RnBeads: uWGBS - prog_v07

Option	Value
analyze.sites	no
region.types	tiling, cpgislands, genes, promoters, ensembleRegBuildBPall, ensembleRegBuildBPallMerged
differential.permutations	0
differential.comparison.columns	cmp_cellnum, cmp_donor_02I_vs_GNN, cmp_donor_02I_vs_GPJ, cmp_donor_02I_vs_2I_, cmp_donor_GNN_vs_GPJ, cmp_donor_GNN_vs_2I_, cmp_donor_GPJ_vs_2I_, cmp_ploidy_2N_vs_4N, cmp_ploidy_2N_vs_8N, cmp_ploidy_2N_vs_16N, cmp_ploidy_2N_vs_32N, cmp_ploidy_4N_vs_8N, cmp_ploidy_8N_vs_16N, cmp_ploidy_16N_vs_32N
differential.comparison.columns.all.pairwise	default
columns.pairing	default
differential.site.test.method	limma
covariate.adjustment.columns	sex, donorId, flowcell, cellSourceCurated, nominalCellNumber
differential.adjustment.sva	yes
differential.adjustment.celltype	yes
differential.enrichment	yes

	comparison	adjustment	covariateTable
1	1 vs. 5 (based on cmp_cellnum)	sex,donorId,flowcell	csv
2	02I vs. GNN (based on cmp_donor_02I_vs_GNN)	flowcell,nominalCellNumber	csv
3	02I vs. GPJ (based on cmp_donor_02I_vs_GPJ)	flowcell,nominalCellNumber	csv
4	02I vs. 2I_ (based on cmp_donor_02I_vs_2I_)	flowcell,nominalCellNumber	csv
5	GNN vs. GPJ (based on cmp_donor_GNN_vs_GPJ)	flowcell	csv
6	2I_ vs. GNN (based on cmp_donor_GNN_vs_2I_)	flowcell	csv
7	2I_ vs. GPJ (based on cmp_donor_GPJ_vs_2I_)	flowcell	csv
8	2N vs. 4N (based on cmp_ploidy_2N_vs_4N)	sex,donorId,flowcell,nominalCellNumber	csv
9	2N vs. 8N (based on cmp_ploidy_2N_vs_8N)	sex,donorId,flowcell,nominalCellNumber	csv
10	16N vs. 2N (based on cmp_ploidy_2N_vs_16N)	sex,donorId,flowcell,nominalCellNumber	csv
11	2N vs. 32N (based on cmp_ploidy_2N_vs_32N)	sex,donorId,flowcell,nominalCellNumber	csv
12	4N vs. 8N (based on cmp_ploidy_4N_vs_8N)	sex,donorId,flowcell,nominalCellNumber	csv
13	16N vs. 8N (based on cmp_ploidy_8N_vs_16N)	sex,donorId,flowcell,nominalCellNumber	csv
14	16N vs. 32N (based on cmp_ploidy_16N_vs_32N)	sex,donorId,flowcell,nominalCellNumber	csv

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 methylation difference in a region of the two groups being and of quotient of mean methylation levelsas well as a p-value obtained from statistical testing (limma or t-test; depending on parameter settings). 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	cpgislands	genes	promoters	ensembleRegBuildBPall	ensembleRegBuildBPallMerged
1 vs. 5 (based on cmp_cellnum)	0	0	0	0	0	0
02I vs. GNN (based on cmp_donor_02I_vs_GNN)	0	0	0	0	0	0
02I vs. GPJ (based on cmp_donor_02I_vs_GPJ)	0	0	0	0	0	0
02I vs. 2I_ (based on cmp_donor_02I_vs_2I_)	0	0	0	0	0	0
GNN vs. GPJ (based on cmp_donor_GNN_vs_GPJ)	0	0	0	0	0	0
2I_ vs. GNN (based on cmp_donor_GNN_vs_2I_)	0	0	0	0	0	0
2I_ vs. GPJ (based on cmp_donor_GPJ_vs_2I_)	0	0	0	0	0	0
2N vs. 4N (based on cmp_ploidy_2N_vs_4N)	0	0	0	0	0	0
2N vs. 8N (based on cmp_ploidy_2N_vs_8N)	0	0	0	0	0	0
16N vs. 2N (based on cmp_ploidy_2N_vs_16N)	0	0	0	0	0	0
2N vs. 32N (based on cmp_ploidy_2N_vs_32N)	0	0	0	0	0	0
4N vs. 8N (based on cmp_ploidy_4N_vs_8N)	0	0	0	0	0	0
16N vs. 8N (based on cmp_ploidy_8N_vs_16N)	0	0	0	0	0	0
16N vs. 32N (based on cmp_ploidy_16N_vs_32N)	0	0	0	0	0	0

