RnBeads report

Option	Value
analyze.sites	yes
differential.report.sites	yes
region.types	default
differential.permutations	0
differential.comparison.columns	Platform, tissue, PrEC_comparison, LNCaP_PrEC_comp
differential.comparison.columns.all.pairwise	default
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
450k vs. non.450k (based on Platform)	25099
EPIC vs. non.EPIC (based on Platform)	17301
WGBS vs. non.WGBS (based on Platform)	143304
infant blood vs. non.infant blood (based on tissue)	121866
non-malignant tissue associated fibroblasts (NAF) vs. non.non-malignant tissue associated fibroblasts (NAF) (based on tissue)	91577
cancer associated fibroblasts (CAF) vs. non.cancer associated fibroblasts (CAF) (based on tissue)	94986
primary prostate epithelial cells (PrEC) vs. non.primary prostate epithelial cells (PrEC) (based on tissue)	72278
prostate cancer cell line (LNCaP) vs. non.prostate cancer cell line (LNCaP) (based on tissue)	113868
Rep1 vs. Rep2 (based on PrEC_comparison)	893
LNCaP vs. PrEC (based on LNCaP_PrEC_comp)	137907

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
450k vs. non.450k (based on Platform)	1821	112	452	347
EPIC vs. non.EPIC (based on Platform)	2377	129	117	132
WGBS vs. non.WGBS (based on Platform)	10884	1899	1241	5746
infant blood vs. non.infant blood (based on tissue)	5009	1703	3391	2557
non-malignant tissue associated fibroblasts (NAF) vs. non.non-malignant tissue associated fibroblasts (NAF) (based on tissue)	7220	1820	3154	789
cancer associated fibroblasts (CAF) vs. non.cancer associated fibroblasts (CAF) (based on tissue)	10552	1663	2262	1272
primary prostate epithelial cells (PrEC) vs. non.primary prostate epithelial cells (PrEC) (based on tissue)	4402	1305	1295	2483
prostate cancer cell line (LNCaP) vs. non.prostate cancer cell line (LNCaP) (based on tissue)	7590	2076	1312	4330
Rep1 vs. Rep2 (based on PrEC_comparison)	452	0	0	263
LNCaP vs. PrEC (based on LNCaP_PrEC_comp)	11615	1987	3029	2197

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

The tables for the individual comparisons can be found here:

	tiling	genes	promoters	cpgislands
450k vs. non.450k (based on Platform)	csv	csv	csv	csv
EPIC vs. non.EPIC (based on Platform)	csv	csv	csv	csv
WGBS vs. non.WGBS (based on Platform)	csv	csv	csv	csv
infant blood vs. non.infant blood (based on tissue)	csv	csv	csv	csv
non-malignant tissue associated fibroblasts (NAF) vs. non.non-malignant tissue associated fibroblasts (NAF) (based on tissue)	csv	csv	csv	csv
cancer associated fibroblasts (CAF) vs. non.cancer associated fibroblasts (CAF) (based on tissue)	csv	csv	csv	csv
primary prostate epithelial cells (PrEC) vs. non.primary prostate epithelial cells (PrEC) (based on tissue)	csv	csv	csv	csv
prostate cancer cell line (LNCaP) vs. non.prostate cancer cell line (LNCaP) (based on tissue)	csv	csv	csv	csv
Rep1 vs. Rep2 (based on PrEC_comparison)	csv	csv	csv	csv
LNCaP vs. PrEC (based on LNCaP_PrEC_comp)	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:1902511	0.0024	Inf	0.0024	1	1	negative regulation of apoptotic DNA fragmentation
GO:0032076	0.0048	427.3421	0.0048	1	2	negative regulation of deoxyribonuclease activity
GO:0050976	0.0048	427.3421	0.0048	1	2	detection of mechanical stimulus involved in sensory perception of touch
GO:0051083	0.0048	427.3421	0.0048	1	2	'de novo' cotranslational protein folding
GO:0060133	0.0048	427.3421	0.0048	1	2	somatotropin secreting cell development
GO:0035803	0.0072	213.6579	0.0072	1	3	egg coat formation
GO:0044571	0.0072	213.6579	0.0072	1	3	[2Fe-2S] cluster assembly

