1 Single cell expression data

Source:
Genome-wide CRISPR Screens in Primary Human T Cells Reveal Key Regulators of Immune Function, GEO accession: GSE119450.

Perturbations:
CRISPR knock-out of 20 genes (2 gRNAs per gene) + 8 non-targeting gRNAs. Guide conditions were defined on the target gene level; target genes were either found to regulate T cell responses in the genome-wide screens, or known checkpoint genes.
Guide RNAs were introduced into T cells through a novel procedure called sgRNA lentiviral infection with Cas9 protein electroporation (SLICE).

Cells:
Primary human CD8+ T cells from two healthy donors, with T cell receptor (TCR) stimulation.
Cells from 2 donors were pooled together into 1 analysis. All cells have only a single type of gRNA readout. Quality control resulted in 13983 cells.

Genes:
Only genes detected in > 10% of cells were kept, resulted in 6062 genes.

Normalization:
Seurat “LogNormalize”: log(count per 10K + 1).
Batch effect, unique UMI count, library size, and mitochondria percentage were all corrected for. The corrected and scaled expression data were used as input for subsequent factor analysis.

2 Guided results

Here, our “guide”, \(G\) matrix, consists of 21 types (20 genes + negative control) of KO conditions across cells.

In each case, Gibbs sampling was conducted for 2000 iterations, and the posterior mean estimates were averaged over the last 500 iterations.

2.1 SVD Initialization

2.1.1 Local False Sign Rate (LFSR)

For a given GSFA inference result, we can estimate the effect a certain KO condition \(m\) has on the expression of gene \(j\) by computing the LFSR of \(\beta_{m\cdot} \cdot W_{j\cdot}\).

Number of genes that passed GSFA LFSR < 0.05 under each perturbation:

GSFA, # of genes that passed LFSR cutoff of 0.05:
KO	ARID1A	BTLA	C10orf54	CBLB	CD3D	CD5	CDKN1B
Num_genes	499	0	0	2484	1238	1264	0
KO	DGKA	DGKZ	HAVCR2	LAG3	LCP2	MEF2D	NonTarget
Num_genes	461	0	0	0	3194	0	0
KO	PDCD1	RASA2	SOCS1	STAT6	TCEB2	TMEM222	TNFRSF9
Num_genes	0	939	0	0	1758	0	0

Number of genes that passed t-test FDR < 0.05 under each perturbation:

Welch’s t-test, # of genes that passed FDR cutoff of 0.05:
KO	ARID1A	BTLA	C10orf54	CBLB	CD3D	CD5	CDKN1B
Num_genes	14	0	0	15	5	6	1
KO	DGKA	DGKZ	HAVCR2	LAG3	LCP2	MEF2D	NonTarget
Num_genes	0	0	0	1	39	0	0
KO	PDCD1	RASA2	SOCS1	STAT6	TCEB2	TMEM222	TNFRSF9
Num_genes	0	9	0	5	73	0	1

2.1.2 Estimate of Factor ~ Perturbation Associations (\(\beta\))

2.1.3 Factor ~ KO Posterior Association

2.1.4 Beta PIP vs P-Value

2.1.5 Correlation btw Factors

2.2 Alternative Initializations and Chain Convergence

Other than initializing GSFA using truncated SVD, we also ran 2 chains with random initialization.

2.2.1 Association results for 2 randomly initialized GSFA runs

2.2.2 Chain mixing and convergence evaluation

	Min.	1st Qu.	Median	Mean	3rd Qu.	Max.
ARID1A	0.999	1.02	1.04	1.06	1.09	1.53
BTLA	0.999	1.02	1.07	1.10	1.19	1.32
C10orf54	0.999	1.00	1.00	1.01	1.01	1.02
CBLB	1.000	1.04	1.09	1.11	1.15	1.70
CD3D	0.999	1.01	1.03	1.05	1.06	1.39
CD5	0.999	1.03	1.09	1.13	1.20	1.75
CDKN1B	1.000	1.05	1.10	1.13	1.17	1.79
DGKA	0.999	1.00	1.02	1.08	1.10	1.88
DGKZ	0.999	1.05	1.12	1.18	1.22	1.96
HAVCR2	1.000	1.03	1.09	1.13	1.18	1.88
LAG3	0.999	1.00	1.00	1.01	1.01	1.13
LCP2	0.999	1.04	1.08	1.10	1.13	1.54
MEF2D	0.999	1.00	1.01	1.03	1.04	1.23
NonTarget	0.999	1.01	1.02	1.03	1.05	1.10
PDCD1	0.999	1.00	1.00	1.00	1.00	1.01
RASA2	1.000	1.03	1.06	1.07	1.10	1.48
SOCS1	1.000	1.05	1.09	1.12	1.16	1.88
STAT6	0.999	1.00	1.00	1.00	1.00	1.01
TCEB2	0.999	1.03	1.08	1.12	1.16	2.04
TMEM222	0.999	1.00	1.00	1.00	1.00	1.02
TNFRSF9	0.999	1.00	1.00	1.01	1.01	1.08
offset	0.999	1.00	1.00	1.00	1.01	1.03

2.2.3 Difference btw methods in factor estimation

For a pair of \(Z\) estimations from 2 inference methods, \(Z_1, Z_2\), we quantify the pairwise estimation difference as \(||Z_1Z_1^T - Z_2Z_2^T||_F/N\), where \(||\cdot||\) is the Frobenius norm of a matrix, and \(N\) is the number of rows (samples) in \(Z\).

Guided SVD vs Rand_01: 0.57

Guided SVD vs Rand_02: 0.438

Rand_01 vs Rand_02: 0.516

3 Unguided Result

In contrast to the guided version, here we provide no guidance (\(G = \vec{0}\)) to our sparse factor analysis model to serve as a comparison.

3.1 Factor ~ KO Posterior Association

3.2 Unguided vs Guided

4 FLASH

4.1 Factor ~ KO Posterior Association

4.2 FLASH vs GSFA

We matched the factors obtained from GFSA with those from FLASH, and conducted pairwise comparisons for both factors and gene loadings.

In the following heatmaps, factors are labeled by the KO condition(s) that they have an association p-value < 1e-4 with.

5 Gene Ontology Enrichment Analysis

Target genes: Genes w/ non-zero loadings in each factor (PIP cutoff at 0.95);
Backgroud genes: all 6062 genes used in factor analysis;
Statistical test: hypergeometric test (over-representation test);
Only GO terms/pathways that satisfy fold change \(\geq\) 2 and test FDR \(<\) 0.05 are shown below.

5.1 GO Slim Over-Representation Analysis

Gene sets: Gene ontology “Biological Process” (non-redundant).

Factor 6 : 2 significant GO terms
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
GO:0061641	CENP-A containing chromatin organization	2.065193	0.0000009	0.0000956	24/27
GO:0022616	DNA strand elongation	2.013563	0.0006495	0.0206995	13/15

Factor 7 : 36 significant GO terms
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
GO:0034113	heterotypic cell-cell adhesion	3.372890	0.0000001	0.0000034	15/16
GO:0042092	type 2 immune response	3.237975	0.0000730	0.0011150	9/10
GO:0032633	interleukin-4 production	2.878200	0.0000388	0.0006607	12/15
GO:0002437	inflammatory response to antigenic stimulus	2.698312	0.0001157	0.0015423	12/16
GO:1990868	response to chemokine	2.698312	0.0001157	0.0015423	12/16
GO:0044091	membrane biogenesis	2.698312	0.0009088	0.0076571	9/12
GO:0001773	myeloid dendritic cell activation	2.638350	0.0003170	0.0035749	11/15
GO:0007200	phospholipase C-activating G protein-coupled receptor signaling pathway	2.518425	0.0066501	0.0314483	7/10
GO:0032941	secretion by tissue	2.518425	0.0066501	0.0314483	7/10
GO:1901522	positive regulation of transcription from RNA polymerase II promoter involved in cellular response to chemical stimulus	2.518425	0.0066501	0.0314483	7/10
GO:0032963	collagen metabolic process	2.461618	0.0002628	0.0031073	13/19
GO:0031579	membrane raft organization	2.398500	0.0056617	0.0286209	8/12
GO:0032528	microvillus organization	2.398500	0.0056617	0.0286209	8/12
GO:0045730	respiratory burst	2.398500	0.0056617	0.0286209	8/12
GO:0033627	cell adhesion mediated by integrin	2.338537	0.0005605	0.0054055	13/20
GO:0006949	syncytium formation	2.327956	0.0016140	0.0114859	11/17
GO:1904019	epithelial cell apoptotic process	2.265250	0.0001385	0.0017597	17/27
GO:0140253	cell-cell fusion	2.248594	0.0038449	0.0220183	10/16
GO:0006959	humoral immune response	2.222139	0.0000341	0.0006253	21/34
GO:0033028	myeloid cell apoptotic process	2.214000	0.0111596	0.0454443	8/13
GO:0032602	chemokine production	2.198625	0.0031143	0.0190234	11/18
GO:0032635	interleukin-6 production	2.139203	0.0000513	0.0008354	22/37
GO:0032609	interferon-gamma production	2.116323	0.0001392	0.0017597	20/34
GO:0007229	integrin-mediated signaling pathway	2.089016	0.0003768	0.0040647	18/31
GO:0032612	interleukin-1 production	2.075625	0.0012768	0.0095548	15/26
GO:0050663	cytokine secretion	2.064283	0.0000010	0.0000381	35/61
GO:0001906	cell killing	2.055857	0.0000034	0.0001043	32/56
GO:0034109	homotypic cell-cell adhesion	2.055857	0.0010152	0.0080889	16/28
GO:0042116	macrophage activation	2.055857	0.0043826	0.0241536	12/21
GO:0042476	odontogenesis	2.055857	0.0043826	0.0241536	12/21
GO:0007187	G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger	2.038725	0.0008062	0.0071195	17/30
GO:0043062	extracellular structure organization	2.036462	0.0000090	0.0002271	30/53
GO:0002065	columnar/cuboidal epithelial cell differentiation	2.014740	0.0027204	0.0170430	14/25
GO:1902579	multi-organism localization	2.014740	0.0027204	0.0170430	14/25
GO:0007162	negative regulation of cell adhesion	2.013027	0.0000000	0.0000031	47/84
GO:0060326	cell chemotaxis	2.004460	0.0000007	0.0000290	39/70

Factor 8 : 27 significant GO terms
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
GO:0070972	protein localization to endoplasmic reticulum	4.372239	0.0000000	0.0000000	91/121
GO:0045730	respiratory burst	3.875758	0.0001917	0.0048455	8/12
GO:0034113	heterotypic cell-cell adhesion	3.633523	0.0000636	0.0019436	10/16
GO:0006413	translational initiation	3.544900	0.0000000	0.0000000	100/164
GO:0002181	cytoplasmic translation	3.535319	0.0000000	0.0000000	45/74
GO:0042116	macrophage activation	3.045238	0.0002418	0.0056219	11/21
GO:0090150	establishment of protein localization to membrane	2.920998	0.0000000	0.0000000	103/205
GO:0006959	humoral immune response	2.906818	0.0000109	0.0005306	17/34
GO:0070671	response to interleukin-12	2.657662	0.0000799	0.0020917	16/35
GO:0033627	cell adhesion mediated by integrin	2.616136	0.0034849	0.0402478	9/20
GO:0070265	necrotic cell death	2.558000	0.0015676	0.0220968	11/25
GO:0006605	protein targeting	2.536451	0.0000000	0.0000000	113/259
GO:0006401	RNA catabolic process	2.475337	0.0000000	0.0000000	109/256
GO:0034341	response to interferon-gamma	2.440292	0.0000001	0.0000104	34/81
GO:1901264	carbohydrate derivative transport	2.422349	0.0041432	0.0453276	10/24
GO:0030101	natural killer cell activation	2.405643	0.0018436	0.0250255	12/29
GO:0046683	response to organophosphorus	2.393850	0.0008278	0.0135372	14/34
GO:0048013	ephrin receptor signaling pathway	2.361790	0.0014686	0.0215292	13/32
GO:0006909	phagocytosis	2.271996	0.0000009	0.0000579	34/87
GO:0014074	response to purine-containing compound	2.260859	0.0016098	0.0222633	14/36
GO:0032609	interferon-gamma production	2.222861	0.0028036	0.0342507	13/34
GO:0008037	cell recognition	2.199754	0.0021873	0.0285736	14/37
GO:0001906	cell killing	2.180114	0.0002172	0.0053061	21/56
GO:1902600	proton transmembrane transport	2.161480	0.0000174	0.0006708	29/78
GO:0038061	NIK/NF-kappaB signaling	2.039872	0.0008311	0.0135372	20/57
GO:0007159	leukocyte cell-cell adhesion	2.038548	0.0000000	0.0000047	54/154
GO:0050900	leukocyte migration	2.022134	0.0000033	0.0001835	40/115