comparison
regions
differential methylation measure

Figure 1

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 2

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
mean.g1,mean.g2: (where g1 and g2 is replaced by the respective group names in the table) mean methylation in each of the two groups
mean.diff: difference in methylation means between the two groups: mean.g1-mean.g2. In case of paired analysis, it is the mean of the pairwise differences.
mean.quot.log2: log2 of the quotient in methylation: log2((mean.g1+epsilon)/(mean.g2+epsilon)), where epsilon:=0.01. In case of paired analysis, it is the mean of the pairwise quotients.
diffmeth.p.val: p-value obtained from linear models employed in the limma package (or alternatively from a two-sided Welch t-test; which type of p-value is computed is specified in the differential.site.test.method option).
max.g1,max.g2: maximum methylation level in group 1 and 2 respectively
min.g1,min.g2: minimum methylation level in group 1 and 2 respectively
sd.g1,sd.g2: standard deviation of methylation levels
min.diff: Minimum of 0 and the smallest pairwise difference between samples of the two groups
diffmeth.p.adj.fdr: FDR adjusted p-value of all sites
combinedRank: mean.diff, mean.quot.log2 and diffmeth.p.val are ranked for all regions. This aggregates them using the maximum, i.e. worst rank of a site among the three measures
num.na.g1,num.na.g2: number of NA methylation values for groups 1 and 2 respectively
mean.covg.g1,mean.covg.g2: mean coverage of groups 1 and 2 respectively (In case of Infinium array methylation data, coverage is defined as combined beadcount.)
min.covg.g1,min.covg.g2: minimum coverage of groups 1 and 2 respectively
max.covg.g1,max.covg.g2: maximum coverage of groups 1 and 2 respectively
covg.thresh.nsamples.g1,covg.thresh.nsamples.g2: number of samples in group 1 and 2 respectively exceeding the coverage threshold (1) for this region.

The tables for the individual comparisons can be found here:

	tiling	cpgislands	genes	promoters	ensembleRegBuildBPall	ensembleRegBuildBPallMerged
1 vs. 5 (based on cmp_cellnum)	csv	csv	csv	csv	csv	csv
02I vs. GNN (based on cmp_donor_02I_vs_GNN)	csv	csv	csv	csv	csv	csv
02I vs. GPJ (based on cmp_donor_02I_vs_GPJ)	csv	csv	csv	csv	csv	csv
02I vs. 2I_ (based on cmp_donor_02I_vs_2I_)	csv	csv	csv	csv	csv	csv
GNN vs. GPJ (based on cmp_donor_GNN_vs_GPJ)	csv	csv	csv	csv	csv	csv
2I_ vs. GNN (based on cmp_donor_GNN_vs_2I_)	csv	csv	csv	csv	csv	csv
2I_ vs. GPJ (based on cmp_donor_GPJ_vs_2I_)	csv	csv	csv	csv	csv	csv
2N vs. 4N (based on cmp_ploidy_2N_vs_4N)	csv	csv	csv	csv	csv	csv
2N vs. 8N (based on cmp_ploidy_2N_vs_8N)	csv	csv	csv	csv	csv	csv
16N vs. 2N (based on cmp_ploidy_2N_vs_16N)	csv	csv	csv	csv	csv	csv
2N vs. 32N (based on cmp_ploidy_2N_vs_32N)	csv	csv	csv	csv	csv	csv
4N vs. 8N (based on cmp_ploidy_4N_vs_8N)	csv	csv	csv	csv	csv	csv
16N vs. 8N (based on cmp_ploidy_8N_vs_16N)	csv	csv	csv	csv	csv	csv
16N vs. 32N (based on cmp_ploidy_16N_vs_32N)	csv	csv	csv	csv	csv	csv

