraction
GO:0050856	0.0078	16.3488	0.1333	2	36	regulation of T cell receptor signaling pathway
GO:0060135	0.0078	16.3488	0.1333	2	36	maternal process involved in female pregnancy
GO:0032675	0.0081	7.8214	0.411	3	111	regulation of interleukin-6 production
GO:0009268	0.0083	15.8807	0.137	2	37	response to pH
GO:0048534	0.0086	3.0075	2.9435	8	795	hematopoietic or lymphoid organ development
GO:0006997	0.0087	7.6086	0.4221	3	114	nucleus organization
GO:0006810	0.0088	1.9929	14.3548	23	3877	transport
GO:0003012	0.0091	4.2057	1.2848	5	347	muscle system process
GO:0051249	0.0091	4.2057	1.2848	5	347	regulation of lymphocyte activation
GO:0002279	0.0091	15.0204	0.1444	2	39	mast cell activation involved in immune response
GO:0030217	0.0095	5.1755	0.8294	4	224	T cell differentiation
GO:0002448	0.0096	14.6242	0.1481	2	40	mast cell mediated immunity
GO:0033003	0.0096	14.6242	0.1481	2	40	regulation of mast cell activation
GO:0044058	0.0096	14.6242	0.1481	2	40	regulation of digestive system process