LOLA Enrichment Analysis

No LOLA Enrichment Analysis was conducted

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0002227	0	178.3077	0.0442	5	18	innate immune response in mucosa
GO:0002251	0	105.3052	0.0663	5	27	organ or tissue specific immune response
GO:0019731	0	74.6912	0.0885	5	36	antibacterial humoral response
GO:0050830	0	41.3555	0.1843	6	75	defense response to Gram-positive bacterium
GO:0061844	0	53.8073	0.1179	5	48	antimicrobial humoral immune response mediated by antimicrobial peptide
GO:0006334	0	22.5672	0.3243	6	132	nucleosome assembly
GO:0006333	0	16.6806	0.4325	6	176	chromatin assembly or disassembly
GO:0006323	0	15.0666	0.4767	6	194	DNA packaging
GO:0071824	0	11.2407	0.6315	6	257	protein-DNA complex subunit organization
GO:0006959	1e-04	11.5147	0.5013	5	204	humoral immune response
GO:0098542	5e-04	6.7623	1.0295	6	419	defense response to other organism
GO:0034622	6e-04	4.4195	2.4817	9	1010	cellular macromolecular complex assembly
GO:0009617	0.0013	5.6363	1.2261	6	499	response to bacterium
GO:0043207	0.0027	4.2326	1.9215	7	782	response to external biotic stimulus
GO:0045900	0.0048	427.2895	0.0048	1	2	negative regulation of translational elongation
GO:1900248	0.0049	416.359	0.0049	1	2	negative regulation of cytoplasmic translational elongation
GO:1902269	0.0049	416.359	0.0049	1	2	positive regulation of polyamine transmembrane transport
GO:1902559	0.0049	416.359	0.0049	1	2	3'-phospho-5'-adenylyl sulfate transmembrane transport
GO:0033387	0.0074	208.1667	0.0074	1	3	putrescine biosynthetic process from ornithine
GO:0035425	0.0074	208.1667	0.0074	1	3	autocrine signaling
GO:0061760	0.0098	138.7692	0.0098	1	4	antifungal innate immune response
GO:1990966	0.0098	138.7692	0.0098	1	4	ATP generation from poly-ADP-D-ribose