Factor 9 : 81 significant GO terms
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
GO:1990868	response to chemokine	5.384391	0.0000000	0.0000004	13/16
GO:0002507	tolerance induction	4.819595	0.0000281	0.0005141	8/11
GO:0050918	positive chemotaxis	4.217145	0.0003282	0.0036850	7/11
GO:0034113	heterotypic cell-cell adhesion	4.141839	0.0000195	0.0003665	10/16
GO:0098742	cell-cell adhesion via plasma-membrane adhesion molecules	3.976166	0.0000050	0.0001082	12/20
GO:0001773	myeloid dendritic cell activation	3.976166	0.0000823	0.0012314	9/15
GO:0007586	digestion	3.865717	0.0006855	0.0068833	7/12
GO:0031579	membrane raft organization	3.865717	0.0006855	0.0068833	7/12
GO:0045730	respiratory burst	3.865717	0.0006855	0.0068833	7/12
GO:0140253	cell-cell fusion	3.727655	0.0001631	0.0020610	9/16
GO:0006949	syncytium formation	3.508382	0.0003004	0.0034410	9/17
GO:0060326	cell chemotaxis	3.502813	0.0000000	0.0000000	37/70
GO:0032615	interleukin-12 production	3.487865	0.0001459	0.0019438	10/19
GO:0006959	humoral immune response	3.313471	0.0000017	0.0000416	17/34
GO:0033627	cell adhesion mediated by integrin	3.313471	0.0002526	0.0029861	10/20
GO:0032602	chemokine production	3.313471	0.0005211	0.0056169	9/18
GO:0044091	membrane biogenesis	3.313471	0.0047331	0.0277549	6/12
GO:0002526	acute inflammatory response	3.190750	0.0000488	0.0008321	13/27
GO:0007585	respiratory gaseous exchange	3.092573	0.0036786	0.0240752	7/15
GO:0032613	interleukin-10 production	3.092573	0.0036786	0.0240752	7/15
GO:0050920	regulation of chemotaxis	2.988621	0.0000003	0.0000096	23/51
GO:0050900	leukocyte migration	2.938905	0.0000000	0.0000000	51/115
GO:0032609	interferon-gamma production	2.923651	0.0000466	0.0008134	15/34
GO:0050866	negative regulation of cell activation	2.920348	0.0000001	0.0000035	26/59
GO:0002437	inflammatory response to antigenic stimulus	2.899288	0.0056997	0.0326399	7/16
GO:0031529	ruffle organization	2.881280	0.0010167	0.0086653	10/23
GO:0043062	extracellular structure organization	2.875843	0.0000006	0.0000196	23/53
GO:0001906	cell killing	2.840118	0.0000005	0.0000154	24/56
GO:0042116	macrophage activation	2.840118	0.0020576	0.0150825	9/21
GO:0045576	mast cell activation	2.840118	0.0020576	0.0150825	9/21
GO:0032612	interleukin-1 production	2.803707	0.0007541	0.0073700	11/26
GO:0032637	interleukin-8 production	2.790292	0.0041677	0.0258895	8/19
GO:0007229	integrin-mediated signaling pathway	2.779041	0.0002791	0.0032473	13/31
GO:0030101	natural killer cell activation	2.742183	0.0005549	0.0058950	12/29
GO:0008037	cell recognition	2.686599	0.0001509	0.0019746	15/37
GO:0007159	leukocyte cell-cell adhesion	2.624958	0.0000000	0.0000000	61/154
GO:0022407	regulation of cell-cell adhesion	2.617009	0.0000000	0.0000000	62/157
GO:0050663	cytokine secretion	2.607322	0.0000031	0.0000734	24/61
GO:0007162	negative regulation of cell adhesion	2.603442	0.0000000	0.0000022	33/84
GO:0034109	homotypic cell-cell adhesion	2.603442	0.0015709	0.0122979	11/28
GO:0032103	positive regulation of response to external stimulus	2.600446	0.0000001	0.0000047	31/79
GO:0070661	leukocyte proliferation	2.530287	0.0000000	0.0000001	42/110
GO:0009308	amine metabolic process	2.524550	0.0084956	0.0450500	8/21
GO:0002791	regulation of peptide secretion	2.522195	0.0000000	0.0000000	51/134
GO:0032635	interleukin-6 production	2.507492	0.0005807	0.0060812	14/37
GO:0042110	T cell activation	2.488993	0.0000000	0.0000000	80/213
GO:2001057	reactive nitrogen species metabolic process	2.485104	0.0059942	0.0340603	9/24
GO:0034341	response to interferon-gamma	2.454423	0.0000008	0.0000231	30/81
GO:0002250	adaptive immune response	2.422262	0.0000000	0.0000000	53/145
GO:0071706	tumor necrosis factor superfamily cytokine production	2.421383	0.0001095	0.0015733	19/52
GO:0070555	response to interleukin-1	2.409797	0.0000784	0.0012220	20/55
GO:0045785	positive regulation of cell adhesion	2.354309	0.0000000	0.0000000	54/152
GO:0050867	positive regulation of cell activation	2.353045	0.0000000	0.0000001	49/138
GO:0090130	tissue migration	2.343675	0.0000038	0.0000880	29/82
GO:0046683	response to organophosphorus	2.338921	0.0028408	0.0194608	12/34
GO:0002237	response to molecule of bacterial origin	2.322846	0.0000007	0.0000210	34/97
GO:0031345	negative regulation of cell projection organization	2.305024	0.0007154	0.0070868	16/46
GO:0070371	ERK1 and ERK2 cascade	2.293942	0.0000131	0.0002592	27/78
GO:0002694	regulation of leukocyte activation	2.273009	0.0000000	0.0000000	71/207
GO:0071887	leukocyte apoptotic process	2.255981	0.0009359	0.0083425	16/47
GO:0001667	ameboidal-type cell migration	2.250660	0.0000008	0.0000229	36/106
GO:0014074	response to purine-containing compound	2.208981	0.0048595	0.0282701	12/36
GO:0033002	muscle cell proliferation	2.168818	0.0007812	0.0075342	18/55
GO:0002449	lymphocyte mediated immunity	2.165239	0.0000061	0.0001284	33/101
GO:0061448	connective tissue development	2.157609	0.0030990	0.0208399	14/43
GO:0048872	homeostasis of number of cells	2.153757	0.0000010	0.0000268	39/120
GO:1901342	regulation of vasculature development	2.149279	0.0001289	0.0018171	24/74
GO:0002683	negative regulation of immune system process	2.139076	0.0000000	0.0000015	51/158
GO:0002521	leukocyte differentiation	2.132432	0.0000000	0.0000000	65/202
GO:0051271	negative regulation of cellular component movement	2.120622	0.0001631	0.0020610	24/75
GO:1901568	fatty acid derivative metabolic process	2.114982	0.0027804	0.0192268	15/47
GO:0051047	positive regulation of secretion	2.111238	0.0000045	0.0001001	36/113
GO:0048771	tissue remodeling	2.092719	0.0078842	0.0428085	12/38
GO:2000147	positive regulation of cell motility	2.062691	0.0000003	0.0000112	47/151
GO:1903706	regulation of hemopoiesis	2.056637	0.0000000	0.0000022	54/174
GO:0043491	protein kinase B signaling	2.039059	0.0009871	0.0086138	20/65
GO:0010959	regulation of metal ion transport	2.033267	0.0001444	0.0019438	27/88
GO:0030099	myeloid cell differentiation	2.027065	0.0000001	0.0000054	52/170
GO:0019932	second-messenger-mediated signaling	2.010421	0.0001782	0.0021776	27/89
GO:0031589	cell-substrate adhesion	2.010421	0.0001782	0.0021776	27/89
GO:0032355	response to estradiol	2.003494	0.0086462	0.0450500	13/43

Factor 11 : 31 significant GO terms
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
GO:0010573	vascular endothelial growth factor production	3.065571	0.0024424	0.0223784	7/11
GO:0050918	positive chemotaxis	3.065571	0.0024424	0.0223784	7/11
GO:0034109	homotypic cell-cell adhesion	2.924805	0.0000045	0.0002007	17/28
GO:0055123	digestive system development	2.846602	0.0000936	0.0021429	13/22
GO:0140253	cell-cell fusion	2.709746	0.0019149	0.0184687	9/16
GO:1990868	response to chemokine	2.709746	0.0019149	0.0184687	9/16
GO:0030101	natural killer cell activation	2.657835	0.0000460	0.0012485	16/29
GO:0043331	response to dsRNA	2.649529	0.0007668	0.0098610	11/20
GO:0001773	myeloid dendritic cell activation	2.569240	0.0053303	0.0394659	8/15
GO:0032613	interleukin-10 production	2.569240	0.0053303	0.0394659	8/15
GO:0006949	syncytium formation	2.550349	0.0033266	0.0280276	9/17
GO:0009581	detection of external stimulus	2.550349	0.0033266	0.0280276	9/17
GO:0032609	interferon-gamma production	2.408663	0.0001371	0.0027915	17/34
GO:0009582	detection of abiotic stimulus	2.408663	0.0054425	0.0396206	9/18
GO:0031532	actin cytoskeleton reorganization	2.335673	0.0003391	0.0052878	16/33
GO:0007229	integrin-mediated signaling pathway	2.330964	0.0005338	0.0078256	15/31
GO:0032970	regulation of actin filament-based process	2.307459	0.0000000	0.0000000	57/119
GO:0007015	actin filament organization	2.295757	0.0000000	0.0000000	61/128
GO:0002576	platelet degranulation	2.288230	0.0001346	0.0027915	19/40
GO:0060326	cell chemotaxis	2.271025	0.0000006	0.0000319	33/70
GO:0032612	interleukin-1 production	2.223381	0.0031783	0.0277348	12/26
GO:0048771	tissue remodeling	2.155119	0.0007246	0.0097594	17/38
GO:0050900	leukocyte migration	2.094489	0.0000000	0.0000021	50/115
GO:0043062	extracellular structure organization	2.090538	0.0001542	0.0029748	23/53
GO:0031214	biomineral tissue development	2.087508	0.0042619	0.0328841	13/30
GO:0032635	interleukin-6 production	2.083168	0.0016109	0.0166552	16/37
GO:0042110	T cell activation	2.058106	0.0000000	0.0000000	91/213
GO:0048017	inositol lipid-mediated signaling	2.016555	0.0013227	0.0149157	18/43
GO:0070555	response to interleukin-1	2.014518	0.0003005	0.0047892	23/55
GO:1902903	regulation of supramolecular fiber organization	2.013800	0.0000001	0.0000044	51/122
GO:0032103	positive regulation of response to external stimulus	2.012301	0.0000160	0.0005338	33/79