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0032722	0	29.9556	0.1568	4	49	positive regulation of chemokine production
GO:0002251	1e-04	49.575	0.0736	3	23	organ or tissue specific immune response
GO:0045347	1e-04	324.1224	0.0128	2	4	negative regulation of MHC class II biosynthetic process
GO:0002823	1e-04	36.706	0.096	3	30	negative regulation of adaptive immune response based on somatic recombination of immune receptors built from immunoglobulin superfamily domains
GO:0042088	3e-04	27.5139	0.1248	3	39	T-helper 1 type immune response
GO:0050715	4e-04	13.0395	0.3425	4	107	positive regulation of cytokine secretion
GO:0043950	4e-04	81	0.032	2	10	positive regulation of cAMP-mediated signaling
GO:0051222	6e-04	5.4942	1.453	7	454	positive regulation of protein transport
GO:0032103	9e-04	7.4638	0.7457	5	233	positive regulation of response to external stimulus
GO:0002227	0.001	49.8305	0.048	2	15	innate immune response in mucosa
GO:0007166	0.001	2.9361	6.3658	15	1989	cell surface receptor signaling pathway
GO:0046827	0.0012	46.2682	0.0512	2	16	positive regulation of protein export from nucleus
GO:1900424	0.0012	46.2682	0.0512	2	16	regulation of defense response to bacterium
GO:0002683	0.0012	5.6061	1.2002	6	375	negative regulation of immune system process
GO:0032760	0.0013	15.4492	0.2144	3	67	positive regulation of tumor necrosis factor production
GO:0031424	0.0017	38.096	0.0608	2	19	keratinization
GO:0032703	0.0017	38.096	0.0608	2	19	negative regulation of interleukin-2 production
GO:0043011	0.0017	38.096	0.0608	2	19	myeloid dendritic cell differentiation
GO:0002702	0.0017	13.9199	0.2368	3	74	positive regulation of production of molecular mediator of immune response
GO:0002367	0.0019	13.353	0.2464	3	77	cytokine production involved in immune response
GO:0071621	0.0019	13.353	0.2464	3	77	granulocyte chemotaxis
GO:0002286	0.0021	12.8304	0.256	3	80	T cell activation involved in immune response
GO:0043207	0.0024	4.251	1.8563	7	580	response to external biotic stimulus
GO:0045638	0.0024	12.3469	0.2656	3	83	negative regulation of myeloid cell differentiation
GO:0060143	0.0024	30.8319	0.0736	2	23	positive regulation of syncytium formation by plasma membrane fusion
GO:0002688	0.0025	12.1937	0.2688	3	84	regulation of leukocyte chemotaxis
GO:2000026	0.0025	2.8338	5.5177	13	1724	regulation of multicellular organismal development
GO:0051149	0.0027	11.756	0.2784	3	87	positive regulation of muscle cell differentiation
GO:0090022	0.0029	28.1473	0.08	2	25	regulation of neutrophil chemotaxis
GO:0008285	0.003	4.0596	1.9395	7	606	negative regulation of cell proliferation
GO:0032733	0.0031	26.9728	0.0832	2	26	positive regulation of interleukin-10 production
GO:2001237	0.0032	11.092	0.2944	3	92	negative regulation of extrinsic apoptotic signaling pathway
GO:0002519	0.0032	Inf	0.0032	1	1	natural killer cell tolerance induction
GO:0002652	0.0032	Inf	0.0032	1	1	regulation of tolerance induction dependent upon immune response
GO:0002732	0.0032	Inf	0.0032	1	1	positive regulation of dendritic cell cytokine production
GO:0002807	0.0032	Inf	0.0032	1	1	positive regulation of antimicrobial peptide biosynthetic process
GO:0002808	0.0032	Inf	0.0032	1	1	regulation of antibacterial peptide biosynthetic process
GO:0006965	0.0032	Inf	0.0032	1	1	positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria
GO:0010607	0.0032	Inf	0.0032	1	1	negative regulation of cytoplasmic mRNA processing body assembly
GO:0032498	0.0032	Inf	0.0032	1	1	detection of muramyl dipeptide
GO:0032712	0.0032	Inf	0.0032	1	1	negative regulation of interleukin-3 production
GO:0070351	0.0032	Inf	0.0032	1	1	negative regulation of white fat cell proliferation
GO:0071656	0.0032	Inf	0.0032	1	1	negative regulation of granulocyte colony-stimulating factor production
GO:0032967	0.0033	25.8922	0.0864	2	27	positive regulation of collagen biosynthetic process
GO:0042832	0.0033	25.8922	0.0864	2	27	defense response to protozoan
GO:0044253	0.0033	25.8922	0.0864	2	27	positive regulation of multicellular organismal metabolic process
GO:0032689	0.0036	24.8948	0.0896	2	28	negative regulation of interferon-gamma production
GO:0061844	0.0036	24.8948	0.0896	2	28	antimicrobial humoral immune response mediated by antimicrobial peptide
GO:1904019	0.0037	10.4987	0.3104	3	97	epithelial cell apoptotic process
GO:0060326	0.0041	6.674	0.6529	4	204	cell chemotaxis
GO:0001906	0.0042	9.9653	0.3265	3	102	cell killing
GO:0002714	0.0044	22.3153	0.0992	2	31	positive regulation of B cell mediated immunity
GO:0032496	0.0046	6.4455	0.6753	4	211	response to lipopolysaccharide
GO:0032732	0.0047	21.5701	0.1024	2	32	positive regulation of interleukin-1 production
GO:1903038	0.0047	9.5758	0.3393	3	106	negative regulation of leukocyte cell-cell adhesion
GO:0002707	0.005	20.8729	0.1056	2	33	negative regulation of lymphocyte mediated immunity
GO:0042092	0.0053	20.2194	0.1088	2	34	type 2 immune response
GO:0030225	0.0056	19.6054	0.112	2	35	macrophage differentiation
GO:0043030	0.0056	19.6054	0.112	2	35	regulation of macrophage activation
GO:0051173	0.0058	2.3486	8.3341	16	2604	positive regulation of nitrogen compound metabolic process
GO:0032757	0.0059	19.0276	0.1152	2	36	positive regulation of interleukin-8 production
GO:0012501	0.0059	2.6136	5.3928	12	1685	programmed cell death
GO:0045926	0.0059	5.9769	0.7265	4	227	negative regulation of growth
GO:0042886	0.006	2.6119	5.396	12	1686	amide transport
GO:1903555	0.0061	8.7229	0.3713	3	116	regulation of tumor necrosis factor superfamily cytokine production
GO:0002752	0.0064	317.66	0.0064	1	2	cell surface pattern recognition receptor signaling pathway
GO:0002859	0.0064	317.66	0.0064	1	2	negative regulation of natural killer cell mediated cytotoxicity directed against tumor cell target
GO:0002879	0.0064	317.66	0.0064	1	2	positive regulation of acute inflammatory response to non-antigenic stimulus
GO:0032701	0.0064	317.66	0.0064	1	2	negative regulation of interleukin-18 production
GO:0035419	0.0064	317.66	0.0064	1	2	activation of MAPK activity involved in innate immune response
GO:0043000	0.0064	317.66	0.0064	1	2	Golgi to plasma membrane CFTR protein transport
GO:1902523	0.0064	317.66	0.0064	1	2	positive regulation of protein K63-linked ubiquitination
GO:2000363	0.0064	317.66	0.0064	1	2	positive regulation of prostaglandin-E synthase activity
GO:2000424	0.0064	317.66	0.0064	1	2	positive regulation of eosinophil chemotaxis
GO:2000521	0.0064	317.66	0.0064	1	2	negative regulation of immunological synapse formation
GO:2001189	0.0064	317.66	0.0064	1	2	negative regulation of T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell
GO:0006357	0.0066	2.5757	5.4633	12	1707	regulation of transcription from RNA polymerase II promoter
GO:0002764	0.0066	5.7924	0.7489	4	234	immune response-regulating signaling pathway
GO:1901224	0.0069	17.4815	0.1248	2	39	positive regulation of NIK/NF-kappaB signaling
GO:0009617	0.0069	4.5325	1.2066	5	377	response to bacterium
GO:1903532	0.0069	4.5325	1.2066	5	377	positive regulation of secretion by cell
GO:0002218	0.007	8.2799	0.3905	3	122	activation of innate immune response
GO:0002252	0.0072	3.8476	1.7219	6	538	immune effector process
GO:0002819	0.008	7.8795	0.4097	3	128	regulation of adaptive immune response
GO:0002833	0.008	16.1673	0.1344	2	42	positive regulation of response to biotic stimulus
GO:0002889	0.008	16.1673	0.1344	2	42	regulation of immunoglobulin mediated immune response
GO:0010712	0.008	16.1673	0.1344	2	42	regulation of collagen metabolic process
GO:0051168	0.0081	7.8165	0.4129	3	129	nuclear export
GO:2000351	0.0083	15.772	0.1376	2	43	regulation of endothelial cell apoptotic process
GO:0070201	0.0085	3.3168	2.3492	7	734	regulation of establishment of protein localization
GO:0031325	0.0088	2.2302	8.699	16	2718	positive regulation of cellular metabolic process
GO:0002793	0.0088	5.3222	0.8129	4	254	positive regulation of peptide secretion
GO:0001525	0.0089	4.2512	1.2834	5	401	angiogenesis
GO:0090087	0.0092	3.2604	2.3876	7	746	regulation of peptide transport
GO:0072359	0.0092	2.9984	2.9957	8	936	circulatory system development
GO:0002381	0.0095	14.6939	0.1472	2	46	immunoglobulin production involved in immunoglobulin mediated immune response
GO:0032720	0.0095	14.6939	0.1472	2	46	negative regulation of tumor necrosis factor production
GO:0000448	0.0096	158.82	0.0096	1	3	cleavage in ITS2 between 5.8S rRNA and LSU-rRNA of tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0002296	0.0096	158.82	0.0096	1	3	T-helper 1 cell lineage commitment
GO:0002784	0.0096	158.82	0.0096	1	3	regulation of antimicrobial peptide production
GO:0002803	0.0096	158.82	0.0096	1	3	positive regulation of antibacterial peptide production
GO:0002838	0.0096	158.82	0.0096	1	3	negative regulation of immune response to tumor cell
GO:0002925	0.0096	158.82	0.0096	1	3	positive regulation of humoral immune response mediated by circulating immunoglobulin
GO:0010482	0.0096	158.82	0.0096	1	3	regulation of epidermal cell division
GO:0035993	0.0096	158.82	0.0096	1	3	deltoid tuberosity development
GO:0051835	0.0096	158.82	0.0096	1	3	positive regulation of synapse structural plasticity
GO:0060585	0.0096	158.82	0.0096	1	3	positive regulation of prostaglandin-endoperoxide synthase activity
GO:1901256	0.0096	158.82	0.0096	1	3	regulation of macrophage colony-stimulating factor production
GO:1903660	0.0096	158.82	0.0096	1	3	negative regulation of complement-dependent cytotoxicity
GO:0046649	0.0096	3.6019	1.8339	6	573	lymphocyte activation
GO:0097529	0.0098	7.2912	0.4417	3	138	myeloid leukocyte migration
GO:1903146	0.0099	14.3664	0.1504	2	47	regulation of autophagy of mitochondrion
GO:0042981	0.0099	2.628	4.3495	10	1359	regulation of apoptotic process