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:1990440	5e-04	75.0926	0.0338	2	11	positive regulation of transcription from RNA polymerase II promoter in response to endoplasmic reticulum stress
GO:0035967	0.0012	9.3843	0.4699	4	153	cellular response to topologically incorrect protein
GO:0031109	0.0027	11.7077	0.2795	3	91	microtubule polymerization or depolymerization
GO:1903508	0.003	3.011	4.3031	11	1401	positive regulation of nucleic acid-templated transcription
GO:0006797	0.0031	Inf	0.0031	1	1	polyphosphate metabolic process
GO:0009992	0.0031	Inf	0.0031	1	1	cellular water homeostasis
GO:0055107	0.0031	Inf	0.0031	1	1	Golgi to secretory granule transport
GO:0060904	0.0031	Inf	0.0031	1	1	regulation of protein folding in endoplasmic reticulum
GO:1905795	0.0031	Inf	0.0031	1	1	cellular response to puromycin
GO:0010468	0.0034	2.2795	13.6311	23	4438	regulation of gene expression
GO:0051254	0.0044	2.851	4.5212	11	1472	positive regulation of RNA metabolic process
GO:0030501	0.0052	20.4495	0.1075	2	35	positive regulation of bone mineralization
GO:0045944	0.0055	3.0699	3.354	9	1092	positive regulation of transcription from RNA polymerase II promoter
GO:1901998	0.0057	19.2786	0.1136	2	37	toxin transport
GO:0001831	0.0061	331.1837	0.0061	1	2	trophectodermal cellular morphogenesis
GO:0010607	0.0061	331.1837	0.0061	1	2	negative regulation of cytoplasmic mRNA processing body assembly
GO:0014835	0.0061	331.1837	0.0061	1	2	myoblast differentiation involved in skeletal muscle regeneration
GO:0021589	0.0061	331.1837	0.0061	1	2	cerebellum structural organization
GO:0051885	0.0061	331.1837	0.0061	1	2	positive regulation of timing of anagen
GO:0071464	0.0061	331.1837	0.0061	1	2	cellular response to hydrostatic pressure
GO:0072272	0.0061	331.1837	0.0061	1	2	proximal/distal pattern formation involved in metanephric nephron development
GO:1903891	0.0061	331.1837	0.0061	1	2	regulation of ATF6-mediated unfolded protein response
GO:1904313	0.0061	331.1837	0.0061	1	2	response to methamphetamine hydrochloride
GO:2000584	0.0061	331.1837	0.0061	1	2	negative regulation of platelet-derived growth factor receptor-alpha signaling pathway
GO:2000791	0.0061	331.1837	0.0061	1	2	negative regulation of mesenchymal cell proliferation involved in lung development
GO:0030968	0.0071	8.2233	0.3931	3	128	endoplasmic reticulum unfolded protein response
GO:0031214	0.0071	8.2233	0.3931	3	128	biomineral tissue development
GO:0006984	0.0081	16.0585	0.1351	2	44	ER-nucleus signaling pathway
GO:0046580	0.0081	16.0585	0.1351	2	44	negative regulation of Ras protein signal transduction
GO:0036023	0.0092	165.5816	0.0092	1	3	embryonic skeletal limb joint morphogenesis
GO:0071409	0.0092	165.5816	0.0092	1	3	cellular response to cycloheximide
GO:0071630	0.0092	165.5816	0.0092	1	3	nuclear protein quality control by the ubiquitin-proteasome system
GO:0010557	0.0096	2.5331	5.028	11	1637	positive regulation of macromolecule biosynthetic process
GO:0000122	0.0097	3.233	2.4111	7	785	negative regulation of transcription from RNA polymerase II promoter
GO:0014074	0.0098	7.2829	0.4423	3	144	response to purine-containing compound
GO:0071320	0.0099	14.3457	0.1505	2	49	cellular response to cAMP