Factor 12 : 7 significant GO terms
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
GO:0032069	regulation of nuclease activity	2.680873	0.0018180	0.0410341	9/15
GO:0061641	CENP-A containing chromatin organization	2.647776	0.0000369	0.0027023	16/27
GO:0051383	kinetochore organization	2.457467	0.0014951	0.0387048	11/20
GO:0036297	interstrand cross-link repair	2.161995	0.0012330	0.0361509	15/31
GO:0071103	DNA conformation change	2.113301	0.0000000	0.0000000	70/148
GO:2000241	regulation of reproductive process	2.094432	0.0018474	0.0410341	15/32
GO:0006260	DNA replication	2.003885	0.0000000	0.0000000	74/165

Factor 13 : 57 significant GO terms
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
GO:0002507	tolerance induction	4.382482	0.0000575	0.0011596	8/11
GO:0034113	heterotypic cell-cell adhesion	4.142815	0.0000048	0.0001767	11/16
GO:0032633	interleukin-4 production	3.615548	0.0001771	0.0028845	9/15
GO:0042092	type 2 immune response	3.615548	0.0023564	0.0179923	6/10
GO:0032612	interleukin-1 production	3.244722	0.0000146	0.0004411	14/26
GO:0032963	collagen metabolic process	3.171533	0.0003292	0.0042056	10/19
GO:1904019	epithelial cell apoptotic process	3.124547	0.0000258	0.0006298	14/27
GO:0033627	cell adhesion mediated by integrin	3.012956	0.0005613	0.0062341	10/20
GO:0002437	inflammatory response to antigenic stimulus	3.012956	0.0020512	0.0170855	8/16
GO:1990868	response to chemokine	3.012956	0.0020512	0.0170855	8/16
GO:0030048	actin filament-based movement	2.892438	0.0002551	0.0037392	12/25
GO:0043062	extracellular structure organization	2.842412	0.0000002	0.0000172	25/53
GO:0006959	humoral immune response	2.835724	0.0000326	0.0007233	16/34
GO:0032609	interferon-gamma production	2.835724	0.0000326	0.0007233	16/34
GO:0001773	myeloid dendritic cell activation	2.812093	0.0063652	0.0392073	7/15
GO:0034109	homotypic cell-cell adhesion	2.797745	0.0002145	0.0032753	13/28
GO:0007229	integrin-mediated signaling pathway	2.721380	0.0001770	0.0028845	14/31
GO:0001906	cell killing	2.690140	0.0000007	0.0000465	25/56
GO:0050663	cytokine secretion	2.568422	0.0000013	0.0000705	26/61
GO:0071706	tumor necrosis factor superfamily cytokine production	2.549425	0.0000096	0.0003341	22/52
GO:0032615	interleukin-12 production	2.537227	0.0075710	0.0436972	8/19
GO:0035456	response to interferon-beta	2.537227	0.0075710	0.0436972	8/19
GO:0045445	myoblast differentiation	2.510797	0.0031575	0.0224704	10/24
GO:0060326	cell chemotaxis	2.496450	0.0000006	0.0000461	29/70
GO:0030101	natural killer cell activation	2.493481	0.0013347	0.0122295	12/29
GO:0032635	interleukin-6 production	2.442938	0.0004444	0.0052542	15/37
GO:0002576	platelet degranulation	2.410365	0.0003456	0.0042934	16/40
GO:0070265	necrotic cell death	2.410365	0.0044935	0.0291480	10/25
GO:0048771	tissue remodeling	2.378650	0.0006234	0.0068207	15/38
GO:0050900	leukocyte migration	2.357966	0.0000000	0.0000011	45/115
GO:0050866	negative regulation of cell activation	2.349085	0.0000301	0.0007111	23/59
GO:0051341	regulation of oxidoreductase activity	2.332611	0.0026320	0.0192927	12/31
GO:0034341	response to interferon-gamma	2.306214	0.0000020	0.0000916	31/81
GO:0046683	response to organophosphorus	2.304025	0.0020098	0.0170855	13/34
GO:0034340	response to type I interferon	2.276456	0.0005047	0.0057805	17/45
GO:0002791	regulation of peptide secretion	2.248475	0.0000000	0.0000011	50/134
GO:0043491	protein kinase B signaling	2.224952	0.0000576	0.0011596	24/65
GO:0034612	response to tumor necrosis factor	2.203022	0.0000022	0.0000916	34/93
GO:0014074	response to purine-containing compound	2.176024	0.0036251	0.0246037	13/36
GO:0002237	response to molecule of bacterial origin	2.174298	0.0000022	0.0000916	35/97
GO:0031032	actomyosin structure organization	2.169329	0.0006855	0.0072818	18/50
GO:0002449	lymphocyte mediated immunity	2.147850	0.0000022	0.0000916	36/101
GO:0071216	cellular response to biotic stimulus	2.146215	0.0000585	0.0011596	26/73
GO:0032103	positive regulation of response to external stimulus	2.135767	0.0000339	0.0007313	28/79
GO:0050920	regulation of chemotaxis	2.126793	0.0008983	0.0088951	18/51
GO:0015850	organic hydroxy compound transport	2.054289	0.0034844	0.0243246	15/44
GO:0042445	hormone metabolic process	2.051375	0.0026263	0.0192927	16/47
GO:0001818	negative regulation of cytokine production	2.050053	0.0000185	0.0005011	33/97
GO:0002250	adaptive immune response	2.036343	0.0000002	0.0000181	49/145
GO:0050817	coagulation	2.029134	0.0000235	0.0005941	33/98
GO:0002683	negative regulation of immune system process	2.021351	0.0000001	0.0000114	53/158
GO:0006909	phagocytosis	2.008638	0.0000898	0.0016448	29/87
GO:0009914	hormone transport	2.008638	0.0001183	0.0021149	28/84
GO:0070371	ERK1 and ERK2 cascade	2.008638	0.0002056	0.0032753	26/78
GO:0009612	response to mechanical stimulus	2.008638	0.0008233	0.0082665	21/63
GO:0060485	mesenchyme development	2.008638	0.0019048	0.0164259	18/54
GO:0003007	heart morphogenesis	2.008638	0.0044435	0.0290809	15/45

Factor 14 : 20 significant GO terms
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
GO:0050918	positive chemotaxis	4.528006	0.0002075	0.0089090	7/11
GO:0051383	kinetochore organization	3.201947	0.0007993	0.0225341	9/20
GO:1904888	cranial skeletal system development	3.201947	0.0007993	0.0225341	9/20
GO:0007292	female gamete generation	2.776756	0.0000652	0.0034137	16/41
GO:0006720	isoprenoid metabolic process	2.736707	0.0017813	0.0373059	10/26
GO:0055088	lipid homeostasis	2.736707	0.0017813	0.0373059	10/26
GO:1902850	microtubule cytoskeleton organization involved in mitosis	2.730342	0.0000000	0.0000028	33/86
GO:0051321	meiotic cell cycle	2.511331	0.0000000	0.0000064	36/102
GO:0008202	steroid metabolic process	2.502132	0.0000003	0.0000274	32/91
GO:0050000	chromosome localization	2.458060	0.0000981	0.0047917	19/55
GO:0070671	response to interleukin-12	2.439579	0.0020285	0.0413017	12/35
GO:0007051	spindle organization	2.371813	0.0000003	0.0000274	35/105
GO:0000910	cytokinesis	2.371813	0.0000035	0.0002117	29/87
GO:0051302	regulation of cell division	2.330919	0.0002188	0.0089090	19/58
GO:0048285	organelle fission	2.274607	0.0000000	0.0000000	78/244
GO:0007059	chromosome segregation	2.268690	0.0000000	0.0000000	66/207
GO:0044839	cell cycle G2/M phase transition	2.193481	0.0000004	0.0000274	41/133
GO:0034502	protein localization to chromosome	2.099638	0.0012918	0.0295913	18/61
GO:1901615	organic hydroxy compound metabolic process	2.098798	0.0000014	0.0000912	41/139
GO:0022412	cellular process involved in reproduction in multicellular organism	2.043796	0.0001453	0.0066550	27/94

Factor 15 : 6 significant GO terms
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
GO:0070972	protein localization to endoplasmic reticulum	2.831150	0.0000000	0.0000000	76/121
GO:0006413	translational initiation	2.226260	0.0000000	0.0000000	81/164
GO:0070671	response to interleukin-12	2.189352	0.0004993	0.0192614	17/35
GO:1902600	proton transmembrane transport	2.138168	0.0000006	0.0000501	37/78
GO:0002181	cytoplasmic translation	2.131921	0.0000014	0.0000901	35/74
GO:0010257	NADH dehydrogenase complex assembly	2.098314	0.0000314	0.0017693	27/58

Factor 16 : 6 significant GO terms
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
GO:0051131	chaperone-mediated protein complex assembly	3.768692	0.0002352	0.0123156	8/12
GO:0051187	cofactor catabolic process	2.975284	0.0005635	0.0236871	10/19
GO:0070972	protein localization to endoplasmic reticulum	2.756440	0.0000000	0.0000000	59/121
GO:0006457	protein folding	2.558310	0.0000000	0.0000000	62/137
GO:0008037	cell recognition	2.291772	0.0008970	0.0311737	15/37
GO:0001906	cell killing	2.018942	0.0009276	0.0311737	20/56