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0006597	0	Inf	0.0049	2	2	spermine biosynthetic process
GO:0008295	1e-04	286.3604	0.0122	2	5	spermidine biosynthetic process
GO:0071468	3e-04	95.4174	0.0269	2	11	cellular response to acidic pH
GO:0006595	4e-04	78.059	0.0318	2	13	polyamine metabolic process
GO:0042401	4e-04	78.059	0.0318	2	13	cellular biogenic amine biosynthetic process
GO:0072755	0.0024	Inf	0.0024	1	1	cellular response to benomyl
GO:0007338	0.0025	12.1821	0.2717	3	111	single fertilization
GO:0009416	0.0028	7.5188	0.5923	4	242	response to light stimulus
GO:0006110	0.0033	25.9836	0.0857	2	35	regulation of glycolytic process
GO:0009268	0.0037	24.4958	0.0906	2	37	response to pH
GO:0006696	0.0049	418.2895	0.0049	1	2	ergosterol biosynthetic process
GO:0036292	0.0049	418.2895	0.0049	1	2	DNA rewinding
GO:0038156	0.0049	418.2895	0.0049	1	2	interleukin-3-mediated signaling pathway
GO:0045338	0.0049	418.2895	0.0049	1	2	farnesyl diphosphate metabolic process
GO:0060733	0.0049	418.2895	0.0049	1	2	regulation of eIF2 alpha phosphorylation by amino acid starvation
GO:0071264	0.0049	418.2895	0.0049	1	2	positive regulation of translational initiation in response to starvation
GO:0042149	0.0054	19.9283	0.1101	2	45	cellular response to glucose starvation
GO:0051193	0.0054	19.9283	0.1101	2	45	regulation of cofactor metabolic process
GO:0016128	0.0073	209.1316	0.0073	1	3	phytosteroid metabolic process
GO:0044107	0.0073	209.1316	0.0073	1	3	cellular alcohol metabolic process
GO:0021888	0.0098	139.4123	0.0098	1	4	hypothalamus gonadotrophin-releasing hormone neuron development
GO:0033026	0.0098	139.4123	0.0098	1	4	negative regulation of mast cell apoptotic process
GO:0070668	0.0098	139.4123	0.0098	1	4	positive regulation of mast cell proliferation
GO:0071494	0.0098	139.4123	0.0098	1	4	cellular response to UV-C
GO:0090315	0.0098	139.4123	0.0098	1	4	negative regulation of protein targeting to membrane

