RnBeads: uWGBS - prog_v08_um

Option	Value
analyze.sites	no
region.types	tiling, cpgislands, genes, promoters, ensembleRegBuildBPall, ensembleRegBuildBPallMerged
differential.permutations	0
differential.comparison.columns	cmp_ct_CMPvGMP, cmp_ct_CMPvCLP, cmp_ct_CLPvMLP0, cmp_ct_HSCvMPP, cmp_ct_MPPvCMP, cmp_ct_MPPvMLP0, cmp_ct_MPPvCLP, cmp_ct_HSCvML
differential.comparison.columns.all.pairwise	default
columns.pairing	default
differential.site.test.method	limma
covariate.adjustment.columns	sex, donorId, flowcell, cellSourceCurated
differential.adjustment.sva	yes
differential.adjustment.celltype	yes
differential.enrichment	yes

	comparison	adjustment	covariateTable
1	CMP vs. GMP (based on cmp_ct_CMPvGMP)		csv
2	CLP vs. CMP (based on cmp_ct_CMPvCLP)		csv
3	CLP vs. MLP0 (based on cmp_ct_CLPvMLP0)		csv
4	HSC vs. MPP (based on cmp_ct_HSCvMPP)		csv
5	CMP vs. MPP (based on cmp_ct_MPPvCMP)		csv
6	MLP0 vs. MPP (based on cmp_ct_MPPvMLP0)		csv
7	CLP vs. MPP (based on cmp_ct_MPPvCLP)		csv
8	HSC vs. ML (based on cmp_ct_HSCvML)	donorId,flowcell	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
CMP vs. GMP (based on cmp_ct_CMPvGMP)	0	0	0	0	0	0
CLP vs. CMP (based on cmp_ct_CMPvCLP)	0	0	0	0	0	0
CLP vs. MLP0 (based on cmp_ct_CLPvMLP0)	0	0	0	0	0	0
HSC vs. MPP (based on cmp_ct_HSCvMPP)	0	0	0	0	0	0
CMP vs. MPP (based on cmp_ct_MPPvCMP)	0	0	0	0	0	0
MLP0 vs. MPP (based on cmp_ct_MPPvMLP0)	0	0	0	0	0	0
CLP vs. MPP (based on cmp_ct_MPPvCLP)	0	0	0	0	0	0
HSC vs. ML (based on cmp_ct_HSCvML)	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
CMP vs. GMP (based on cmp_ct_CMPvGMP)	csv	csv	csv	csv	csv	csv
CLP vs. CMP (based on cmp_ct_CMPvCLP)	csv	csv	csv	csv	csv	csv
CLP vs. MLP0 (based on cmp_ct_CLPvMLP0)	csv	csv	csv	csv	csv	csv
HSC vs. MPP (based on cmp_ct_HSCvMPP)	csv	csv	csv	csv	csv	csv
CMP vs. MPP (based on cmp_ct_MPPvCMP)	csv	csv	csv	csv	csv	csv
MLP0 vs. MPP (based on cmp_ct_MPPvMLP0)	csv	csv	csv	csv	csv	csv
CLP vs. MPP (based on cmp_ct_MPPvCLP)	csv	csv	csv	csv	csv	csv
HSC vs. ML (based on cmp_ct_HSCvML)	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:0043456	0	359.6782	0.0099	2	5	regulation of pentose-phosphate shunt
GO:0006006	1e-04	14.0704	0.427	5	216	glucose metabolic process
GO:0010675	3e-04	14.8091	0.3143	4	159	regulation of cellular carbohydrate metabolic process
GO:0005996	3e-04	10.1494	0.5852	5	296	monosaccharide metabolic process
GO:0043101	3e-04	89.8678	0.0277	2	14	purine-containing compound salvage
GO:0009310	4e-04	77.0197	0.0316	2	16	amine catabolic process
GO:0014912	4e-04	77.0197	0.0316	2	16	negative regulation of smooth muscle cell migration
GO:0001708	6e-04	20.0938	0.17	3	86	cell fate specification
GO:0019682	7e-04	59.8889	0.0395	2	20	glyceraldehyde-3-phosphate metabolic process
GO:0051156	0.0012	44.8994	0.0514	2	26	glucose 6-phosphate metabolic process
GO:1901575	0.0014	3.8114	3.4559	10	1748	organic substance catabolic process
GO:0019439	0.0015	6.8227	0.858	5	434	aromatic compound catabolic process
GO:0019362	0.0016	14.4727	0.2333	3	118	pyridine nucleotide metabolic process
GO:1901564	0.0016	3.5485	4.1735	11	2111	organonitrogen compound metabolic process
GO:0043603	0.0017	4.7406	1.807	7	914	cellular amide metabolic process
GO:0006739	0.0019	34.7453	0.0652	2	33	NADP metabolic process
GO:0006148	0.002	Inf	0.002	1	1	inosine catabolic process
GO:0006168	0.002	Inf	0.002	1	1	adenine salvage
GO:0006738	0.002	Inf	0.002	1	1	nicotinamide riboside catabolic process
GO:0019428	0.002	Inf	0.002	1	1	allantoin biosynthetic process
GO:0019628	0.002	Inf	0.002	1	1	urate catabolic process
GO:0034356	0.002	Inf	0.002	1	1	NAD biosynthesis via nicotinamide riboside salvage pathway
GO:0034418	0.002	Inf	0.002	1	1	urate biosynthetic process
GO:0035262	0.002	Inf	0.002	1	1	gonad morphogenesis
GO:0050983	0.002	Inf	0.002	1	1	deoxyhypusine biosynthetic process from spermidine
GO:0070637	0.002	Inf	0.002	1	1	pyridine nucleoside metabolic process
GO:1904205	0.002	Inf	0.002	1	1	negative regulation of skeletal muscle hypertrophy
GO:0060795	0.0022	32.6353	0.0692	2	35	cell fate commitment involved in formation of primary germ layer
GO:0009058	0.0023	2.9921	11.7337	20	5935	biosynthetic process
GO:0006144	0.0024	30.9762	0.0727	2	38	purine nucleobase metabolic process
GO:0042278	0.003	7.5286	0.605	4	306	purine nucleoside metabolic process
GO:0043470	0.0032	26.254	0.085	2	43	regulation of carbohydrate catabolic process