Enrichment Analysis

Enrichment Analysis was conducted. The wordclouds and tables below contains significant GO terms as determined by a hypergeometric test.

comparison
Hypermethylation/hypomethylation
ontology
regions
differential methylation measure

Figure 3

Wordclouds for GO enrichment terms.

comparison
Hypermethylation/hypomethylation
ontology
regions
differential methylation measure

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0006370	2e-04	126.2097	0.021	2	33	7-methylguanosine mRNA capping
GO:0036260	2e-04	111.7571	0.0236	2	37	RNA capping
GO:0097310	6e-04	Inf	6e-04	1	1	cap2 mRNA methylation
GO:1901676	6e-04	Inf	6e-04	1	1	positive regulation of histone H3-K27 acetylation
GO:0048861	0.0025	580.6667	0.0025	1	4	leukemia inhibitory factor signaling pathway
GO:0072108	0.0025	580.6667	0.0025	1	4	positive regulation of mesenchymal to epithelial transition involved in metanephros morphogenesis
GO:0051461	0.0032	435.4722	0.0032	1	5	positive regulation of corticotropin secretion
GO:0060708	0.0032	435.4722	0.0032	1	5	spongiotrophoblast differentiation
GO:1903025	0.0032	435.4722	0.0032	1	5	regulation of RNA polymerase II regulatory region sequence-specific DNA binding
GO:0009249	0.0038	348.3556	0.0038	1	6	protein lipoylation
GO:0080009	0.0038	348.3556	0.0038	1	6	mRNA methylation
GO:0019827	0.0042	25.0419	0.1001	2	157	stem cell population maintenance
GO:0072307	0.0045	290.2778	0.0045	1	7	regulation of metanephric nephron tubule epithelial cell differentiation
GO:0006123	0.0051	248.7937	0.0051	1	8	mitochondrial electron transport, cytochrome c to oxygen
GO:0008635	0.0051	248.7937	0.0051	1	8	activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c
GO:0060426	0.0051	248.7937	0.0051	1	8	lung vasculature development
GO:0060463	0.0051	248.7937	0.0051	1	8	lung lobe morphogenesis
GO:0006108	0.0057	217.6806	0.0057	1	9	malate metabolic process
GO:0006122	0.0057	217.6806	0.0057	1	9	mitochondrial electron transport, ubiquinol to cytochrome c
GO:0060290	0.0057	217.6806	0.0057	1	9	transdifferentiation
GO:0045333	0.0059	21.0557	0.1185	2	186	cellular respiration
GO:0060180	0.0064	193.4815	0.0064	1	10	female mating behavior
GO:0006107	0.007	174.1222	0.007	1	11	oxaloacetate metabolic process
GO:0042511	0.007	174.1222	0.007	1	11	positive regulation of tyrosine phosphorylation of Stat1 protein
GO:0045835	0.007	174.1222	0.007	1	11	negative regulation of meiotic nuclear division
GO:0048711	0.0076	158.2828	0.0076	1	12	positive regulation of astrocyte differentiation
GO:0045651	0.0083	145.0833	0.0083	1	13	positive regulation of macrophage differentiation
GO:0060707	0.0083	145.0833	0.0083	1	13	trophoblast giant cell differentiation
GO:2000696	0.0089	133.9145	0.0089	1	14	regulation of epithelial cell differentiation involved in kidney development
GO:0015671	0.0095	124.3413	0.0096	1	15	oxygen transport
GO:0072160	0.0095	124.3413	0.0096	1	15	nephron tubule epithelial cell differentiation
GO:0072283	0.0095	124.3413	0.0096	1	15	metanephric renal vesicle morphogenesis
GO:0044706	0.0097	16.2216	0.153	2	240	multi-multicellular organism process