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0050911	0	17.3611	0.3688	5	261	detection of chemical stimulus involved in sensory perception of smell
GO:0007195	1e-04	193.4286	0.0141	2	10	adenylate cyclase-inhibiting dopamine receptor signaling pathway
GO:0009593	1e-04	13.4473	0.4719	5	334	detection of chemical stimulus
GO:0050906	1e-04	12.8488	0.4931	5	349	detection of stimulus involved in sensory perception
GO:0007606	1e-04	12.773	0.4959	5	351	sensory perception of chemical stimulus
GO:0060158	1e-04	154.7238	0.017	2	12	phospholipase C-activating dopamine receptor signaling pathway
GO:0051481	1e-04	140.6494	0.0184	2	13	negative regulation of cytosolic calcium ion concentration
GO:0051967	1e-04	140.6494	0.0184	2	13	negative regulation of synaptic transmission, glutamatergic
GO:0048149	2e-04	128.9206	0.0198	2	14	behavioral response to ethanol
GO:1901386	2e-04	110.4898	0.0226	2	16	negative regulation of voltage-gated calcium channel activity
GO:0009636	2e-04	15.7072	0.3094	4	219	response to toxic substance
GO:0048148	3e-04	90.9748	0.0268	2	19	behavioral response to cocaine
GO:0014059	7e-04	61.8324	0.0381	2	27	regulation of dopamine secretion
GO:0001963	9e-04	53.2906	0.0438	2	31	synaptic transmission, dopaminergic
GO:0007194	0.001	49.8464	0.0466	2	33	negative regulation of adenylate cyclase activity
GO:0015872	0.0014	41.7477	0.0551	2	39	dopamine transport
GO:1903170	0.0015	39.602	0.0579	2	41	negative regulation of calcium ion transmembrane transport
GO:0030803	0.002	34.309	0.0664	2	47	negative regulation of cyclic nucleotide biosynthetic process
GO:0030815	0.0022	32.845	0.0692	2	49	negative regulation of cAMP metabolic process
GO:0050432	0.0022	32.845	0.0692	2	49	catecholamine secretion
GO:1900372	0.0022	32.1587	0.0706	2	50	negative regulation of purine nucleotide biosynthetic process
GO:0050877	0.0038	4.802	1.581	6	1119	nervous system process
GO:0032413	0.0041	23.3622	0.0961	2	68	negative regulation of ion transmembrane transporter activity
GO:0009624	0.0042	369.4091	0.0042	1	3	response to nematode
GO:0009822	0.0042	369.4091	0.0042	1	3	alkaloid catabolic process
GO:0045980	0.0047	21.7103	0.1031	2	73	negative regulation of nucleotide metabolic process
GO:0015844	0.0048	21.4074	0.1046	2	74	monoamine transport
GO:0051952	0.0048	21.4074	0.1046	2	74	regulation of amine transport
GO:0010466	0.0052	9.6428	0.356	3	252	negative regulation of peptidase activity
GO:0015672	0.0059	6.3331	0.7446	4	527	monovalent inorganic cation transport
GO:0043086	0.0063	4.979	1.2207	5	864	negative regulation of catalytic activity
GO:1901019	0.0065	18.3356	0.1215	2	86	regulation of calcium ion transmembrane transporter activity
GO:0034763	0.0076	16.9178	0.1314	2	93	negative regulation of transmembrane transport
GO:0031279	0.0077	16.7329	0.1328	2	94	regulation of cyclase activity
GO:0043266	0.0077	16.7329	0.1328	2	94	regulation of potassium ion transport
GO:0051339	0.0079	16.552	0.1342	2	95	regulation of lyase activity
GO:0002933	0.0084	147.7364	0.0085	1	6	lipid hydroxylation
GO:0006805	0.0087	15.7026	0.1413	2	100	xenobiotic metabolic process
GO:0050804	0.0088	7.8975	0.4323	3	306	modulation of chemical synaptic transmission
GO:0043279	0.0097	14.7912	0.1498	2	106	response to alkaloid

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0035137	0	102.2773	0.0386	3	37	hindlimb morphogenesis
GO:0048935	1e-04	196.9818	0.0136	2	13	peripheral nervous system neuron development
GO:0030326	3e-04	27.8882	0.1326	3	127	embryonic limb morphogenesis
GO:0035107	4e-04	23.9851	0.1535	3	147	appendage morphogenesis
GO:0009954	5e-04	74.6345	0.0324	2	31	proximal/distal pattern formation
GO:0035136	8e-04	56.9263	0.0418	2	40	forelimb morphogenesis
GO:0021763	0.001	Inf	0.001	1	1	subthalamic nucleus development
GO:0060127	0.001	Inf	0.001	1	1	prolactin secreting cell differentiation
GO:0060578	0.001	Inf	0.001	1	1	superior vena cava morphogenesis
GO:0071444	0.001	Inf	0.001	1	1	cellular response to pheromone
GO:0035993	0.0021	1016.3125	0.0021	1	2	deltoid tuberosity development
GO:0060460	0.0021	1016.3125	0.0021	1	2	left lung morphogenesis
GO:0060577	0.0021	1016.3125	0.0021	1	2	pulmonary vein morphogenesis
GO:0071461	0.0021	1016.3125	0.0021	1	2	cellular response to redox state
GO:0007422	0.0024	31.2908	0.0741	2	71	peripheral nervous system development
GO:0032481	0.0027	29.9815	0.0773	2	74	positive regulation of type I interferon production
GO:0008344	0.0029	28.7769	0.0804	2	77	adult locomotory behavior
GO:0003350	0.0031	508.125	0.0031	1	3	pulmonary myocardium development
GO:0061031	0.0031	508.125	0.0031	1	3	endodermal digestive tract morphogenesis
GO:0048704	0.0042	23.6938	0.0971	2	93	embryonic skeletal system morphogenesis
GO:0021855	0.0042	338.7292	0.0042	1	4	hypothalamus cell migration
GO:0061325	0.0042	338.7292	0.0042	1	4	cell proliferation involved in outflow tract morphogenesis
GO:0002074	0.0052	254.0312	0.0052	1	5	extraocular skeletal muscle development
GO:0060126	0.0052	254.0312	0.0052	1	5	somatotropin secreting cell differentiation
GO:0070221	0.0052	254.0312	0.0052	1	5	sulfide oxidation, using sulfide:quinone oxidoreductase
GO:1901164	0.0052	254.0312	0.0052	1	5	negative regulation of trophoblast cell migration
GO:0060537	0.0063	9.255	0.3874	3	371	muscle tissue development
GO:0007517	0.0064	9.1785	0.3906	3	374	muscle organ development
GO:0043900	0.0066	9.0783	0.3947	3	378	regulation of multi-organism process
GO:0003253	0.0073	169.3333	0.0073	1	7	cardiac neural crest cell migration involved in outflow tract morphogenesis
GO:0055009	0.0073	169.3333	0.0073	1	7	atrial cardiac muscle tissue morphogenesis
GO:0007389	0.0089	8.1224	0.4396	3	421	pattern specification process
GO:0048568	0.009	8.1025	0.4407	3	422	embryonic organ development
GO:0007338	0.0091	15.6934	0.1452	2	139	single fertilization
GO:0060050	0.0094	126.9844	0.0094	1	9	positive regulation of protein glycosylation
GO:2000288	0.0094	126.9844	0.0094	1	9	positive regulation of myoblast proliferation
GO:0007519	0.0094	15.4449	0.1485	2	151	skeletal muscle tissue development