GO:0007519	0.0037	10.6408	0.3143	3	159	skeletal muscle tissue development
GO:0009119	0.0039	6.9634	0.6524	4	330	ribonucleoside metabolic process
GO:0002302	0.004	521.6	0.004	1	2	CD8-positive, alpha-beta T cell differentiation involved in immune response
GO:0044209	0.004	521.6	0.004	1	2	AMP salvage
GO:0046083	0.004	521.6	0.004	1	2	adenine metabolic process
GO:0060809	0.004	521.6	0.004	1	2	mesodermal to mesenchymal transition involved in gastrulation
GO:1902732	0.004	521.6	0.004	1	2	positive regulation of chondrocyte proliferation
GO:0051196	0.004	23.3928	0.0949	2	48	regulation of coenzyme metabolic process
GO:0071320	0.004	23.3928	0.0949	2	48	cellular response to cAMP
GO:0051186	0.0046	6.6307	0.6841	4	346	cofactor metabolic process
GO:2001238	0.0049	21.0926	0.1048	2	53	positive regulation of extrinsic apoptotic signaling pathway
GO:0019748	0.0055	19.917	0.1107	2	56	secondary metabolic process
GO:0006576	0.0055	9.2077	0.3618	3	183	cellular biogenic amine metabolic process
GO:1901657	0.0058	6.1862	0.7315	4	370	glycosyl compound metabolic process
GO:0019674	0.0058	19.2032	0.1147	2	58	NAD metabolic process
GO:0021912	0.0059	260.7833	0.0059	1	3	regulation of transcription from RNA polymerase II promoter involved in spinal cord motor neuron fate specification
GO:0033512	0.0059	260.7833	0.0059	1	3	L-lysine catabolic process to acetyl-CoA via saccharopine
GO:0097168	0.0059	260.7833	0.0059	1	3	mesenchymal stem cell proliferation
GO:2001022	0.0069	17.6235	0.1246	2	63	positive regulation of response to DNA damage stimulus
GO:0006082	0.007	3.6094	2.327	7	1177	organic acid metabolic process
GO:0006096	0.0073	17.0619	0.1285	2	65	glycolytic process
GO:0001707	0.0075	16.7942	0.1305	2	66	mesoderm formation
GO:0014812	0.0075	16.7942	0.1305	2	66	muscle cell migration
GO:0006598	0.0079	173.8444	0.0079	1	4	polyamine catabolic process
GO:0008612	0.0079	173.8444	0.0079	1	4	peptidyl-lysine modification to peptidyl-hypusine
GO:0010917	0.0079	173.8444	0.0079	1	4	negative regulation of mitochondrial membrane potential
GO:0019477	0.0079	173.8444	0.0079	1	4	L-lysine catabolic process
GO:0021913	0.0079	173.8444	0.0079	1	4	regulation of transcription from RNA polymerase II promoter involved in ventral spinal cord interneuron specification
GO:1902093	0.0079	173.8444	0.0079	1	4	positive regulation of sperm motility
GO:0044270	0.0081	5.6182	0.8057	4	421	cellular nitrogen compound catabolic process
GO:0046700	0.0081	5.6182	0.8057	4	421	heterocycle catabolic process
GO:0044275	0.0086	15.5722	0.1404	2	71	cellular carbohydrate catabolic process
GO:0055086	0.0089	4.4022	1.3048	5	660	nucleobase-containing small molecule metabolic process
GO:0048608	0.0091	5.4115	0.8323	4	421	reproductive structure development
GO:0046031	0.0094	14.9205	0.1463	2	74	ADP metabolic process
GO:0072526	0.0098	130.375	0.0099	1	5	pyridine-containing compound catabolic process
GO:0097052	0.0098	130.375	0.0099	1	5	L-kynurenine metabolic process
GO:1903898	0.0098	130.375	0.0099	1	5	negative regulation of PERK-mediated unfolded protein response
GO:1903912	0.0098	130.375	0.0099	1	5	negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0030947	3e-04	89.3657	0.0276	2	27	regulation of vascular endothelial growth factor receptor signaling pathway
GO:0061301	0.001	Inf	0.001	1	1	cerebellum vasculature morphogenesis
GO:0071806	0.0013	44.6114	0.0531	2	52	protein transmembrane transport
GO:0035470	0.002	1044.2	0.002	1	2	positive regulation of vascular wound healing
GO:1903378	0.0031	522.0667	0.0031	1	3	positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway
GO:0007223	0.0041	348.0222	0.0041	1	4	Wnt signaling pathway, calcium modulating pathway
GO:0035426	0.0041	348.0222	0.0041	1	4	extracellular matrix-cell signaling
GO:0042701	0.0041	348.0222	0.0041	1	4	progesterone secretion
GO:0042760	0.0051	261	0.0051	1	5	very long-chain fatty acid catabolic process
GO:0060754	0.0051	261	0.0051	1	5	positive regulation of mast cell chemotaxis
GO:0061304	0.0051	261	0.0051	1	5	retinal blood vessel morphogenesis
GO:0008203	0.0064	18.9829	0.1214	2	119	cholesterol metabolic process
GO:0006633	0.009	15.8408	0.1449	2	142	fatty acid biosynthetic process
GO:0046322	0.0091	130.4667	0.0092	1	9	negative regulation of fatty acid oxidation
GO:1903209	0.0091	130.4667	0.0092	1	9	positive regulation of oxidative stress-induced cell death