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

LOLA Enrichment Analysis

References

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0009615	0.0012	9.6113	0.469	4	202	response to virus
GO:1903900	0.0019	13.3999	0.2484	3	107	regulation of viral life cycle
GO:0003147	0.0023	Inf	0.0023	1	1	neural crest cell migration involved in heart formation
GO:0061713	0.0023	Inf	0.0023	1	1	anterior neural tube closure
GO:0071231	0.0023	Inf	0.0023	1	1	cellular response to folic acid
GO:0045071	0.0028	28.3321	0.0789	2	34	negative regulation of viral genome replication
GO:0009855	0.0028	11.6997	0.2833	3	122	determination of bilateral symmetry
GO:0043901	0.0042	10.0767	0.3274	3	141	negative regulation of multi-organism process
GO:1900176	0.0046	441.5833	0.0046	1	2	negative regulation of nodal signaling pathway involved in determination of lateral mesoderm left/right asymmetry
GO:0048678	0.0065	18.112	0.1207	2	52	response to axon injury
GO:0097176	0.007	220.7778	0.007	1	3	epoxide metabolic process
GO:0043903	0.0076	8.1151	0.404	3	174	regulation of symbiosis, encompassing mutualism through parasitism
GO:0098542	0.009	5.3689	0.8243	4	355	defense response to other organism
GO:0050688	0.0091	15.0838	0.144	2	62	regulation of defense response to virus
GO:0003419	0.0093	147.1759	0.0093	1	4	growth plate cartilage chondrocyte proliferation
GO:0035582	0.0093	147.1759	0.0093	1	4	sequestering of BMP in extracellular matrix
GO:0044838	0.0093	147.1759	0.0093	1	4	cell quiescence
GO:0046655	0.0093	147.1759	0.0093	1	4	folic acid metabolic process
GO:0050689	0.0093	147.1759	0.0093	1	4	negative regulation of defense response to virus by host
GO:1900108	0.0093	147.1759	0.0093	1	4	negative regulation of nodal signaling pathway
GO:1900145	0.0093	147.1759	0.0093	1	4	regulation of nodal signaling pathway involved in determination of left/right asymmetry
GO:0061371	0.0094	14.8356	0.1463	2	63	determination of heart left/right asymmetry