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0034660	1e-04	99.9781	0.1173	3	460	ncRNA metabolic process
GO:0006364	5e-04	107.1862	0.0375	2	147	rRNA processing
GO:0070940	0.0013	1306.9167	0.0013	1	5	dephosphorylation of RNA polymerase II C-terminal domain
GO:0009301	0.0025	580.6667	0.0025	1	10	snRNA transcription
GO:0022613	0.003	43.1887	0.091	2	357	ribonucleoprotein complex biogenesis
GO:0000028	0.0041	348.2667	0.0041	1	16	ribosomal small subunit assembly
GO:0000462	0.0064	217.5417	0.0064	1	25	maturation of SSU-rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0007186	0.0015	37.8516	0.2944	3	1155	G-protein coupled receptor signaling pathway
GO:0050911	0.0031	42.2149	0.093	2	365	detection of chemical stimulus involved in sensory perception of smell
GO:0009593	0.0047	34.3311	0.1137	2	446	detection of chemical stimulus
GO:0007606	0.0049	33.326	0.117	2	459	sensory perception of chemical stimulus
GO:0050906	0.0049	33.326	0.117	2	459	detection of stimulus involved in sensory perception
GO:0071377	0.0097	140.991	0.0097	1	38	cellular response to glucagon stimulus

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0030185	0.001	1960.5	0.001	1	3	nitric oxide transport
GO:0018298	0.0032	435.4722	0.0032	1	10	protein-chromophore linkage
GO:0015671	0.0048	279.8571	0.0048	1	15	oxygen transport
GO:0070293	0.0051	261.1833	0.0051	1	16	renal absorption
GO:0042744	0.0073	178	0.0073	1	23	hydrogen peroxide catabolic process
GO:0034109	0.0095	20.2899	0.1596	2	501	homotypic cell-cell adhesion

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0016260	0.0011	Inf	0.0011	1	1	selenocysteine biosynthetic process
GO:0043624	0.0029	12.2716	0.2947	3	272	cellular protein complex disassembly
GO:0060112	0.0032	489.75	0.0033	1	3	generation of ovulation cycle rhythm
GO:0032984	0.0044	10.5854	0.3402	3	314	macromolecular complex disassembly
GO:0001887	0.0062	19.2173	0.1192	2	110	selenium compound metabolic process
GO:0014050	0.0065	195.8625	0.0065	1	6	negative regulation of glutamate secretion
GO:0009069	0.0074	17.4286	0.1311	2	121	serine family amino acid metabolic process
GO:0032229	0.0076	163.2083	0.0076	1	7	negative regulation of synaptic transmission, GABAergic
GO:0021891	0.0086	139.8839	0.0087	1	8	olfactory bulb interneuron development