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0032918	0.001	Inf	0.001	1	1	spermidine acetylation
GO:0032919	0.001	Inf	0.001	1	1	spermine acetylation
GO:0032920	0.001	Inf	0.001	1	1	putrescine acetylation
GO:0038158	0.001	Inf	0.001	1	1	granulocyte colony-stimulating factor signaling pathway
GO:0046204	0.001	Inf	0.001	1	1	nor-spermidine metabolic process
GO:0009447	0.0019	1118.8571	0.0019	1	2	putrescine catabolic process
GO:1903378	0.0029	559.3929	0.0029	1	3	positive regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway
GO:0030223	0.0048	279.6607	0.0048	1	5	neutrophil differentiation
GO:0045217	0.0067	186.4167	0.0067	1	7	cell-cell junction maintenance
GO:2001020	0.0079	17.0604	0.1358	2	142	regulation of response to DNA damage stimulus
GO:1903209	0.0086	139.7946	0.0086	1	9	positive regulation of oxidative stress-induced cell death
GO:0007156	0.0089	16.0207	0.1445	2	151	homophilic cell adhesion via plasma membrane adhesion molecules
GO:0048552	0.0095	124.254	0.0096	1	10	regulation of metalloenzyme activity
GO:1903203	0.0095	124.254	0.0096	1	10	regulation of oxidative stress-induced neuron death