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0022612	4e-04	23.3957	0.1522	3	118	gland morphogenesis
GO:0060571	5e-04	71.2018	0.0335	2	26	morphogenesis of an epithelial fold
GO:0060429	5e-04	6.3715	1.5351	7	1190	epithelium development
GO:0048729	0.001	7.9353	0.8011	5	621	tissue morphogenesis
GO:0021509	0.0013	Inf	0.0013	1	1	roof plate formation
GO:0071444	0.0013	Inf	0.0013	1	1	cellular response to pheromone
GO:2001051	0.0013	Inf	0.0013	1	1	positive regulation of tendon cell differentiation
GO:0061138	0.0015	15.2292	0.2309	3	179	morphogenesis of a branching epithelium
GO:0021515	0.002	34.1221	0.0671	2	52	cell differentiation in spinal cord
GO:0009952	0.0021	13.4497	0.2606	3	202	anterior/posterior pattern specification
GO:0015891	0.0039	406.4	0.0039	1	3	siderophore transport
GO:0035992	0.0039	406.4	0.0039	1	3	tendon formation
GO:0048619	0.0039	406.4	0.0039	1	3	embryonic hindgut morphogenesis
GO:0045165	0.0039	10.7594	0.3238	3	251	cell fate commitment
GO:0010046	0.0052	270.9167	0.0052	1	4	response to mycotoxin
GO:0072376	0.0052	20.7651	0.1084	2	84	protein activation cascade
GO:0010628	0.0056	4.049	2.3143	7	1794	positive regulation of gene expression
GO:0060157	0.0064	203.175	0.0065	1	5	urinary bladder development
GO:0070221	0.0064	203.175	0.0065	1	5	sulfide oxidation, using sulfide:quinone oxidoreductase
GO:0015840	0.0077	162.53	0.0077	1	6	urea transport
GO:0060527	0.0077	162.53	0.0077	1	6	prostate epithelial cord arborization involved in prostate glandular acinus morphogenesis
GO:0009635	0.009	135.4333	0.009	1	7	response to herbicide
GO:0060687	0.009	135.4333	0.009	1	7	regulation of branching involved in prostate gland morphogenesis
GO:0035239	0.0095	7.7332	0.4463	3	346	tube morphogenesis
GO:0048513	0.0098	3.2864	3.9929	9	3249	animal organ development