Factor 17 : 106 significant GO terms
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
GO:0007200	phospholipase C-activating G protein-coupled receptor signaling pathway	6.558974	0.0000866	0.0012450	6/10
GO:0034113	heterotypic cell-cell adhesion	6.149038	0.0000027	0.0000748	9/16
GO:0050918	positive chemotaxis	5.962704	0.0001759	0.0021864	6/11
GO:0055094	response to lipoprotein particle	5.465812	0.0010712	0.0095752	5/10
GO:0071402	cellular response to lipoprotein particle stimulus	5.465812	0.0010712	0.0095752	5/10
GO:0006959	humoral immune response	5.465812	0.0000000	0.0000000	17/34
GO:0002437	inflammatory response to antigenic stimulus	5.465812	0.0000307	0.0005926	8/16
GO:0003170	heart valve development	5.045365	0.0005568	0.0056389	6/13
GO:0030101	natural killer cell activation	4.900383	0.0000005	0.0000153	13/29
GO:0042116	macrophage activation	4.684982	0.0000449	0.0007647	9/21
GO:0001906	cell killing	4.489774	0.0000000	0.0000000	23/56
GO:0033627	cell adhesion mediated by integrin	4.372650	0.0002161	0.0025142	8/20
GO:0032633	interleukin-4 production	4.372650	0.0013851	0.0120711	6/15
GO:0032609	interferon-gamma production	4.179739	0.0000041	0.0001113	13/34
GO:0002526	acute inflammatory response	4.048750	0.0000752	0.0011486	10/27
GO:0032615	interleukin-12 production	4.027440	0.0009732	0.0090301	7/19
GO:0007187	G protein-coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger	4.008262	0.0000365	0.0006519	11/30
GO:0043062	extracellular structure organization	3.918884	0.0000001	0.0000031	19/53
GO:0001570	vasculogenesis	3.904151	0.0062469	0.0391812	5/14
GO:0006720	isoprenoid metabolic process	3.784024	0.0003143	0.0034543	9/26
GO:0032612	interleukin-1 production	3.784024	0.0003143	0.0034543	9/26
GO:0034341	response to interferon-gamma	3.778833	0.0000000	0.0000000	28/81
GO:0050866	negative regulation of cell activation	3.705635	0.0000001	0.0000039	20/59
GO:2001057	reactive nitrogen species metabolic process	3.643875	0.0009080	0.0086434	8/24
GO:0042110	T cell activation	3.592553	0.0000000	0.0000000	70/213
GO:0070661	leukocyte proliferation	3.577622	0.0000000	0.0000000	36/110
GO:0002449	lymphocyte mediated immunity	3.571719	0.0000000	0.0000000	33/101
GO:0007159	leukocyte cell-cell adhesion	3.549228	0.0000000	0.0000000	50/154
GO:0055123	digestive system development	3.478244	0.0025852	0.0201587	7/22
GO:0035456	response to interferon-beta	3.452092	0.0054710	0.0358297	6/19
GO:0051187	cofactor catabolic process	3.452092	0.0054710	0.0358297	6/19
GO:0060191	regulation of lipase activity	3.452092	0.0054710	0.0358297	6/19
GO:0022407	regulation of cell-cell adhesion	3.411781	0.0000000	0.0000000	49/157
GO:0050727	regulation of inflammatory response	3.380915	0.0000000	0.0000000	30/97
GO:0097696	STAT cascade	3.327016	0.0000364	0.0006519	14/46
GO:0048017	inositol lipid-mediated signaling	3.304910	0.0000747	0.0011486	13/43
GO:0060326	cell chemotaxis	3.279487	0.0000005	0.0000173	21/70
GO:0098742	cell-cell adhesion via plasma-membrane adhesion molecules	3.279487	0.0072239	0.0437616	6/20
GO:0008037	cell recognition	3.249942	0.0003157	0.0034543	11/37
GO:0045785	positive regulation of cell adhesion	3.236336	0.0000000	0.0000000	45/152
GO:0050900	leukocyte migration	3.231958	0.0000000	0.0000000	34/115
GO:0050663	cytokine secretion	3.225725	0.0000046	0.0001165	18/61
GO:0070371	ERK1 and ERK2 cascade	3.223428	0.0000002	0.0000077	23/78
GO:0002694	regulation of leukocyte activation	3.221396	0.0000000	0.0000000	61/207
GO:0050920	regulation of chemotaxis	3.215184	0.0000302	0.0005926	15/51
GO:0007229	integrin-mediated signaling pathway	3.173697	0.0013395	0.0118295	9/31
GO:0050867	positive regulation of cell activation	3.168587	0.0000000	0.0000000	40/138
GO:0045165	cell fate commitment	3.164417	0.0004084	0.0044027	11/38
GO:0071706	tumor necrosis factor superfamily cytokine production	3.153353	0.0000390	0.0006799	15/52
GO:0034109	homotypic cell-cell adhesion	3.123321	0.0027660	0.0205503	8/28
GO:0002065	columnar/cuboidal epithelial cell differentiation	3.060855	0.0057252	0.0364921	7/25
GO:0032103	positive regulation of response to external stimulus	3.044250	0.0000012	0.0000352	22/79
GO:0002250	adaptive immune response	3.015620	0.0000000	0.0000000	40/145
GO:0003205	cardiac chamber development	3.015620	0.0035206	0.0250542	8/29
GO:0009791	post-embryonic development	2.915100	0.0044253	0.0308926	8/30
GO:0003158	endothelium development	2.893665	0.0027201	0.0205503	9/34
GO:0030856	regulation of epithelial cell differentiation	2.876743	0.0016777	0.0135139	10/38
GO:0043491	protein kinase B signaling	2.859040	0.0000485	0.0008076	17/65
GO:0043583	ear development	2.802980	0.0020759	0.0165396	10/39
GO:0032623	interleukin-2 production	2.732906	0.0067595	0.0419894	8/32
GO:0002683	negative regulation of immune system process	2.698312	0.0000000	0.0000002	39/158
GO:0031348	negative regulation of defense response	2.690861	0.0001760	0.0021864	16/65
GO:0021915	neural tube development	2.666250	0.0030998	0.0224962	10/41
GO:0002764	immune response-regulating signaling pathway	2.656283	0.0000000	0.0000000	52/214
GO:0001819	positive regulation of cytokine production	2.629125	0.0000000	0.0000005	38/158
GO:0032102	negative regulation of response to external stimulus	2.623590	0.0000998	0.0014066	18/75
GO:0019932	second-messenger-mediated signaling	2.579372	0.0000350	0.0006519	21/89
GO:0050817	coagulation	2.565585	0.0000163	0.0003859	23/98
GO:0071887	leukocyte apoptotic process	2.558465	0.0027755	0.0205503	11/47
GO:1901568	fatty acid derivative metabolic process	2.558465	0.0027755	0.0205503	11/47
GO:0090130	tissue migration	2.532937	0.0001070	0.0014794	19/82
GO:0006909	phagocytosis	2.513017	0.0000796	0.0011908	20/87
GO:0002521	leukocyte differentiation	2.489380	0.0000000	0.0000001	46/202
GO:0001667	ameboidal-type cell migration	2.475085	0.0000204	0.0004454	24/106
GO:0007162	negative regulation of cell adhesion	2.472629	0.0001507	0.0019731	19/84
GO:0002697	regulation of immune effector process	2.470846	0.0000006	0.0000180	33/146
GO:0042113	B cell activation	2.429250	0.0000284	0.0005786	24/108
GO:0002064	epithelial cell development	2.408663	0.0021202	0.0167104	13/59
GO:0008202	steroid metabolic process	2.402555	0.0001547	0.0019896	20/91
GO:0002285	lymphocyte activation involved in immune response	2.395972	0.0007196	0.0071277	16/73
GO:0048872	homeostasis of number of cells	2.368518	0.0000213	0.0004454	26/120
GO:0042063	gliogenesis	2.363594	0.0008426	0.0081262	16/74
GO:0003013	circulatory system process	2.360237	0.0002875	0.0032932	19/88
GO:0034612	response to tumor necrosis factor	2.350887	0.0002117	0.0025032	20/93
GO:0072507	divalent inorganic cation homeostasis	2.324046	0.0000213	0.0004454	27/127
GO:0031349	positive regulation of defense response	2.301394	0.0000045	0.0001165	32/152
GO:0038061	NIK/NF-kappaB signaling	2.301394	0.0046233	0.0319704	12/57
GO:0008544	epidermis development	2.292115	0.0033766	0.0242654	13/62
GO:0045088	regulation of innate immune response	2.271506	0.0000061	0.0001486	32/154
GO:0007015	actin filament organization	2.220486	0.0000689	0.0010982	26/128
GO:0031589	cell-substrate adhesion	2.210890	0.0009440	0.0088708	18/89
GO:0002791	regulation of peptide secretion	2.202641	0.0000580	0.0009450	27/134
GO:0051271	negative regulation of cellular component movement	2.186325	0.0027611	0.0205503	15/75
GO:0048871	multicellular organismal homeostasis	2.143456	0.0007586	0.0074143	20/102
GO:0001818	negative regulation of cytokine production	2.141246	0.0010348	0.0094814	19/97
GO:0050878	regulation of body fluid levels	2.137009	0.0001346	0.0017943	26/133
GO:0019216	regulation of lipid metabolic process	2.135083	0.0001835	0.0022418	25/128
GO:0051047	positive regulation of secretion	2.128281	0.0004645	0.0047960	22/113
GO:0048880	sensory system development	2.102235	0.0040969	0.0288754	15/78
GO:0001505	regulation of neurotransmitter levels	2.096476	0.0056078	0.0363180	14/73
GO:0072593	reactive oxygen species metabolic process	2.077008	0.0015138	0.0127540	19/100
GO:1902903	regulation of supramolecular fiber organization	2.060880	0.0005616	0.0056389	23/122
GO:0002009	morphogenesis of an epithelium	2.043294	0.0014163	0.0120711	20/107
GO:0018212	peptidyl-tyrosine modification	2.043294	0.0014163	0.0120711	20/107
GO:0097305	response to alcohol	2.040570	0.0071799	0.0437616	14/75
GO:0043087	regulation of GTPase activity	2.011955	0.0001325	0.0017943	30/163

Factor 18 : 50 significant GO terms
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
GO:0070972	protein localization to endoplasmic reticulum	8.072743	0.0000000	0.0000000	80/121
GO:0006413	translational initiation	6.551720	0.0000000	0.0000000	88/164
GO:0002181	cytoplasmic translation	6.270012	0.0000000	0.0000000	38/74
GO:0050918	positive chemotaxis	5.550011	0.0010973	0.0161849	5/11
GO:0090150	establishment of protein localization to membrane	5.181815	0.0000000	0.0000000	87/205
GO:0031579	membrane raft organization	5.087510	0.0017556	0.0235669	5/12
GO:0006959	humoral immune response	5.027657	0.0000001	0.0000111	14/34
GO:0046939	nucleotide phosphorylation	4.440009	0.0000002	0.0000111	16/44
GO:0006605	protein targeting	4.337151	0.0000000	0.0000000	92/259
GO:0070206	protein trimerization	4.070008	0.0009926	0.0151582	7/21
GO:0006401	RNA catabolic process	4.006414	0.0000000	0.0000000	84/256
GO:0009132	nucleoside diphosphate metabolic process	3.991739	0.0000004	0.0000205	17/52
GO:0006090	pyruvate metabolic process	3.916423	0.0000005	0.0000260	17/53
GO:0048678	response to axon injury	3.663007	0.0041838	0.0471804	6/20
GO:0016052	carbohydrate catabolic process	3.402794	0.0000045	0.0001661	17/61
GO:0072524	pyridine-containing compound metabolic process	3.139720	0.0000082	0.0002845	18/70
GO:0071887	leukocyte apoptotic process	3.117453	0.0002878	0.0062054	12/47
GO:0050920	regulation of chemotaxis	3.112359	0.0001643	0.0037646	13/51
GO:0034404	nucleobase-containing small molecule biosynthetic process	2.951874	0.0000025	0.0001066	22/91
GO:0072522	purine-containing compound biosynthetic process	2.915827	0.0000000	0.0000017	32/134
GO:0008637	apoptotic mitochondrial changes	2.872947	0.0000842	0.0021279	16/68
GO:0048017	inositol lipid-mediated signaling	2.839540	0.0019903	0.0255952	10/43
GO:0046434	organophosphate catabolic process	2.829152	0.0000232	0.0007085	19/82
GO:1902600	proton transmembrane transport	2.817698	0.0000403	0.0010951	18/78
GO:0060326	cell chemotaxis	2.790863	0.0001219	0.0029231	16/70
GO:0090559	regulation of membrane permeability	2.713339	0.0028562	0.0337680	10/45
GO:0070482	response to oxygen levels	2.703648	0.0000002	0.0000120	31/140
GO:0046390	ribose phosphate biosynthetic process	2.662336	0.0000006	0.0000315	29/133
GO:0035821	modification of morphology or physiology of other organism	2.560166	0.0012480	0.0179365	13/62
GO:0070371	ERK1 and ERK2 cascade	2.504620	0.0004586	0.0085121	16/78
GO:0043491	protein kinase B signaling	2.442005	0.0019675	0.0255952	13/65
GO:0046677	response to antibiotic	2.422624	0.0000225	0.0007085	25/126
GO:0005996	monosaccharide metabolic process	2.394122	0.0001764	0.0039188	20/102
GO:0009123	nucleoside monophosphate metabolic process	2.382444	0.0000001	0.0000108	40/205
GO:0009141	nucleoside triphosphate metabolic process	2.379389	0.0000003	0.0000157	38/195
GO:0050900	leukocyte migration	2.335831	0.0001236	0.0029231	22/115
GO:0007006	mitochondrial membrane organization	2.332252	0.0007340	0.0118971	17/89
GO:1901293	nucleoside phosphate biosynthetic process	2.311957	0.0000045	0.0001661	32/169
GO:0009636	response to toxic substance	2.232690	0.0000097	0.0003247	32/175
GO:0097193	intrinsic apoptotic signaling pathway	2.226986	0.0000271	0.0007932	29/159
GO:0071826	ribonucleoprotein complex subunit organization	2.214253	0.0000045	0.0001661	35/193
GO:0010821	regulation of mitochondrion organization	2.162192	0.0017683	0.0235669	17/96
GO:0048872	homeostasis of number of cells	2.136754	0.0006248	0.0111634	21/120
GO:2001233	regulation of apoptotic signaling pathway	2.100649	0.0000353	0.0009954	32/186
GO:0002791	regulation of peptide secretion	2.095750	0.0004645	0.0085121	23/134
GO:0072331	signal transduction by p53 class mediator	2.082330	0.0006731	0.0112134	22/129
GO:0016053	organic acid biosynthetic process	2.063666	0.0004445	0.0085121	24/142
GO:0051188	cofactor biosynthetic process	2.049858	0.0006424	0.0111634	23/137
GO:0070997	neuron death	2.035004	0.0009273	0.0144620	22/132
GO:0022407	regulation of cell-cell adhesion	2.022042	0.0003608	0.0073458	26/157