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0070301	4e-04	22.8772	0.1501	3	76	cellular response to hydrogen peroxide
GO:0016045	5e-04	71.931	0.0336	2	17	detection of bacterium
GO:0098581	9e-04	51.3596	0.0454	2	23	detection of external biotic stimulus
GO:0007344	0.002	Inf	0.002	1	1	pronuclear fusion
GO:0038158	0.002	Inf	0.002	1	1	granulocyte colony-stimulating factor signaling pathway
GO:0046380	0.002	Inf	0.002	1	1	N-acetylneuraminate biosynthetic process
GO:0048006	0.002	Inf	0.002	1	1	antigen processing and presentation, endogenous lipid antigen via MHC class Ib
GO:0006040	0.0023	31.6957	0.0711	2	36	amino sugar metabolic process
GO:1903037	0.0025	7.9074	0.5769	4	292	regulation of leukocyte cell-cell adhesion
GO:0034110	0.0028	7.6633	0.5947	4	301	regulation of homotypic cell-cell adhesion
GO:0006045	0.0039	521.9667	0.004	1	2	N-acetylglucosamine biosynthetic process
GO:0006227	0.0039	521.9667	0.004	1	2	dUDP biosynthetic process
GO:0006233	0.0039	521.9667	0.004	1	2	dTDP biosynthetic process
GO:0009139	0.0039	521.9667	0.004	1	2	pyrimidine nucleoside diphosphate biosynthetic process
GO:0009196	0.0039	521.9667	0.004	1	2	pyrimidine deoxyribonucleoside diphosphate metabolic process
GO:0034124	0.0039	521.9667	0.004	1	2	regulation of MyD88-dependent toll-like receptor signaling pathway
GO:0032655	0.0047	21.531	0.1027	2	52	regulation of interleukin-12 production
GO:0019884	0.0048	9.7049	0.3438	3	174	antigen processing and presentation of exogenous antigen
GO:0051249	0.0058	6.1734	0.733	4	371	regulation of lymphocyte activation
GO:0002486	0.0059	260.9667	0.0059	1	3	antigen processing and presentation of endogenous peptide antigen via MHC class I via ER pathway, TAP-independent
GO:0014038	0.0059	260.9667	0.0059	1	3	regulation of Schwann cell differentiation
GO:0015891	0.0059	260.9667	0.0059	1	3	siderophore transport
GO:0045590	0.0059	260.9667	0.0059	1	3	negative regulation of regulatory T cell differentiation
GO:0071586	0.0059	260.9667	0.0059	1	3	CAAX-box protein processing
GO:0050870	0.0067	8.5864	0.3872	3	196	positive regulation of T cell activation
GO:0051707	0.0072	3.9972	1.7643	6	893	response to other organism
GO:0006235	0.0079	173.9667	0.0079	1	4	dTTP biosynthetic process
GO:0009189	0.0079	173.9667	0.0079	1	4	deoxyribonucleoside diphosphate biosynthetic process
GO:0010046	0.0079	173.9667	0.0079	1	4	response to mycotoxin
GO:1903751	0.0079	173.9667	0.0079	1	4	negative regulation of intrinsic apoptotic signaling pathway in response to hydrogen peroxide
GO:1903753	0.0079	173.9667	0.0079	1	4	negative regulation of p38MAPK cascade
GO:2000564	0.0079	173.9667	0.0079	1	4	regulation of CD8-positive, alpha-beta T cell proliferation
GO:0046634	0.0079	16.2947	0.1343	2	68	regulation of alpha-beta T cell activation
GO:0000302	0.0087	7.7701	0.4267	3	216	response to reactive oxygen species
GO:0009607	0.0087	3.8319	1.8354	6	929	response to biotic stimulus
GO:0034599	0.009	7.6607	0.4327	3	219	cellular response to oxidative stress
GO:0006488	0.0091	15.1423	0.1442	2	73	dolichol-linked oligosaccharide biosynthetic process
GO:1900034	0.0098	14.5256	0.1501	2	76	regulation of cellular response to heat
GO:0009211	0.0098	130.4667	0.0099	1	5	pyrimidine deoxyribonucleoside triphosphate metabolic process
GO:0030223	0.0098	130.4667	0.0099	1	5	neutrophil differentiation
GO:0045345	0.0098	130.4667	0.0099	1	5	positive regulation of MHC class I biosynthetic process
GO:0051135	0.0098	130.4667	0.0099	1	5	positive regulation of NK T cell activation
GO:1903748	0.0098	130.4667	0.0099	1	5	negative regulation of establishment of protein localization to mitochondrion
GO:0070489	0.0099	5.2724	0.8535	4	432	T cell aggregation