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:0042102	0	27.4287	0.2205	5	97	positive regulation of T cell proliferation
GO:0032946	0	19.6704	0.3023	5	133	positive regulation of mononuclear cell proliferation
GO:0002274	0	30.854	0.1562	4	82	myeloid leukocyte activation
GO:0050867	1e-04	10.4628	0.6841	6	301	positive regulation of cell activation
GO:0050670	1e-04	12.7918	0.4568	5	201	regulation of lymphocyte proliferation
GO:0002263	1e-04	6.6067	1.4978	8	659	cell activation involved in immune response
GO:0070663	1e-04	12.1632	0.4796	5	211	regulation of leukocyte proliferation
GO:1903039	1e-04	12.1037	0.4818	5	212	positive regulation of leukocyte cell-cell adhesion
GO:1902715	1e-04	154.6286	0.0182	2	8	positive regulation of interferon-gamma secretion
GO:0002684	2e-04	5.2922	2.1342	9	939	positive regulation of immune system process
GO:0050900	2e-04	7.9505	0.891	6	392	leukocyte migration
GO:0006600	3e-04	103.0667	0.025	2	11	creatine metabolic process
GO:0051251	3e-04	9.8351	0.5887	5	259	positive regulation of lymphocyte activation
GO:0001787	3e-04	92.7543	0.0273	2	12	natural killer cell proliferation
GO:0045087	4e-04	5.3248	1.8365	8	808	innate immune response
GO:0002694	5e-04	6.7768	1.0387	6	457	regulation of leukocyte activation
GO:0050863	6e-04	8.3314	0.691	5	304	regulation of T cell activation
GO:0043312	6e-04	6.5093	1.0796	6	475	neutrophil degranulation
GO:0042119	7e-04	6.3556	1.1046	6	486	neutrophil activation
GO:0032940	8e-04	3.9699	3.1729	10	1396	secretion by cell
GO:0002275	9e-04	6.0582	1.1612	6	525	myeloid cell activation involved in immune response
GO:0032649	0.0011	16.5759	0.2023	3	89	regulation of interferon-gamma production
GO:0010758	0.0011	46.3486	0.05	2	22	regulation of macrophage chemotaxis
GO:0046640	0.0011	46.3486	0.05	2	22	regulation of alpha-beta T cell proliferation
GO:0002444	0.0012	5.7716	1.2114	6	533	myeloid leukocyte mediated immunity
GO:0001774	0.0012	44.1388	0.0523	2	23	microglial cell activation
GO:0042330	0.0015	5.4604	1.2774	6	562	taxis
GO:0045785	0.0016	6.6113	0.8637	5	380	positive regulation of cell adhesion
GO:0007200	0.0019	13.5605	0.2455	3	108	phospholipase C-activating G-protein coupled receptor signaling pathway
GO:0022407	0.0021	6.2042	0.9182	5	404	regulation of cell-cell adhesion
GO:0014739	0.0023	Inf	0.0023	1	1	positive regulation of muscle hyperplasia
GO:0071663	0.0023	Inf	0.0023	1	1	positive regulation of granzyme B production
GO:1903997	0.0023	Inf	0.0023	1	1	positive regulation of non-membrane spanning protein tyrosine kinase activity
GO:1904140	0.0023	Inf	0.0023	1	1	negative regulation of microglial cell migration
GO:1904151	0.0023	Inf	0.0023	1	1	positive regulation of microglial cell mediated cytotoxicity
GO:2001264	0.0023	Inf	0.0023	1	1	negative regulation of C-C chemokine binding
GO:0045937	0.0025	3.9116	2.4502	8	1078	positive regulation of phosphate metabolic process
GO:0060326	0.0025	7.8172	0.5728	4	252	cell chemotaxis
GO:0097178	0.0025	29.882	0.075	2	33	ruffle assembly