Factor 19 : 120 significant GO terms
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
GO:1990868	response to chemokine	6.297046	0.0000022	0.0000658	9/16
GO:0050918	positive chemotaxis	6.106226	0.0001539	0.0018802	6/11
GO:0032633	interleukin-4 production	5.224216	0.0001478	0.0018365	7/15
GO:0002507	tolerance induction	5.088522	0.0016313	0.0125864	5/11
GO:0033627	cell adhesion mediated by integrin	5.037637	0.0000230	0.0004108	9/20
GO:0032602	chemokine production	4.975444	0.0000746	0.0010937	8/18
GO:0034113	heterotypic cell-cell adhesion	4.897702	0.0002427	0.0027973	7/16
GO:0045730	respiratory burst	4.664479	0.0025931	0.0181021	5/12
GO:0055123	digestive system development	4.579670	0.0000578	0.0009100	9/22
GO:0090077	foam cell differentiation	4.477899	0.0085288	0.0453015	4/10
GO:0001773	myeloid dendritic cell activation	4.477899	0.0012214	0.0098382	6/15
GO:0003170	heart valve development	4.305672	0.0039080	0.0246947	5/13
GO:0033028	myeloid cell apoptotic process	4.305672	0.0039080	0.0246947	5/13
GO:0043062	extracellular structure organization	4.224433	0.0000000	0.0000006	20/53
GO:0002437	inflammatory response to antigenic stimulus	4.198031	0.0018086	0.0132569	6/16
GO:0007229	integrin-mediated signaling pathway	3.972330	0.0000416	0.0006928	11/31
GO:0006959	humoral immune response	3.951088	0.0000197	0.0003707	12/34
GO:0098742	cell-cell adhesion via plasma-membrane adhesion molecules	3.918162	0.0011987	0.0097629	7/20
GO:0032623	interleukin-2 production	3.848195	0.0000583	0.0009100	11/32
GO:0071887	leukocyte apoptotic process	3.810978	0.0000014	0.0000483	16/47
GO:0042116	macrophage activation	3.731583	0.0016618	0.0126885	7/21
GO:0046847	filopodium assembly	3.731583	0.0078481	0.0426120	5/15
GO:0032103	positive regulation of response to external stimulus	3.684348	0.0000000	0.0000002	26/79
GO:0060326	cell chemotaxis	3.678275	0.0000000	0.0000007	23/70
GO:0002065	columnar/cuboidal epithelial cell differentiation	3.582320	0.0010513	0.0087864	8/25
GO:0030101	natural killer cell activation	3.474232	0.0006595	0.0061977	9/29
GO:0070555	response to interleukin-1	3.460195	0.0000030	0.0000717	17/55
GO:0002576	platelet degranulation	3.358424	0.0001221	0.0015646	12/40
GO:0050900	leukocyte migration	3.309752	0.0000000	0.0000000	34/115
GO:0045445	myoblast differentiation	3.265135	0.0039076	0.0246947	7/24
GO:0050727	regulation of inflammatory response	3.231474	0.0000000	0.0000006	28/97
GO:0009308	amine metabolic process	3.198500	0.0083391	0.0446171	6/21
GO:0007159	leukocyte cell-cell adhesion	3.125806	0.0000000	0.0000000	43/154
GO:0050663	cytokine secretion	3.119848	0.0000144	0.0002848	17/61
GO:0050920	regulation of chemotaxis	3.073068	0.0000987	0.0013157	14/51
GO:0002285	lymphocyte activation involved in immune response	3.067054	0.0000034	0.0000772	20/73
GO:0070661	leukocyte proliferation	3.053113	0.0000000	0.0000007	30/110
GO:0031532	actin cytoskeleton reorganization	3.053113	0.0018389	0.0133453	9/33
GO:0050866	negative regulation of cell activation	3.035864	0.0000373	0.0006356	16/59
GO:0070371	ERK1 and ERK2 cascade	3.013971	0.0000026	0.0000682	21/78
GO:0032612	interleukin-1 production	3.013971	0.0063508	0.0355351	7/26
GO:0072507	divalent inorganic cation homeostasis	2.997019	0.0000000	0.0000002	34/127
GO:0031214	biomineral tissue development	2.985266	0.0038195	0.0246947	8/30
GO:0038061	NIK/NF-kappaB signaling	2.945986	0.0000951	0.0012908	15/57
GO:0042110	T cell activation	2.943220	0.0000000	0.0000000	56/213
GO:0007162	negative regulation of cell adhesion	2.931958	0.0000025	0.0000676	22/84
GO:0022407	regulation of cell-cell adhesion	2.923469	0.0000000	0.0000000	41/157
GO:0002526	acute inflammatory response	2.902342	0.0079297	0.0427387	7/27
GO:0050867	positive regulation of cell activation	2.839248	0.0000000	0.0000005	35/138
GO:0045785	positive regulation of cell adhesion	2.798687	0.0000000	0.0000002	38/152
GO:0001906	cell killing	2.798687	0.0002921	0.0031951	14/56
GO:0007272	ensheathment of neurons	2.798687	0.0058571	0.0338049	8/32
GO:2000241	regulation of reproductive process	2.798687	0.0058571	0.0338049	8/32
GO:0034109	homotypic cell-cell adhesion	2.798687	0.0097802	0.0497842	7/28
GO:0001667	ameboidal-type cell migration	2.745882	0.0000012	0.0000461	26/106
GO:0009615	response to virus	2.741571	0.0000000	0.0000006	36/147
GO:0034340	response to type I interferon	2.736494	0.0015767	0.0123055	11/45
GO:0090130	tissue migration	2.730426	0.0000227	0.0004108	20/82
GO:0002521	leukocyte differentiation	2.715558	0.0000000	0.0000000	49/202
GO:0051271	negative regulation of cellular component movement	2.686740	0.0000731	0.0010937	18/75
GO:0001655	urogenital system development	2.665416	0.0003186	0.0034345	15/63
GO:0030856	regulation of epithelial cell differentiation	2.651388	0.0052011	0.0312495	9/38
GO:0033002	muscle cell proliferation	2.646031	0.0008532	0.0077209	13/55
GO:0031589	cell-substrate adhesion	2.641458	0.0000244	0.0004258	21/89
GO:0003158	endothelium development	2.634058	0.0086307	0.0455132	8/34
GO:0002250	adaptive immune response	2.624976	0.0000001	0.0000037	34/145
GO:0048872	homeostasis of number of cells	2.612108	0.0000014	0.0000483	28/120
GO:0002244	hematopoietic progenitor cell differentiation	2.603430	0.0037812	0.0246947	10/43
GO:0044706	multi-multicellular organism process	2.598781	0.0010228	0.0087179	13/56
GO:0043583	ear development	2.583404	0.0062413	0.0355351	9/39
GO:0051235	maintenance of location	2.575783	0.0000043	0.0000966	26/113
GO:0032102	negative regulation of response to external stimulus	2.537476	0.0002442	0.0027973	17/75
GO:2000027	regulation of animal organ morphogenesis	2.518818	0.0074343	0.0406668	9/40
GO:1903706	regulation of hemopoiesis	2.509168	0.0000000	0.0000016	39/174
GO:0002694	regulation of leukocyte activation	2.487722	0.0000000	0.0000002	46/207
GO:0001503	ossification	2.460384	0.0001114	0.0014575	20/91
GO:0007015	actin filament organization	2.448851	0.0000053	0.0001115	28/128
GO:0072511	divalent inorganic cation transport	2.433641	0.0000192	0.0003700	25/115
GO:0097696	STAT cascade	2.433641	0.0063084	0.0355351	10/46
GO:0001818	negative regulation of cytokine production	2.423605	0.0000949	0.0012908	21/97
GO:0002791	regulation of peptide secretion	2.422744	0.0000045	0.0000976	29/134
GO:1901342	regulation of vasculature development	2.420486	0.0006489	0.0061773	16/74
GO:0010959	regulation of metal ion transport	2.417048	0.0002111	0.0024953	19/88
GO:0040013	negative regulation of locomotion	2.408997	0.0004700	0.0047195	17/79
GO:0042445	hormone metabolic process	2.381861	0.0073925	0.0406668	10/47
GO:0098542	defense response to other organism	2.372397	0.0000023	0.0000658	32/151
GO:2000147	positive regulation of cell motility	2.372397	0.0000023	0.0000658	32/151
GO:0007219	Notch signaling pathway	2.368120	0.0053003	0.0313316	11/52
GO:0031349	positive regulation of defense response	2.356789	0.0000027	0.0000684	32/152
GO:0002831	regulation of response to biotic stimulus	2.356789	0.0038073	0.0246947	12/57
GO:0034341	response to interferon-gamma	2.349515	0.0006386	0.0061773	17/81
GO:0035821	modification of morphology or physiology of other organism	2.347286	0.0027389	0.0189397	13/62
GO:0001525	angiogenesis	2.316155	0.0000660	0.0010078	24/116
GO:0002237	response to molecule of bacterial origin	2.308196	0.0002794	0.0031030	20/97
GO:0043900	regulation of multi-organism process	2.306797	0.0000022	0.0000658	34/165
GO:0009636	response to toxic substance	2.302920	0.0000011	0.0000461	36/175
GO:0034612	response to tumor necrosis factor	2.287099	0.0004466	0.0045463	19/93
GO:0097191	extrinsic apoptotic signaling pathway	2.287099	0.0004466	0.0045463	19/93
GO:0042113	B cell activation	2.280412	0.0001684	0.0020237	22/108
GO:0001819	positive regulation of cytokine production	2.267291	0.0000065	0.0001320	32/158
GO:0043491	protein kinase B signaling	2.238950	0.0042278	0.0262627	13/65
GO:0043270	positive regulation of ion transport	2.198968	0.0094426	0.0484017	11/56
GO:0002009	morphogenesis of an epithelium	2.197100	0.0004037	0.0042278	21/107
GO:0032970	regulation of actin filament-based process	2.163691	0.0002737	0.0030870	23/119
GO:0003013	circulatory system process	2.162622	0.0016954	0.0128116	17/88
GO:0002764	immune response-regulating signaling pathway	2.144788	0.0000014	0.0000483	41/214
GO:1902532	negative regulation of intracellular signal transduction	2.140172	0.0000028	0.0000684	39/204
GO:0019932	second-messenger-mediated signaling	2.138323	0.0019274	0.0138511	17/89
GO:0002683	negative regulation of immune system process	2.125585	0.0000468	0.0007622	30/158
GO:0048568	embryonic organ development	2.121110	0.0015781	0.0123055	18/95
GO:0042063	gliogenesis	2.117925	0.0051505	0.0312495	14/74
GO:0002449	lymphocyte mediated immunity	2.105943	0.0012907	0.0102839	19/101
GO:0052547	regulation of peptidase activity	2.094501	0.0000827	0.0011663	29/155
GO:0018212	peptidyl-tyrosine modification	2.092476	0.0010548	0.0087864	20/107
GO:0006909	phagocytosis	2.058804	0.0038600	0.0246947	16/87
GO:0045861	negative regulation of proteolysis	2.052370	0.0007909	0.0072470	22/120
GO:0046677	response to antibiotic	2.043486	0.0006444	0.0061773	23/126
GO:0030099	myeloid cell differentiation	2.041395	0.0000783	0.0011260	31/170
GO:1902903	regulation of supramolecular fiber organization	2.018725	0.0009958	0.0087179	22/122
GO:0072593	reactive oxygen species metabolic process	2.015055	0.0028632	0.0194325	18/100