Differential Methylation

Parameter Overview

Introduction: Differential Methylation of Sample Groups

Comparisons

P-values

Region Level

Differential Methylation Tables

Enrichment Analysis

References

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0019538	6e-04	2.7912	15.0359	26	5362	protein metabolic process
GO:0044260	9e-04	2.9082	22.3716	33	7978	cellular macromolecule metabolic process
GO:0002758	0.001	7.357	0.7655	5	273	innate immune response-activating signal transduction
GO:0051437	0.0011	16.2826	0.2047	3	73	positive regulation of ubiquitin-protein ligase activity involved in regulation of mitotic cell cycle transition
GO:0050849	0.0011	46.5208	0.0505	2	18	negative regulation of calcium-mediated signaling
GO:0031145	0.0017	13.8891	0.2384	3	85	anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process
GO:0045089	0.002	6.1801	0.9057	5	323	positive regulation of innate immune response
GO:0051436	0.002	13.0866	0.2524	3	90	negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle
GO:0045859	0.0022	3.9221	2.3751	8	847	regulation of protein kinase activity
GO:2000058	0.0024	12.3714	0.2664	3	95	regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process
GO:0000188	0.0024	30.998	0.0729	2	26	inactivation of MAPK activity
GO:0002253	0.0024	4.9048	1.3853	6	494	activation of immune response
GO:0051351	0.0025	12.1066	0.272	3	97	positive regulation of ligase activity
GO:0051352	0.0026	11.9784	0.2748	3	98	negative regulation of ligase activity
GO:0001193	0.0028	Inf	0.0028	1	1	maintenance of transcriptional fidelity during DNA-templated transcription elongation from RNA polymerase II promoter
GO:0038061	0.003	11.3759	0.2888	3	103	NIK/NF-kappaB signaling
GO:0051348	0.0033	5.4909	1.0151	5	362	negative regulation of transferase activity
GO:0001933	0.004	5.2499	1.06	5	378	negative regulation of protein phosphorylation
GO:0002223	0.0045	9.7967	0.3337	3	119	stimulatory C-type lectin receptor signaling pathway
GO:0090068	0.0047	6.4469	0.6814	4	243	positive regulation of cell cycle process
GO:0007050	0.005	6.3127	0.6954	4	248	cell cycle arrest
GO:0071901	0.005	9.3888	0.3477	3	124	negative regulation of protein serine/threonine kinase activity
GO:0006227	0.0056	363.8605	0.0056	1	2	dUDP biosynthetic process
GO:0006233	0.0056	363.8605	0.0056	1	2	dTDP biosynthetic process
GO:0009139	0.0056	363.8605	0.0056	1	2	pyrimidine nucleoside diphosphate biosynthetic process
GO:0009196	0.0056	363.8605	0.0056	1	2	pyrimidine deoxyribonucleoside diphosphate metabolic process
GO:0034124	0.0056	363.8605	0.0056	1	2	regulation of MyD88-dependent toll-like receptor signaling pathway
GO:0044743	0.0056	19.5602	0.1122	2	40	intracellular protein transmembrane import
GO:0006413	0.0056	6.1091	0.7179	4	256	translational initiation
GO:0051438	0.0059	8.8714	0.3673	3	131	regulation of ubiquitin-protein transferase activity
GO:0032269	0.0061	3.2724	2.8126	8	1003	negative regulation of cellular protein metabolic process
GO:0002764	0.0069	3.9123	1.7189	6	613	immune response-regulating signaling pathway
GO:0031397	0.0075	8.1047	0.401	3	143	negative regulation of protein ubiquitination
GO:0043043	0.0079	3.8014	1.7666	6	630	peptide biosynthetic process
GO:1901987	0.0079	5.5284	0.7908	4	282	regulation of cell cycle phase transition
GO:0045590	0.0084	181.9186	0.0084	1	3	negative regulation of regulatory T cell differentiation
GO:0043405	0.0084	4.3495	1.2703	5	453	regulation of MAP kinase activity
GO:0071806	0.0093	14.8543	0.1458	2	52	protein transmembrane transport
GO:0050852	0.0096	7.3613	0.4403	3	157	T cell receptor signaling pathway