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0048387	7e-04	57.8926	0.0407	2	29	negative regulation of retinoic acid receptor signaling pathway
GO:0006148	0.0014	Inf	0.0014	1	1	inosine catabolic process
GO:0006738	0.0014	Inf	0.0014	1	1	nicotinamide riboside catabolic process
GO:0032646	0.0014	Inf	0.0014	1	1	regulation of hepatocyte growth factor production
GO:0034356	0.0014	Inf	0.0014	1	1	NAD biosynthesis via nicotinamide riboside salvage pathway
GO:0034418	0.0014	Inf	0.0014	1	1	urate biosynthetic process
GO:0048178	0.0014	Inf	0.0014	1	1	negative regulation of hepatocyte growth factor biosynthetic process
GO:0070637	0.0014	Inf	0.0014	1	1	pyridine nucleoside metabolic process
GO:0045645	0.0028	745.5714	0.0028	1	2	positive regulation of eosinophil differentiation
GO:0045659	0.0028	745.5714	0.0028	1	2	negative regulation of neutrophil differentiation
GO:1902732	0.0028	745.5714	0.0028	1	2	positive regulation of chondrocyte proliferation
GO:0060279	0.0042	372.7619	0.0042	1	3	positive regulation of ovulation
GO:0097168	0.0042	372.7619	0.0042	1	3	mesenchymal stem cell proliferation
GO:0034653	0.0056	248.4921	0.0056	1	4	retinoic acid catabolic process
GO:0046881	0.0056	248.4921	0.0056	1	4	positive regulation of follicle-stimulating hormone secretion
GO:0033578	0.007	186.3571	0.007	1	5	protein glycosylation in Golgi
GO:0046882	0.007	186.3571	0.007	1	5	negative regulation of follicle-stimulating hormone secretion
GO:0072526	0.007	186.3571	0.007	1	5	pyridine-containing compound catabolic process
GO:0016115	0.0084	149.0762	0.0084	1	6	terpenoid catabolic process
GO:0034382	0.0098	124.2222	0.0098	1	7	chylomicron remnant clearance
GO:0072038	0.0098	124.2222	0.0098	1	7	mesenchymal stem cell maintenance involved in nephron morphogenesis
GO:0072161	0.0098	124.2222	0.0098	1	7	mesenchymal cell differentiation involved in kidney development