Factor 20 : 75 significant GO terms
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
GO:0045730	respiratory burst	6.538855	0.0005558	0.0079333	5/12
GO:0042092	type 2 immune response	6.277301	0.0024994	0.0277763	4/10
GO:0070265	necrotic cell death	5.021840	0.0001035	0.0022311	8/25
GO:0034341	response to interferon-gamma	4.456109	0.0000000	0.0000001	23/81
GO:0032602	chemokine production	4.359236	0.0043757	0.0445469	5/18
GO:0030101	natural killer cell activation	4.329173	0.0003279	0.0054633	8/29
GO:0070972	protein localization to endoplasmic reticulum	4.279978	0.0000000	0.0000000	33/121
GO:0060326	cell chemotaxis	4.259597	0.0000000	0.0000033	19/70
GO:0032612	interleukin-1 production	4.225106	0.0009153	0.0119807	7/26
GO:0006959	humoral immune response	4.154096	0.0001961	0.0034224	9/34
GO:0050920	regulation of chemotaxis	4.000241	0.0000118	0.0003745	13/51
GO:0001906	cell killing	3.923313	0.0000069	0.0002664	14/56
GO:0034109	homotypic cell-cell adhesion	3.923313	0.0014752	0.0176614	7/28
GO:0032609	interferon-gamma production	3.692530	0.0010482	0.0132465	8/34
GO:0071887	leukocyte apoptotic process	3.672889	0.0001297	0.0026405	11/47
GO:0006413	translational initiation	3.444860	0.0000000	0.0000000	36/164
GO:0050900	leukocyte migration	3.411576	0.0000000	0.0000033	25/115
GO:0043062	extracellular structure organization	3.257090	0.0004021	0.0061409	11/53
GO:0046683	response to organophosphorus	3.230964	0.0048185	0.0470299	7/34
GO:0070371	ERK1 and ERK2 cascade	3.219129	0.0000234	0.0006850	16/78
GO:0030902	hindbrain development	3.219129	0.0026866	0.0293923	8/39
GO:0034612	response to tumor necrosis factor	3.206148	0.0000042	0.0002075	19/93
GO:0070555	response to interleukin-1	3.138650	0.0005628	0.0079333	11/55
GO:0002576	platelet degranulation	3.138650	0.0031763	0.0337429	8/40
GO:0072507	divalent inorganic cation homeostasis	3.089223	0.0000003	0.0000162	25/127
GO:0071241	cellular response to inorganic substance	3.051466	0.0001398	0.0026968	14/72
GO:0003012	muscle system process	3.031651	0.0000297	0.0008372	17/88
GO:0070482	response to oxygen levels	3.026556	0.0000001	0.0000090	27/140
GO:0071706	tumor necrosis factor superfamily cytokine production	3.017933	0.0013731	0.0170594	10/52
GO:0002285	lymphocyte activation involved in immune response	3.009665	0.0001632	0.0029906	14/73
GO:0032103	positive regulation of response to external stimulus	2.979731	0.0001077	0.0022546	15/79
GO:0002181	cytoplasmic translation	2.968993	0.0001899	0.0033950	14/74
GO:0042110	T cell activation	2.947090	0.0000000	0.0000001	40/213
GO:0048872	homeostasis of number of cells	2.877096	0.0000049	0.0002120	22/120
GO:0090150	establishment of protein localization to membrane	2.832441	0.0000000	0.0000006	37/205
GO:0002449	lymphocyte mediated immunity	2.796817	0.0000539	0.0012739	18/101
GO:0045785	positive regulation of cell adhesion	2.787617	0.0000008	0.0000433	27/152
GO:0042063	gliogenesis	2.756923	0.0006793	0.0092215	13/74
GO:0031099	regeneration	2.753202	0.0028218	0.0304177	10/57
GO:0070661	leukocyte proliferation	2.710653	0.0000524	0.0012739	19/110
GO:0003013	circulatory system process	2.674986	0.0003748	0.0058445	15/88
GO:0019882	antigen processing and presentation	2.667853	0.0001593	0.0029906	17/100
GO:0050866	negative regulation of cell activation	2.659873	0.0036658	0.0378452	10/59
GO:0002521	leukocyte differentiation	2.641438	0.0000001	0.0000076	34/202
GO:0010038	response to metal ion	2.638688	0.0000768	0.0017590	19/113
GO:0052547	regulation of peptidase activity	2.632416	0.0000038	0.0001990	26/155
GO:0050867	positive regulation of cell activation	2.615542	0.0000156	0.0004778	23/138
GO:0042113	B cell activation	2.615542	0.0001333	0.0026405	18/108
GO:0022407	regulation of cell-cell adhesion	2.598882	0.0000049	0.0002120	26/157
GO:0051346	negative regulation of hydrolase activity	2.598221	0.0000075	0.0002740	25/151
GO:0002250	adaptive immune response	2.597504	0.0000115	0.0003745	24/145
GO:0002237	response to molecule of bacterial origin	2.588578	0.0003543	0.0056457	16/97
GO:0050727	regulation of inflammatory response	2.588578	0.0003543	0.0056457	16/97
GO:0006401	RNA catabolic process	2.574674	0.0000000	0.0000008	42/256
GO:0055076	transition metal ion homeostasis	2.572664	0.0046985	0.0470299	10/61
GO:0051271	negative regulation of cellular component movement	2.510920	0.0025010	0.0277763	12/75
GO:0007159	leukocyte cell-cell adhesion	2.445702	0.0000325	0.0008820	24/154
GO:0006605	protein targeting	2.423668	0.0000001	0.0000069	40/259
GO:0001819	positive regulation of cytokine production	2.383785	0.0000499	0.0012622	24/158
GO:0002683	negative regulation of immune system process	2.383785	0.0000499	0.0012622	24/158
GO:0045861	negative regulation of proteolysis	2.353988	0.0005145	0.0075424	18/120
GO:0072593	reactive oxygen species metabolic process	2.353988	0.0014881	0.0176614	15/100
GO:0002694	regulation of leukocyte activation	2.350197	0.0000052	0.0002126	31/207
GO:0002791	regulation of peptide secretion	2.342276	0.0002716	0.0046298	20/134
GO:0007249	I-kappaB kinase/NF-kappaB signaling	2.329467	0.0004140	0.0061928	19/128
GO:0010959	regulation of metal ion transport	2.318321	0.0034742	0.0363793	13/88
GO:0002764	immune response-regulating signaling pathway	2.273322	0.0000105	0.0003669	31/214
GO:0009636	response to toxic substance	2.241893	0.0000981	0.0021798	25/175
GO:0005996	monosaccharide metabolic process	2.153976	0.0048856	0.0470299	14/102
GO:0048871	multicellular organismal homeostasis	2.153976	0.0048856	0.0470299	14/102
GO:0002697	regulation of immune effector process	2.149761	0.0008482	0.0113036	20/146
GO:1903706	regulation of hemopoiesis	2.074395	0.0005896	0.0081550	23/174
GO:0030099	myeloid cell differentiation	2.030891	0.0010327	0.0132465	22/170
GO:0009615	response to virus	2.028379	0.0022789	0.0261005	19/147
GO:0019058	viral life cycle	2.028379	0.0022789	0.0261005	19/147

Summary:
Factor	1	2	3	4	5	6	7	8	9	10
Signif_GO_terms	0	0	0	0	0	2	36	27	81	0
Factor	11	12	13	14	15	16	17	18	19	20
Signif_GO_terms	31	7	57	20	6	6	106	50	120	75

5.1.1 Factors of interest

7: immune response, interleukin production, response to chemokine, cell killing
8: cell killing, leukocyte migration
9: response to chemokine, interleukin production, leukocyte migration, cell killing, T cell activation
11: cell chemotaxis, interleukin production, leukocyte migration, T cell activation
12: DNA conformation change, DNA replication
13: interleukin production, cell killing, cell chemotaxis, leukocyte migration
14: meiotic cell cycle, cytokinesis, chromosome segregation, cell cycle G2/M phase transition
16: (cell killing)
17: cell killing, interleukin production, T cell activation, leukocyte proliferation, cell-cell adhesion, leukocyte migration, adaptive immune response, ……
18: cell chemotaxis, leukocyte migration, signal transduction by p53 class mediator
19: interleukin production, leukocyte migration, leukocyte proliferation, cell killing, B cell activation
20: cell chemotaxis, cell killing, leukocyte migration, leukocyte proliferation, T cell activation

From the reference study:

Targeting CD5, RASA2, SOCS1, and CBLB promoted programs that are characterized by the induction of markers of activation states (e.g. IL2RA, TNFRSF18/GITR), cell cycle genes (e.g. MKI67, UBE2S, CENPF and TOP2A), and effector molecules (e.g GZMB).

Associated factors in GSFA:

CD5: 7, 9
RASA2: 11, 13, 19, 20
SOCS1: 11
CBLB: 7, 9, 11

From the reference study:

Targeting CD3D or LCP2 inhibited the cluster 10 activation program and promoted programs characterized by expression of resting state markers such as IL7R and CCR7.

Associated factors in GSFA

CD3D: 7, 13
LCP2: 2, 4, 7, 13

5.2 Reactome Pathway Over-Representation Analysis

Gene sets: The Reactome pathway database.

Factor 4 : 8 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-176974	Unwinding of DNA	2.253105	0.0002922	0.0092682	10/10
R-HSA-445355	Smooth Muscle Contraction	2.127932	0.0000101	0.0026273	17/18
R-HSA-446728	Cell junction organization	2.092169	0.0002086	0.0074105	13/14
R-HSA-9008059	Interleukin-37 signaling	2.048277	0.0019219	0.0348290	10/11
R-HSA-174411	Polymerase switching on the C-strand of the telomere	2.048277	0.0019219	0.0348290	10/11
R-HSA-69091	Polymerase switching	2.048277	0.0019219	0.0348290	10/11
R-HSA-69109	Leading Strand Synthesis	2.048277	0.0019219	0.0348290	10/11
R-HSA-446353	Cell-extracellular matrix interactions	2.048277	0.0019219	0.0348290	10/11

Factor 5 : 1 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-176974	Unwinding of DNA	2.106136	0.0005747	0.0085057	10/10