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0006612	0	16.1059	0.3732	5	183	protein targeting to membrane
GO:0006364	2e-04	15.5005	0.2998	4	147	rRNA processing
GO:0022613	7e-04	8.0529	0.7281	5	357	ribonucleoprotein complex biogenesis
GO:1901566	0.001	4.2683	2.7001	9	1324	organonitrogen compound biosynthetic process
GO:0006614	0.0012	16.2591	0.208	3	102	SRP-dependent cotranslational protein targeting to membrane
GO:0006412	0.0012	5.7919	1.2359	6	606	translation
GO:0014861	0.002	Inf	0.002	1	1	regulation of skeletal muscle contraction via regulation of action potential
GO:0033552	0.002	Inf	0.002	1	1	response to vitamin B3
GO:0035684	0.002	Inf	0.002	1	1	helper T cell extravasation
GO:0001912	0.0022	32.5562	0.0693	2	34	positive regulation of leukocyte mediated cytotoxicity
GO:0034660	0.0022	6.188	0.9381	5	460	ncRNA metabolic process
GO:0043604	0.0027	4.9315	1.4398	6	706	amide biosynthetic process
GO:0006518	0.0036	4.6328	1.5275	6	749	peptide metabolic process
GO:0002434	0.0041	505.0968	0.0041	1	2	immune complex clearance
GO:0006542	0.0041	505.0968	0.0041	1	2	glutamine biosynthetic process
GO:0071403	0.0041	505.0968	0.0041	1	2	cellular response to high density lipoprotein particle stimulus
GO:0090076	0.0041	505.0968	0.0041	1	2	relaxation of skeletal muscle
GO:0090265	0.0041	505.0968	0.0041	1	2	positive regulation of immune complex clearance by monocytes and macrophages
GO:0042255	0.0043	22.6275	0.0979	2	48	ribosome assembly
GO:0045085	0.0061	252.5323	0.0061	1	3	negative regulation of interleukin-2 biosynthetic process
GO:2000502	0.0061	252.5323	0.0061	1	3	negative regulation of natural killer cell chemotaxis
GO:0031341	0.0062	18.575	0.1183	2	58	regulation of cell killing
GO:0044802	0.0072	3.9809	1.762	6	864	single-organism membrane organization
GO:0045047	0.0074	185.2024	0.0074	1	4	protein targeting to ER
GO:0045039	0.0081	168.3441	0.0082	1	4	protein import into mitochondrial inner membrane
GO:0072594	0.0087	4.4104	1.297	5	636	establishment of protein localization to organelle

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0006414	0	21.8147	0.2961	5	202	translational elongation
GO:0072599	0	30.9076	0.1612	4	110	establishment of protein localization to endoplasmic reticulum
GO:0006415	1e-04	19.4236	0.2521	4	172	translational termination
GO:0043043	2e-04	8.509	0.9235	6	630	peptide biosynthetic process
GO:0016259	2e-04	28.8648	0.1231	3	84	selenocysteine metabolic process
GO:0006614	4e-04	23.5894	0.1495	3	102	SRP-dependent cotranslational protein targeting to membrane
GO:0006413	5e-04	12.8789	0.3752	4	256	translational initiation
GO:0000184	6e-04	21.023	0.1671	3	114	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0043241	9e-04	10.7846	0.4456	4	304	protein complex disassembly
GO:0071584	0.0015	Inf	0.0015	1	1	negative regulation of zinc ion transmembrane import
GO:0071585	0.0015	Inf	0.0015	1	1	detoxification of cadmium ion
GO:2000872	0.0015	Inf	0.0015	1	1	positive regulation of progesterone secretion
GO:0043603	0.0016	5.7507	1.3368	6	912	cellular amide metabolic process
GO:0010324	0.0018	36.2997	0.063	2	43	membrane invagination
GO:0050911	0.0018	8.9267	0.535	4	365	detection of chemical stimulus involved in sensory perception of smell
GO:0006612	0.0019	14.0554	0.2483	3	177	protein targeting to membrane
GO:0019083	0.0024	12.6926	0.2726	3	186	viral transcription
GO:0071580	0.0029	712.1364	0.0029	1	2	regulation of zinc ion transmembrane transport
GO:0071582	0.0029	712.1364	0.0029	1	2	negative regulation of zinc ion transport
GO:0097501	0.0029	712.1364	0.0029	1	2	stress response to metal ion
GO:0006402	0.0031	11.6601	0.2961	3	202	mRNA catabolic process
GO:0044033	0.0033	11.3706	0.3034	3	207	multi-organism metabolic process
GO:0019058	0.0034	7.425	0.6391	4	436	viral life cycle
GO:0009593	0.0037	7.2522	0.6538	4	446	detection of chemical stimulus
GO:0007606	0.0041	7.039	0.6728	4	459	sensory perception of chemical stimulus
GO:0050906	0.0041	7.039	0.6728	4	459	detection of stimulus involved in sensory perception
GO:0006407	0.0044	356.0455	0.0044	1	3	rRNA export from nucleus
GO:0070574	0.0059	237.3485	0.0059	1	4	cadmium ion transmembrane transport
GO:0044802	0.0073	4.7888	1.2665	5	864	single-organism membrane organization
GO:0006620	0.0088	142.3909	0.0088	1	6	posttranslational protein targeting to membrane