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0006335	0	1314.3243	0.1199	24	32	DNA replication-dependent nucleosome assembly
GO:0000183	0	750.7645	0.1424	24	38	chromatin silencing at rDNA
GO:0051290	0	525.3405	0.1649	24	44	protein heterotetramerization
GO:0045815	0	187.2046	0.2998	24	80	positive regulation of gene expression, epigenetic
GO:1902036	0	132.5132	0.386	24	103	regulation of hematopoietic stem cell differentiation
GO:0060964	0	127.6414	0.3972	24	106	regulation of gene silencing by miRNA
GO:0045814	0	104.5492	0.4646	24	124	negative regulation of gene expression, epigenetic
GO:0060968	0	98.5946	0.4871	24	130	regulation of gene silencing
GO:0031497	0	82.1843	0.5658	24	151	chromatin assembly
GO:0032200	0	73.4343	0.622	24	166	telomere organization
GO:0045653	0	1207.4255	0.0674	14	18	negative regulation of megakaryocyte differentiation
GO:0002244	0	63.4964	0.7045	24	188	hematopoietic progenitor cell differentiation
GO:0048863	0	47.028	0.978	25	261	stem cell differentiation
GO:0065004	0	51.4295	0.8469	24	226	protein-DNA complex assembly
GO:0035194	0	49.4456	0.8768	24	234	posttranscriptional gene silencing by RNA
GO:0071103	0	41.4305	1.0267	24	274	DNA conformation change
GO:0017148	0	34.6526	1.2066	24	322	negative regulation of translation
GO:0034080	0	172.234	0.1574	14	42	CENP-A containing nucleosome assembly
GO:1904837	0	160.7319	0.1649	14	44	beta-catenin-TCF complex assembly
GO:0030099	0	28.2519	1.4539	24	388	myeloid cell differentiation
GO:0034724	0	120.4745	0.2023	14	54	DNA replication-independent nucleosome organization
GO:0016233	0	117.5288	0.2061	14	55	telomere capping
GO:0051259	0	22.1504	1.941	25	518	protein oligomerization
GO:0006303	0	78.8971	0.281	14	75	double-strand break repair via nonhomologous end joining
GO:0043044	0	75.1848	0.2923	14	78	ATP-dependent chromatin remodeling
GO:0034248	0	19.6991	2.0272	24	541	regulation of cellular amide metabolic process
GO:0010608	0	17.9213	2.3607	25	630	posttranscriptional regulation of gene expression
GO:0045892	0	12.5407	4.2043	29	1122	negative regulation of transcription, DNA-templated
GO:1902679	0	12.0889	4.3467	29	1160	negative regulation of RNA biosynthetic process
GO:1903707	0	39.2996	0.5096	14	136	negative regulation of hemopoiesis
GO:0048534	0	12.8748	3.2038	25	855	hematopoietic or lymphoid organ development
GO:0038111	0	113.3754	0.1424	10	38	interleukin-7-mediated signaling pathway
GO:0098760	0	109.4591	0.1461	10	39	response to interleukin-7
GO:0043043	0	13.2848	2.919	24	779	peptide biosynthetic process
GO:0045652	0	92.9672	0.1648	10	57	regulation of megakaryocyte differentiation
GO:0045934	0	9.8849	5.2123	29	1391	negative regulation of nucleobase-containing compound metabolic process
GO:0006352	0	23.3891	0.8918	15	238	DNA-templated transcription, initiation
GO:0051248	0	9.6174	4.7364	27	1264	negative regulation of protein metabolic process
GO:0070271	0	9.1666	5.2535	28	1402	protein complex biogenesis