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0007218	4e-04	23.8498	0.1467	3	92	neuropeptide signaling pathway
GO:0007194	7e-04	61.7905	0.0383	2	24	negative regulation of adenylate cyclase activity
GO:0018106	0.0016	Inf	0.0016	1	1	peptidyl-histidine phosphorylation
GO:0019046	0.0016	Inf	0.0016	1	1	release from viral latency
GO:0071881	0.0016	Inf	0.0016	1	1	adenylate cyclase-inhibiting adrenergic receptor signaling pathway
GO:0071882	0.0016	Inf	0.0016	1	1	phospholipase C-activating adrenergic receptor signaling pathway
GO:2000057	0.0016	Inf	0.0016	1	1	negative regulation of Wnt signaling pathway involved in digestive tract morphogenesis
GO:2000326	0.0016	Inf	0.0016	1	1	negative regulation of ligand-dependent nuclear receptor transcription coactivator activity
GO:0030803	0.0017	37.7271	0.0606	2	38	negative regulation of cyclic nucleotide biosynthetic process
GO:0030815	0.0018	35.7368	0.0638	2	40	negative regulation of cAMP metabolic process
GO:1900372	0.0018	35.7368	0.0638	2	40	negative regulation of purine nucleotide biosynthetic process
GO:0002302	0.0032	652.25	0.0032	1	2	CD8-positive, alpha-beta T cell differentiation involved in immune response
GO:0048213	0.0032	652.25	0.0032	1	2	Golgi vesicle prefusion complex stabilization
GO:0060809	0.0032	652.25	0.0032	1	2	mesodermal to mesenchymal transition involved in gastrulation
GO:0070473	0.0032	652.25	0.0032	1	2	negative regulation of uterine smooth muscle contraction
GO:0071373	0.0032	652.25	0.0032	1	2	cellular response to luteinizing hormone stimulus
GO:0051224	0.0036	10.9246	0.3125	3	196	negative regulation of protein transport
GO:0019637	0.0042	4.6328	1.6024	6	1005	organophosphate metabolic process
GO:0042308	0.0048	21.521	0.1036	2	65	negative regulation of protein import into nucleus
GO:0014717	0.0048	326.1042	0.0048	1	3	regulation of satellite cell activation involved in skeletal muscle regeneration
GO:0071314	0.0048	326.1042	0.0048	1	3	cellular response to cocaine
GO:0071878	0.0048	326.1042	0.0048	1	3	negative regulation of adrenergic receptor signaling pathway
GO:0071883	0.0048	326.1042	0.0048	1	3	activation of MAPK activity by adrenergic receptor signaling pathway
GO:0045980	0.0049	21.1834	0.1052	2	66	negative regulation of nucleotide metabolic process
GO:0009152	0.0059	9.1051	0.3731	3	234	purine ribonucleotide biosynthetic process
GO:0046888	0.006	19.0863	0.1164	2	73	negative regulation of hormone secretion
GO:0006990	0.0064	217.3889	0.0064	1	4	positive regulation of transcription from RNA polymerase II promoter involved in unfolded protein response
GO:0035625	0.0064	217.3889	0.0064	1	4	epidermal growth factor-activated receptor transactivation by G-protein coupled receptor signaling pathway
GO:0050955	0.0064	217.3889	0.0064	1	4	thermoception
GO:0031279	0.0068	17.8249	0.1244	2	78	regulation of cyclase activity
GO:0046390	0.0069	8.6127	0.3938	3	247	ribose phosphate biosynthetic process
GO:0051339	0.0071	17.3657	0.1276	2	80	regulation of lyase activity
GO:0072522	0.0073	8.4027	0.4034	3	253	purine-containing compound biosynthetic process
GO:0014719	0.0079	163.0312	0.008	1	5	skeletal muscle satellite cell activation
GO:0045198	0.0095	130.4167	0.0096	1	6	establishment of epithelial cell apical/basal polarity
GO:0071712	0.0095	130.4167	0.0096	1	6	ER-associated misfolded protein catabolic process
GO:1990314	0.0095	130.4167	0.0096	1	6	cellular response to insulin-like growth factor stimulus

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0090155	0.0017	979.3125	0.0017	1	3	negative regulation of sphingolipid biosynthetic process
GO:0032277	0.0052	244.7344	0.0052	1	9	negative regulation of gonadotropin secretion
GO:0048245	0.0063	195.7625	0.0063	1	11	eosinophil chemotaxis
GO:0016558	0.0074	163.1146	0.0075	1	13	protein import into peroxisome matrix
GO:0050930	0.008	150.5577	0.008	1	14	induction of positive chemotaxis
GO:1904874	0.008	150.5577	0.008	1	14	positive regulation of telomerase RNA localization to Cajal body
GO:0090670	0.0086	139.7946	0.0086	1	15	RNA localization to Cajal body
GO:0090672	0.0086	139.7946	0.0086	1	15	telomerase RNA localization
GO:0001522	0.0091	130.4667	0.0092	1	16	pseudouridine synthesis
GO:0043574	0.0097	122.3047	0.0098	1	17	peroxisomal transport
GO:0072663	0.0097	122.3047	0.0098	1	17	establishment of protein localization to peroxisome