Factor 6 : 21 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-174411	Polymerase switching on the C-strand of the telomere	2.230679	0.0001444	0.0018055	11/11
R-HSA-69091	Polymerase switching	2.230679	0.0001444	0.0018055	11/11
R-HSA-69109	Leading Strand Synthesis	2.230679	0.0001444	0.0018055	11/11
R-HSA-176974	Unwinding of DNA	2.230679	0.0003231	0.0036315	10/10
R-HSA-912446	Meiotic recombination	2.144884	0.0000000	0.0000021	25/26
R-HSA-69190	DNA strand elongation	2.144884	0.0000000	0.0000021	25/26
R-HSA-5693554	Resolution of D-loop Structures through Synthesis-Dependent Strand Annealing (SDSA)	2.099463	0.0000252	0.0004151	16/17
R-HSA-69186	Lagging Strand Synthesis	2.091262	0.0000534	0.0007648	15/16
R-HSA-5334118	DNA methylation	2.044789	0.0010230	0.0094627	11/12
R-HSA-73728	RNA Polymerase I Promoter Opening	2.044789	0.0010230	0.0094627	11/12
R-HSA-5625886	Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3	2.027890	0.0021102	0.0169976	10/11
R-HSA-5358508	Mismatch Repair	2.027890	0.0021102	0.0169976	10/11
R-HSA-69183	Processive synthesis on the lagging strand	2.027890	0.0021102	0.0169976	10/11
R-HSA-2299718	Condensation of Prophase Chromosomes	2.018234	0.0000159	0.0002996	19/21
R-HSA-5693579	Homologous DNA Pairing and Strand Exchange	2.007611	0.0000003	0.0000117	27/30
R-HSA-5696397	Gap-filling DNA repair synthesis and ligation in GG-NER	2.007611	0.0000323	0.0005014	18/20
R-HSA-156711	Polo-like kinase mediated events	2.007611	0.0043201	0.0297384	9/10
R-HSA-5358565	Mismatch repair (MMR) directed by MSH2:MSH6 (MutSalpha)	2.007611	0.0043201	0.0297384	9/10
R-HSA-5358606	Mismatch repair (MMR) directed by MSH2:MSH3 (MutSbeta)	2.007611	0.0043201	0.0297384	9/10
R-HSA-69166	Removal of the Flap Intermediate	2.007611	0.0043201	0.0297384	9/10
R-HSA-75035	Chk1/Chk2(Cds1) mediated inactivation of Cyclin B:Cdk1 complex	2.007611	0.0043201	0.0297384	9/10

Factor 7 : 34 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-373076	Class A/1 (Rhodopsin-like receptors)	2.777444	0.0000019	0.0000631	17/22
R-HSA-375276	Peptide ligand-binding receptors	2.695755	0.0009114	0.0149873	9/12
R-HSA-389948	PD-1 signaling	2.635849	0.0003177	0.0065598	11/15
R-HSA-446353	Cell-extracellular matrix interactions	2.614065	0.0025008	0.0341653	8/11
R-HSA-446728	Cell junction organization	2.567385	0.0008525	0.0142826	10/14
R-HSA-216083	Integrin cell surface interactions	2.567385	0.0008525	0.0142826	10/14
R-HSA-622312	Inflammasomes	2.488389	0.0022322	0.0309713	9/13
R-HSA-500792	GPCR ligand binding	2.471109	0.0000016	0.0000563	22/32
R-HSA-202427	Phosphorylation of CD3 and TCR zeta chains	2.471109	0.0007616	0.0135253	11/16
R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	2.396226	0.0000012	0.0000481	24/36
R-HSA-2172127	DAP12 interactions	2.396226	0.0019221	0.0279801	10/15
R-HSA-2424491	DAP12 signaling	2.396226	0.0019221	0.0279801	10/15
R-HSA-1474228	Degradation of the extracellular matrix	2.325749	0.0016180	0.0243525	11/17
R-HSA-163210	Formation of ATP by chemiosmotic coupling	2.325749	0.0016180	0.0243525	11/17
R-HSA-1500931	Cell-Cell communication	2.318929	0.0000207	0.0005264	20/31
R-HSA-156842	Eukaryotic Translation Elongation	2.313598	0.0000000	0.0000000	56/87
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	2.296384	0.0000062	0.0001839	23/36
R-HSA-156902	Peptide chain elongation	2.283463	0.0000000	0.0000000	54/85
R-HSA-192823	Viral mRNA Translation	2.283463	0.0000000	0.0000000	54/85
R-HSA-202733	Cell surface interactions at the vascular wall	2.279337	0.0000019	0.0000631	26/41
R-HSA-202433	Generation of second messenger molecules	2.246462	0.0003895	0.0078613	15/24
R-HSA-2408557	Selenocysteine synthesis	2.198890	0.0000000	0.0000000	52/85
R-HSA-977225	Amyloid fiber formation	2.156604	0.0007255	0.0131472	15/25
R-HSA-1474244	Extracellular matrix organization	2.137175	0.0000510	0.0011602	22/37
R-HSA-72689	Formation of a pool of free 40S subunits	2.134139	0.0000000	0.0000000	57/96
R-HSA-72764	Eukaryotic Translation Termination	2.123928	0.0000000	0.0000000	52/88
R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	2.116667	0.0000000	0.0000000	53/90
R-HSA-72695	Formation of the ternary complex, and subsequently, the 43S complex	2.096698	0.0000080	0.0002159	28/48
R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	2.068441	0.0000000	0.0000000	61/106
R-HSA-5357905	Regulation of TNFR1 signaling	2.031583	0.0034617	0.0452057	13/23
R-HSA-168643	Nucleotide-binding domain, leucine rich repeat containing receptor (NLR) signaling pathways	2.021816	0.0006389	0.0120710	18/32
R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	2.015518	0.0000000	0.0000000	60/107
R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane	2.015518	0.0000000	0.0000000	60/107
R-HSA-416476	G alpha (q) signalling events	2.006143	0.0000960	0.0020803	24/43

Factor 8 : 58 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-156842	Eukaryotic Translation Elongation	5.137738	0.0000000	0.0000000	84/87
R-HSA-156902	Peptide chain elongation	5.133421	0.0000000	0.0000000	82/85
R-HSA-192823	Viral mRNA Translation	5.008216	0.0000000	0.0000000	80/85
R-HSA-2408557	Selenocysteine synthesis	5.008216	0.0000000	0.0000000	80/85
R-HSA-72689	Formation of a pool of free 40S subunits	4.933223	0.0000000	0.0000000	89/96
R-HSA-72764	Eukaryotic Translation Termination	4.837481	0.0000000	0.0000000	80/88
R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	4.789106	0.0000000	0.0000000	81/90
R-HSA-72695	Formation of the ternary complex, and subsequently, the 43S complex	4.656075	0.0000000	0.0000000	42/48
R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	4.618425	0.0000000	0.0000000	92/106
R-HSA-389948	PD-1 signaling	4.611732	0.0000000	0.0000006	13/15
R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	4.525531	0.0000000	0.0000000	91/107
R-HSA-2408522	Selenoamino acid metabolism	4.461232	0.0000000	0.0000000	83/99
R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane	4.426069	0.0000000	0.0000000	89/107
R-HSA-72613	Eukaryotic Translation Initiation	4.341003	0.0000000	0.0000000	93/114
R-HSA-72737	Cap-dependent Translation Initiation	4.341003	0.0000000	0.0000000	93/114
R-HSA-202427	Phosphorylation of CD3 and TCR zeta chains	4.323499	0.0000001	0.0000027	13/16
R-HSA-72662	Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	4.275988	0.0000000	0.0000000	45/56
R-HSA-72649	Translation initiation complex formation	4.256983	0.0000000	0.0000000	44/55
R-HSA-202430	Translocation of ZAP-70 to Immunological synapse	4.180966	0.0000020	0.0000460	11/14
R-HSA-72702	Ribosomal scanning and start codon recognition	4.160234	0.0000000	0.0000000	43/55
R-HSA-927802	Nonsense-Mediated Decay (NMD)	4.089463	0.0000000	0.0000000	83/108
R-HSA-975957	Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)	4.089463	0.0000000	0.0000000	83/108
R-HSA-168273	Influenza Viral RNA Transcription and Replication	3.707414	0.0000000	0.0000000	85/122
R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	3.547486	0.0000000	0.0000000	24/36
R-HSA-168255	Influenza Life Cycle	3.533946	0.0000000	0.0000000	87/131
R-HSA-3928662	EPHB-mediated forward signaling	3.458799	0.0000069	0.0001465	13/20
R-HSA-9010553	Regulation of expression of SLITs and ROBOs	3.415654	0.0000000	0.0000000	95/148
R-HSA-168254	Influenza Infection	3.382781	0.0000000	0.0000000	89/140
R-HSA-983170	Antigen Presentation: Folding, assembly and peptide loading of class I MHC	3.192737	0.0000508	0.0009811	12/20
R-HSA-376176	Signaling by ROBO receptors	3.167398	0.0000000	0.0000000	100/168
R-HSA-427359	SIRT1 negatively regulates rRNA expression	3.104050	0.0026428	0.0340121	7/12
R-HSA-5627117	RHO GTPases Activate ROCKs	3.104050	0.0026428	0.0340121	7/12
R-HSA-445355	Smooth Muscle Contraction	2.956238	0.0005245	0.0081709	10/18
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol	2.844682	0.0000000	0.0000000	85/159
R-HSA-2682334	EPH-Ephrin signaling	2.800647	0.0000026	0.0000574	20/38
R-HSA-5663213	RHO GTPases Activate WASPs and WAVEs	2.767039	0.0001826	0.0031182	13/25
R-HSA-8868773	rRNA processing in the nucleus and cytosol	2.707844	0.0000000	0.0000000	86/169
R-HSA-422475	Axon guidance	2.660614	0.0000000	0.0000000	130/260
R-HSA-877300	Interferon gamma signaling	2.660614	0.0000015	0.0000345	23/46
R-HSA-202433	Generation of second messenger molecules	2.660614	0.0005196	0.0081709	12/24
R-HSA-72312	rRNA processing	2.600146	0.0000000	0.0000000	86/176
R-HSA-71291	Metabolism of amino acids and derivatives	2.586018	0.0000000	0.0000000	104/214
R-HSA-5625740	RHO GTPases activate PKNs	2.568869	0.0002842	0.0046727	14/29
R-HSA-388841	Costimulation by the CD28 family	2.465935	0.0000482	0.0009505	19/41
R-HSA-8950505	Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation	2.403136	0.0006689	0.0100671	14/31
R-HSA-72766	Translation	2.400555	0.0000000	0.0000000	120/266
R-HSA-977225	Amyloid fiber formation	2.341341	0.0032587	0.0407567	11/25
R-HSA-202733	Cell surface interactions at the vascular wall	2.336149	0.0001808	0.0031182	18/41
R-HSA-9020591	Interleukin-12 signaling	2.280527	0.0008507	0.0121835	15/35
R-HSA-447115	Interleukin-12 family signaling	2.261522	0.0004367	0.0070503	17/40
R-HSA-2029482	Regulation of actin dynamics for phagocytic cup formation	2.240518	0.0007273	0.0107638	16/38
R-HSA-1236975	Antigen processing-Cross presentation	2.217179	0.0000050	0.0001075	30/72
R-HSA-5663205	Infectious disease	2.194143	0.0000000	0.0000000	127/308
R-HSA-1266738	Developmental Biology	2.170110	0.0000000	0.0000000	146/358
R-HSA-1236974	ER-Phagosome pathway	2.112841	0.0000419	0.0008570	27/68
R-HSA-114608	Platelet degranulation	2.106320	0.0006024	0.0092225	19/48
R-HSA-5668541	TNFR2 non-canonical NF-kB pathway	2.015617	0.0001970	0.0033010	25/66
R-HSA-2029480	Fcgamma receptor (FCGR) dependent phagocytosis	2.010242	0.0021204	0.0281038	17/45