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0045653	0	2273.04	0.0431	14	18	negative regulation of megakaryocyte differentiation
GO:0006335	0	504.6844	0.0767	14	32	DNA replication-dependent nucleosome assembly
GO:0000183	0	378.3733	0.091	14	38	chromatin silencing at rDNA
GO:0034080	0	324.24	0.1006	14	42	CENP-A containing nucleosome assembly
GO:0051290	0	302.5867	0.1054	14	44	protein heterotetramerization
GO:1904837	0	302.5867	0.1054	14	44	beta-catenin-TCF complex assembly
GO:0034724	0	226.8	0.1294	14	54	DNA replication-independent nucleosome organization
GO:0016233	0	221.2546	0.1318	14	55	telomere capping
GO:0006303	0	148.5285	0.1797	14	75	double-strand break repair via nonhomologous end joining
GO:0043044	0	141.54	0.1869	14	78	ATP-dependent chromatin remodeling
GO:0045815	0	137.2339	0.1917	14	80	positive regulation of gene expression, epigenetic
GO:1903707	0	83.2593	0.3258	15	136	negative regulation of hemopoiesis
GO:1902036	0	101.6243	0.2468	14	103	regulation of hematopoietic stem cell differentiation
GO:0060964	0	98.2922	0.2539	14	106	regulation of gene silencing by miRNA
GO:0045814	0	82.1164	0.2971	14	124	negative regulation of gene expression, epigenetic
GO:0060968	0	77.84	0.3114	14	130	regulation of gene silencing
GO:0031497	0	65.8225	0.3618	14	151	chromatin assembly
GO:0032200	0	59.2716	0.3977	14	166	telomere organization
GO:0045596	0	26.7437	1.5213	20	635	negative regulation of cell differentiation
GO:0006352	0	44.8907	0.5702	15	238	DNA-templated transcription, initiation
GO:0045637	0	44.4861	0.575	15	240	regulation of myeloid cell differentiation
GO:0002244	0	51.7067	0.4504	14	188	hematopoietic progenitor cell differentiation
GO:0048863	0	40.6352	0.6253	15	261	stem cell differentiation
GO:0065004	0	42.3381	0.5414	14	226	protein-DNA complex assembly
GO:0035194	0	40.7782	0.5606	14	234	posttranscriptional gene silencing by RNA
GO:0071103	0	34.4185	0.6564	14	274	DNA conformation change
GO:0017148	0	28.9673	0.7714	14	322	negative regulation of translation
GO:0060249	0	24.7726	0.8936	14	373	anatomical structure homeostasis
GO:0006281	0	19.5539	1.241	15	518	DNA repair
GO:0051259	0	19.5539	1.241	15	518	protein oligomerization
GO:0048534	0	14.2023	2.0483	17	855	hematopoietic or lymphoid organ development
GO:0034248	0	16.6969	1.2961	14	541	regulation of cellular amide metabolic process
GO:0010608	0	14.2036	1.5093	14	630	posttranscriptional regulation of gene expression
GO:0070271	0	9.2007	3.3588	18	1402	protein complex biogenesis
GO:0006325	0	12.0361	1.7633	14	736	chromatin organization
GO:0043043	0	11.3281	1.8663	14	779	peptide biosynthetic process
GO:2000026	0	8.5243	4.1109	19	1803	regulation of multicellular organismal development
GO:0045892	0	9.519	2.688	16	1122	negative regulation of transcription, DNA-templated
GO:1902679	0	9.1797	2.779	16	1160	negative regulation of RNA biosynthetic process

GOMFID	Pvalue	OddsRatio	ExpCount	Count	Size	Term
GO:0030887	0.0017	Inf	0.0017	1	1	positive regulation of myeloid dendritic cell activation
GO:0038002	0.0017	Inf	0.0017	1	1	endocrine signaling
GO:0021897	0.0033	625.0385	0.0033	1	2	forebrain astrocyte development
GO:0050992	0.0033	625.0385	0.0033	1	2	dimethylallyl diphosphate biosynthetic process
GO:1904381	0.005	312.5	0.005	1	3	Golgi apparatus mannose trimming
GO:0006695	0.0055	19.9225	0.1111	2	67	cholesterol biosynthetic process
GO:0035022	0.0066	208.3205	0.0066	1	4	positive regulation of Rac protein signal transduction
GO:1990966	0.0066	208.3205	0.0066	1	4	ATP generation from poly-ADP-D-ribose
GO:0050810	0.0079	16.3777	0.1343	2	81	regulation of steroid biosynthetic process
GO:0009240	0.0083	156.2308	0.0083	1	5	isopentenyl diphosphate biosynthetic process
GO:0035900	0.0099	124.9769	0.01	1	6	response to isolation stress