Differential Methylation

Parameter Overview

Introduction: Differential Methylation of Sample Groups

Comparisons

P-values

Region Level

Differential Methylation Tables

Enrichment Analysis

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:1903723	8e-04	Inf	8e-04	1	1	negative regulation of centriole elongation
GO:0050911	0.0023	14.1339	0.2786	3	364	detection of chemical stimulus involved in sensory perception of smell
GO:0009593	0.0041	11.4827	0.3406	3	445	detection of chemical stimulus
GO:0007606	0.0045	11.1451	0.3505	3	458	sensory perception of chemical stimulus
GO:0050906	0.0045	11.1451	0.3505	3	458	detection of stimulus involved in sensory perception
GO:0051783	0.0071	18.5641	0.1293	2	169	regulation of nuclear division
GO:0010826	0.0076	158.1717	0.0077	1	10	negative regulation of centrosome duplication
GO:0048552	0.0076	158.1717	0.0077	1	10	regulation of metalloenzyme activity
GO:0070886	0.0076	158.1717	0.0077	1	10	positive regulation of calcineurin-NFAT signaling cascade
GO:1904903	0.0076	158.1717	0.0077	1	10	ESCRT III complex disassembly
GO:0045741	0.0084	142.3455	0.0084	1	11	positive regulation of epidermal growth factor-activated receptor activity
GO:1901673	0.0084	142.3455	0.0084	1	11	regulation of mitotic spindle assembly
GO:0007186	0.0089	6.3181	0.8824	4	1153	G-protein coupled receptor signaling pathway
GO:0046599	0.0099	118.6061	0.0099	1	13	regulation of centriole replication

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0009649	0.0011	46.2993	0.0499	2	27	entrainment of circadian clock
GO:0006413	0.0012	9.7771	0.4735	4	256	translational initiation
GO:0015742	0.0037	558.9286	0.0037	1	2	alpha-ketoglutarate transport
GO:0060474	0.0037	558.9286	0.0037	1	2	positive regulation of sperm motility involved in capacitation
GO:0071931	0.0037	558.9286	0.0037	1	2	positive regulation of transcription involved in G1/S transition of mitotic cell cycle
GO:0016071	0.0041	5.3749	1.0893	5	589	mRNA metabolic process
GO:0000956	0.0049	9.6992	0.3459	3	187	nuclear-transcribed mRNA catabolic process
GO:0030185	0.0055	279.4464	0.0055	1	3	nitric oxide transport
GO:0034473	0.0055	279.4464	0.0055	1	3	U1 snRNA 3'-end processing
GO:0034476	0.0055	279.4464	0.0055	1	3	U5 snRNA 3'-end processing
GO:0061030	0.0055	279.4464	0.0055	1	3	epithelial cell differentiation involved in mammary gland alveolus development
GO:0043043	0.0056	4.992	1.1689	5	632	peptide biosynthetic process
GO:0015711	0.0061	6.1319	0.7435	4	402	organic anion transport
GO:0003166	0.0074	186.2857	0.0074	1	4	bundle of His development
GO:0061031	0.0074	186.2857	0.0074	1	4	endodermal digestive tract morphogenesis
GO:0071042	0.0074	186.2857	0.0074	1	4	nuclear polyadenylation-dependent mRNA catabolic process
GO:0006401	0.0087	7.8052	0.4272	3	231	RNA catabolic process
GO:0000467	0.0092	139.7054	0.0092	1	5	exonucleolytic trimming to generate mature 3'-end of 5.8S rRNA from tricistronic rRNA transcript (SSU-rRNA, 5.8S rRNA, LSU-rRNA)
GO:0045578	0.0092	139.7054	0.0092	1	5	negative regulation of B cell differentiation
GO:0071038	0.0092	139.7054	0.0092	1	5	nuclear polyadenylation-dependent tRNA catabolic process
GO:1903898	0.0092	139.7054	0.0092	1	5	negative regulation of PERK-mediated unfolded protein response
GO:1903912	0.0092	139.7054	0.0092	1	5	negative regulation of endoplasmic reticulum stress-induced eIF2 alpha phosphorylation

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:1904431	0	921.1176	0.0048	2	4	positive regulation of t-circle formation
GO:0010792	0	460.5	0.0073	2	6	DNA double-strand break processing involved in repair via single-strand annealing
GO:0050911	8e-04	11.3341	0.4411	4	364	detection of chemical stimulus involved in sensory perception of smell
GO:0036297	0.0012	45.9441	0.0509	2	42	interstrand cross-link repair
GO:0031424	0.0015	39.9361	0.0582	2	48	keratinization
GO:0009593	0.0018	9.2033	0.5392	4	445	detection of chemical stimulus
GO:0018149	0.0019	35.3145	0.0654	2	54	peptide cross-linking
GO:0007606	0.002	8.9322	0.555	4	458	sensory perception of chemical stimulus
GO:0050906	0.002	8.9322	0.555	4	458	detection of stimulus involved in sensory perception
GO:0060474	0.0024	870	0.0024	1	2	positive regulation of sperm motility involved in capacitation
GO:0032204	0.0027	29.5996	0.0776	2	64	regulation of telomere maintenance
GO:0000726	0.0034	26.2034	0.0872	2	72	non-recombinational repair
GO:0003008	0.0048	4.289	2.2805	7	1882	system process
GO:1901317	0.0085	144.9537	0.0085	1	7	regulation of sperm motility