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0048208	2e-04	29.3492	0.1183	3	58	COPII vesicle coating
GO:0043241	3e-04	9.5132	0.62	5	304	protein complex disassembly
GO:0048199	4e-04	23.3733	0.1468	3	72	vesicle targeting, to, from or within Golgi
GO:1902591	6e-04	20.6645	0.1652	3	81	single-organism membrane budding
GO:1903020	7e-04	61.3412	0.0387	2	19	positive regulation of glycoprotein metabolic process
GO:0051668	8e-04	18.7326	0.1815	3	89	localization within membrane
GO:0010509	0.002	Inf	0.002	1	1	polyamine homeostasis
GO:0018153	0.002	Inf	0.002	1	1	isopeptide cross-linking via N6-(L-isoglutamyl)-L-lysine
GO:2000872	0.002	Inf	0.002	1	1	positive regulation of progesterone secretion
GO:0019068	0.0028	28.1477	0.0795	2	39	virion assembly
GO:0022411	0.0035	4.6591	1.5193	6	745	cellular component disassembly
GO:0000964	0.0041	505.0968	0.0041	1	2	mitochondrial RNA 5'-end processing
GO:0042418	0.0041	505.0968	0.0041	1	2	epinephrine biosynthetic process
GO:0006888	0.0043	10.0846	0.3304	3	162	ER to Golgi vesicle-mediated transport
GO:0006415	0.0044	9.9985	0.3339	3	169	translational termination
GO:0001510	0.0045	22.1447	0.0999	2	49	RNA methylation
GO:0031424	0.0045	22.1447	0.0999	2	49	keratinization
GO:0018149	0.0056	19.6302	0.1122	2	55	peptide cross-linking
GO:0009913	0.006	8.896	0.3732	3	183	epidermal cell differentiation
GO:0006452	0.0061	252.5323	0.0061	1	3	translational frameshifting
GO:0045905	0.0061	252.5323	0.0061	1	3	positive regulation of translational termination
GO:0060061	0.0061	252.5323	0.0061	1	3	Spemann organizer formation
GO:0060715	0.0061	252.5323	0.0061	1	3	syncytiotrophoblast cell differentiation involved in labyrinthine layer development
GO:1901382	0.0061	252.5323	0.0061	1	3	regulation of chorionic trophoblast cell proliferation
GO:0006414	0.0069	8.4951	0.3913	3	198	translational elongation
GO:0043933	0.0074	2.8159	5.0312	11	2467	macromolecular complex subunit organization
GO:0000045	0.008	16.2448	0.1346	2	66	autophagosome assembly
GO:0008612	0.0081	168.3441	0.0082	1	4	peptidyl-lysine modification to peptidyl-hypusine
GO:0045901	0.0081	168.3441	0.0082	1	4	positive regulation of translational elongation
GO:0090646	0.0081	168.3441	0.0082	1	4	mitochondrial tRNA processing
GO:1903251	0.0081	168.3441	0.0082	1	4	multi-ciliated epithelial cell differentiation
GO:0043043	0.0084	4.4545	1.2848	5	630	peptide biosynthetic process
GO:0051650	0.0089	7.6845	0.4303	3	211	establishment of vesicle localization