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0005125	0.001	9.9771	0.4437	4	144	cytokine activity
GO:0032500	0.0031	Inf	0.0031	1	1	muramyl dipeptide binding
GO:0042007	0.0031	Inf	0.0031	1	1	interleukin-18 binding
GO:0030545	0.0042	5.1388	1.0723	5	348	receptor regulator activity
GO:0005547	0.0052	20.401	0.1078	2	35	phosphatidylinositol-3,4,5-trisphosphate binding
GO:0004014	0.0062	330.2708	0.0062	1	2	adenosylmethionine decarboxylase activity
GO:0008650	0.0062	330.2708	0.0062	1	2	rRNA (uridine-2'-O-)-methyltransferase activity
GO:0019810	0.0062	330.2708	0.0062	1	2	putrescine binding
GO:0048248	0.0062	330.2708	0.0062	1	2	CXCR3 chemokine receptor binding
GO:0050436	0.0062	330.2708	0.0062	1	2	microfibril binding
GO:0008083	0.0066	8.4799	0.3821	3	124	growth factor activity
GO:0008201	0.008	7.8883	0.4098	3	133	heparin binding
GO:0004459	0.0092	165.125	0.0092	1	3	L-lactate dehydrogenase activity
GO:0004566	0.0092	165.125	0.0092	1	3	beta-glucuronidase activity
GO:0005136	0.0092	165.125	0.0092	1	3	interleukin-4 receptor binding
GO:0005160	0.01	14.3115	0.151	2	49	transforming growth factor beta receptor binding

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0032500	0.0033	Inf	0.0033	1	1	muramyl dipeptide binding
GO:0042007	0.0033	Inf	0.0033	1	1	interleukin-18 binding
GO:0102076	0.0033	Inf	0.0033	1	1	beta,beta-carotene-9',10'-cleaving oxygenase activity
GO:0030545	0.0059	4.7094	1.1598	5	348	receptor regulator activity
GO:0004020	0.0067	304.7885	0.0067	1	2	adenylylsulfate kinase activity
GO:0004781	0.0067	304.7885	0.0067	1	2	sulfate adenylyltransferase (ATP) activity
GO:0016501	0.0067	304.7885	0.0067	1	2	prostacyclin receptor activity
GO:0048248	0.0067	304.7885	0.0067	1	2	CXCR3 chemokine receptor binding
GO:0050436	0.0067	304.7885	0.0067	1	2	microfibril binding
GO:0030544	0.0075	16.7599	0.13	2	39	Hsp70 protein binding
GO:0005136	0.01	152.3846	0.01	1	3	interleukin-4 receptor binding
GO:0015057	0.01	152.3846	0.01	1	3	thrombin-activated receptor activity

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0045296	0.0025	5.8124	0.9493	5	296	cadherin binding
GO:0032500	0.0032	Inf	0.0032	1	1	muramyl dipeptide binding
GO:0042007	0.0032	Inf	0.0032	1	1	interleukin-18 binding
GO:0001205	0.0053	20.1786	0.109	2	34	transcriptional activator activity, RNA polymerase II distal enhancer sequence-specific binding
GO:0016501	0.0064	317.02	0.0064	1	2	prostacyclin receptor activity
GO:0048248	0.0064	317.02	0.0064	1	2	CXCR3 chemokine receptor binding
GO:0050436	0.0064	317.02	0.0064	1	2	microfibril binding
GO:0004459	0.0096	158.5	0.0096	1	3	L-lactate dehydrogenase activity
GO:0005136	0.0096	158.5	0.0096	1	3	interleukin-4 receptor binding