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0019083	1e-04	22.6799	0.2254	4	186	viral transcription
GO:0044033	1e-04	20.3061	0.2508	4	207	multi-organism metabolic process
GO:0016259	1e-04	36.0648	0.1018	3	84	selenocysteine metabolic process
GO:0030593	1e-04	35.1913	0.1042	3	86	neutrophil chemotaxis
GO:0006614	2e-04	29.4735	0.1236	3	102	SRP-dependent cotranslational protein targeting to membrane
GO:0072599	3e-04	27.2558	0.1333	3	110	establishment of protein localization to endoplasmic reticulum
GO:0097530	3e-04	27.2558	0.1333	3	110	granulocyte migration
GO:0000184	3e-04	26.2669	0.1381	3	114	nuclear-transcribed mRNA catabolic process, nonsense-mediated decay
GO:0071346	6e-04	21.891	0.1648	3	136	cellular response to interferon-gamma
GO:0006415	0.0011	17.1879	0.2084	3	172	translational termination
GO:0043085	0.0012	5.6061	1.797	7	1483	positive regulation of catalytic activity
GO:0007634	0.0012	Inf	0.0012	1	1	optokinetic behavior
GO:0021560	0.0012	Inf	0.0012	1	1	abducens nerve development
GO:0021599	0.0012	Inf	0.0012	1	1	abducens nerve formation
GO:0032113	0.0012	Inf	0.0012	1	1	regulation of carbohydrate phosphatase activity
GO:0032812	0.0012	Inf	0.0012	1	1	positive regulation of epinephrine secretion
GO:0032918	0.0012	Inf	0.0012	1	1	spermidine acetylation
GO:0032919	0.0012	Inf	0.0012	1	1	spermine acetylation
GO:0032920	0.0012	Inf	0.0012	1	1	putrescine acetylation
GO:0046204	0.0012	Inf	0.0012	1	1	nor-spermidine metabolic process
GO:0060550	0.0012	Inf	0.0012	1	1	positive regulation of fructose 1,6-bisphosphate 1-phosphatase activity
GO:0060552	0.0012	Inf	0.0012	1	1	positive regulation of fructose 1,6-bisphosphate metabolic process
GO:0090035	0.0012	Inf	0.0012	1	1	positive regulation of chaperone-mediated protein complex assembly
GO:0006612	0.0013	16.126	0.2217	3	183	protein targeting to membrane
GO:0046677	0.0014	41.7567	0.0557	2	46	response to antibiotic
GO:0019058	0.0016	9.4006	0.5283	4	436	viral life cycle
GO:0048247	0.0016	38.2672	0.0606	2	50	lymphocyte chemotaxis
GO:0006402	0.0018	14.5685	0.2448	3	202	mRNA catabolic process
GO:0006414	0.0018	14.5685	0.2448	3	202	translational elongation
GO:0032760	0.002	34.6459	0.0666	2	55	positive regulation of tumor necrosis factor production
GO:0031401	0.002	5.7323	1.4214	6	1173	positive regulation of protein modification process
GO:0016482	0.0022	5.6176	1.448	6	1195	cytoplasmic transport
GO:0002548	0.0023	32.2064	0.0715	2	59	monocyte chemotaxis
GO:0044403	0.0023	6.5737	0.9839	5	812	symbiosis, encompassing mutualism through parasitism
GO:0002302	0.0024	870	0.0024	1	2	CD8-positive, alpha-beta T cell differentiation involved in immune response
GO:0009447	0.0024	870	0.0024	1	2	putrescine catabolic process
GO:0021754	0.0024	870	0.0024	1	2	facial nucleus development
GO:0032829	0.0024	870	0.0024	1	2	regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation
GO:0032834	0.0024	870	0.0024	1	2	positive regulation of CD4-positive, CD25-positive, alpha-beta regulatory T cell differentiation involved in immune response