Factor 9 : 40 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-202430	Translocation of ZAP-70 to Immunological synapse	5.056709	0.0000003	0.0000303	11/14
R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	5.005631	0.0000000	0.0000000	28/36
R-HSA-202427	Phosphorylation of CD3 and TCR zeta chains	4.826858	0.0000002	0.0000290	12/16
R-HSA-389948	PD-1 signaling	4.719595	0.0000009	0.0000781	11/15
R-HSA-6783783	Interleukin-10 signaling	4.505068	0.0001652	0.0035779	7/10
R-HSA-202433	Generation of second messenger molecules	4.290540	0.0000000	0.0000062	16/24
R-HSA-2142753	Arachidonic acid metabolism	4.095516	0.0003936	0.0075976	7/11
R-HSA-373076	Class A/1 (Rhodopsin-like receptors)	3.802979	0.0000035	0.0001594	13/22
R-HSA-375276	Peptide ligand-binding receptors	3.754223	0.0008186	0.0145387	7/12
R-HSA-216083	Integrin cell surface interactions	3.677606	0.0004080	0.0077080	8/14
R-HSA-912526	Interleukin receptor SHC signaling	3.510442	0.0031492	0.0473975	6/11
R-HSA-451927	Interleukin-2 family signaling	3.371139	0.0000924	0.0023439	11/21
R-HSA-2219530	Constitutive Signaling by Aberrant PI3K in Cancer	3.217905	0.0026676	0.0408420	7/14
R-HSA-877300	Interferon gamma signaling	3.077996	0.0000002	0.0000290	22/46
R-HSA-983695	Antigen activates B Cell Receptor (BCR) leading to generation of second messengers	3.064672	0.0005269	0.0097480	10/21
R-HSA-500792	GPCR ligand binding	3.016786	0.0000267	0.0009893	15/32
R-HSA-202733	Cell surface interactions at the vascular wall	2.982449	0.0000028	0.0001531	19/41
R-HSA-212300	PRC2 methylates histones and DNA	2.896115	0.0016652	0.0273826	9/20
R-HSA-445355	Smooth Muscle Contraction	2.860360	0.0033348	0.0485454	8/18
R-HSA-1500931	Cell-Cell communication	2.698888	0.0003698	0.0074634	13/31
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	2.681588	0.0001432	0.0031787	15/36
R-HSA-388841	Costimulation by the CD28 family	2.668507	0.0000557	0.0015444	17/41
R-HSA-1474244	Extracellular matrix organization	2.609113	0.0002069	0.0043740	15/37
R-HSA-72695	Formation of the ternary complex, and subsequently, the 43S complex	2.547508	0.0000443	0.0013565	19/48
R-HSA-72649	Translation initiation complex formation	2.457310	0.0000336	0.0011922	21/55
R-HSA-373760	L1CAM interactions	2.451738	0.0003004	0.0062030	16/42
R-HSA-156842	Eukaryotic Translation Elongation	2.441170	0.0000002	0.0000290	33/87
R-HSA-72662	Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	2.413429	0.0000460	0.0013625	21/56
R-HSA-909733	Interferon alpha/beta signaling	2.413429	0.0020013	0.0317344	12/32
R-HSA-156902	Peptide chain elongation	2.347178	0.0000015	0.0000925	31/85
R-HSA-192823	Viral mRNA Translation	2.347178	0.0000015	0.0000925	31/85
R-HSA-2408557	Selenocysteine synthesis	2.347178	0.0000015	0.0000925	31/85
R-HSA-72702	Ribosomal scanning and start codon recognition	2.340295	0.0001154	0.0028466	20/55
R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	2.288288	0.0000019	0.0001115	32/90
R-HSA-72764	Eukaryotic Translation Termination	2.267161	0.0000034	0.0001594	31/88
R-HSA-447115	Interleukin-12 family signaling	2.252534	0.0018710	0.0302090	14/40
R-HSA-76005	Response to elevated platelet cytosolic Ca2+	2.104015	0.0015059	0.0252310	17/52
R-HSA-72689	Formation of a pool of free 40S subunits	2.078231	0.0000260	0.0009893	31/96
R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	2.064317	0.0000124	0.0005249	34/106
R-HSA-2408522	Selenoamino acid metabolism	2.015254	0.0000510	0.0014610	31/99

Factor 10 : 2 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-8864260	Transcriptional regulation by the AP-2 (TFAP2) family of transcription factors	2.004304	0.0041693	0.0402428	11/15
R-HSA-5627123	RHO GTPases activate PAKs	2.004304	0.0041693	0.0402428	11/15

Factor 11 : 33 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-445355	Smooth Muscle Contraction	3.605028	0.0000005	0.0000695	14/18
R-HSA-6783783	Interleukin-10 signaling	3.244525	0.0013758	0.0219961	7/10
R-HSA-5627123	RHO GTPases activate PAKs	3.090024	0.0002144	0.0050099	10/15
R-HSA-389948	PD-1 signaling	3.090024	0.0002144	0.0050099	10/15
R-HSA-202430	Translocation of ZAP-70 to Immunological synapse	2.979666	0.0006762	0.0133430	9/14
R-HSA-912526	Interleukin receptor SHC signaling	2.949569	0.0030817	0.0437308	7/11
R-HSA-202427	Phosphorylation of CD3 and TCR zeta chains	2.896898	0.0004617	0.0102498	10/16
R-HSA-622312	Inflammasomes	2.852330	0.0020605	0.0310128	8/13
R-HSA-2871809	FCERI mediated Ca+2 mobilization	2.726492	0.0009060	0.0167613	10/17
R-HSA-202433	Generation of second messenger molecules	2.703771	0.0000939	0.0030735	14/24
R-HSA-5626467	RHO GTPases activate IQGAPs	2.607208	0.0025352	0.0375203	9/16
R-HSA-5663213	RHO GTPases Activate WASPs and WAVEs	2.595620	0.0001714	0.0043489	14/25
R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	2.575020	0.0000080	0.0005090	20/36
R-HSA-3928662	EPHB-mediated forward signaling	2.549270	0.0010730	0.0186814	11/20
R-HSA-191273	Cholesterol biosynthesis	2.549270	0.0010730	0.0186814	11/20
R-HSA-983695	Antigen activates B Cell Receptor (BCR) leading to generation of second messengers	2.427876	0.0018192	0.0278521	11/21
R-HSA-114608	Platelet degranulation	2.414081	0.0000029	0.0002554	25/48
R-HSA-76005	Response to elevated platelet cytosolic Ca2+	2.406654	0.0000012	0.0001224	27/52
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	2.317518	0.0001450	0.0039011	18/36
R-HSA-397014	Muscle contraction	2.260993	0.0000969	0.0030735	20/41
R-HSA-388841	Costimulation by the CD28 family	2.147944	0.0003372	0.0076774	19/41
R-HSA-76002	Platelet activation, signaling and aggregation	2.139248	0.0000000	0.0000055	48/104
R-HSA-156842	Eukaryotic Translation Elongation	2.131051	0.0000003	0.0000450	40/87
R-HSA-1474244	Extracellular matrix organization	2.129611	0.0007807	0.0150715	17/37
R-HSA-156902	Peptide chain elongation	2.126664	0.0000004	0.0000569	39/85
R-HSA-1655829	Regulation of cholesterol biosynthesis by SREBP (SREBF)	2.093242	0.0027598	0.0401758	14/31
R-HSA-2029482	Regulation of actin dynamics for phagocytic cup formation	2.073569	0.0011338	0.0189971	17/38
R-HSA-202733	Cell surface interactions at the vascular wall	2.034894	0.0010694	0.0186814	18/41
R-HSA-8957322	Metabolism of steroids	2.032911	0.0001222	0.0033914	25/57
R-HSA-192823	Viral mRNA Translation	2.017604	0.0000037	0.0002741	37/85
R-HSA-2408557	Selenocysteine synthesis	2.017604	0.0000037	0.0002741	37/85
R-HSA-877300	Interferon gamma signaling	2.015233	0.0006650	0.0133430	20/46
R-HSA-418594	G alpha (i) signalling events	2.008516	0.0001146	0.0032833	26/60

Factor 12 : 36 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-176974	Unwinding of DNA	3.759868	0.0000197	0.0009126	9/10
R-HSA-73728	RNA Polymerase I Promoter Opening	3.481360	0.0000242	0.0009126	10/12
R-HSA-5625886	Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3	3.418062	0.0000852	0.0027712	9/11
R-HSA-2514853	Condensation of Prometaphase Chromosomes	3.342105	0.0002949	0.0068922	8/10
R-HSA-202430	Translocation of ZAP-70 to Immunological synapse	3.282425	0.0000247	0.0009126	11/14
R-HSA-2299718	Condensation of Prophase Chromosomes	3.182957	0.0000006	0.0000601	16/21
R-HSA-5626467	RHO GTPases activate IQGAPs	3.133224	0.0000228	0.0009126	12/16
R-HSA-157858	Gap junction trafficking and regulation	3.133224	0.0002682	0.0064366	9/12
R-HSA-190828	Gap junction trafficking	3.133224	0.0002682	0.0064366	9/12
R-HSA-5334118	DNA methylation	3.133224	0.0002682	0.0064366	9/12
R-HSA-156711	Polo-like kinase mediated events	2.924342	0.0026438	0.0454320	7/10
R-HSA-983189	Kinesins	2.906179	0.0000045	0.0002636	16/23
R-HSA-389948	PD-1 signaling	2.785088	0.0005329	0.0112662	10/15
R-HSA-171306	Packaging Of Telomere Ends	2.785088	0.0020266	0.0359923	8/12
R-HSA-427359	SIRT1 negatively regulates rRNA expression	2.785088	0.0020266	0.0359923	8/12
R-HSA-212300	PRC2 methylates histones and DNA	2.715460	0.0001090	0.0033378	13/20
R-HSA-68962	Activation of the pre-replicative complex	2.673684	0.0000225	0.0009126	16/25
R-HSA-606279	Deposition of new CENPA-containing nucleosomes at the centromere	2.658493	0.0000013	0.0000885	21/33
R-HSA-774815	Nucleosome assembly	2.658493	0.0000013	0.0000885	21/33
R-HSA-202427	Phosphorylation of CD3 and TCR zeta chains	2.611020	0.0011178	0.0215777	10/16
R-HSA-912446	Meiotic recombination	2.570850	0.0000457	0.0015593	16/26
R-HSA-176187	Activation of ATR in response to replication stress	2.475633	0.0000874	0.0027712	16/27
R-HSA-201722	Formation of the beta-catenin:TCF transactivating complex	2.410172	0.0002217	0.0059647	15/26
R-HSA-3214858	RMTs methylate histone arginines	2.290959	0.0001966	0.0054567	17/31
R-HSA-202433	Generation of second messenger molecules	2.262884	0.0013178	0.0248979	13/24
R-HSA-1221632	Meiotic synapsis	2.249494	0.0009290	0.0183317	14/26
R-HSA-69190	DNA strand elongation	2.249494	0.0009290	0.0183317	14/26
R-HSA-5250924	B-WICH complex positively regulates rRNA expression	2.228070	0.0004629	0.0102758	16/30
R-HSA-2500257	Resolution of Sister Chromatid Cohesion	2.201118	0.0000000	0.0000004	49/93
R-HSA-2559586	DNA Damage/Telomere Stress Induced Senescence	2.152113	0.0005262	0.0112662	17/33
R-HSA-1500620	Meiosis	2.088816	0.0001437	0.0041174	22/44
R-HSA-5663220	RHO GTPases Activate Formins	2.088816	0.0000000	0.0000045	47/94
R-HSA-141424	Amplification of signal from the kinetochores	2.060965	0.0000012	0.0000885	37/75
R-HSA-141444	Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal	2.060965	0.0000012	0.0000885	37/75
R-HSA-3371497	HSP90 chaperone cycle for steroid hormone receptors (SHR)	2.025518	0.0017694	0.0327333	16/33
R-HSA-73886	Chromosome Maintenance	2.019189	0.0000293	0.0010394	29/60

Factor 13 : 33 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	4.464844	0.0000000	0.0000000	27/36
R-HSA-216083	Integrin cell surface interactions	4.252232	0.0000088	0.0006017	10/14
R-HSA-445355	Smooth Muscle Contraction	3.968750	0.0000032	0.0003160	12/18
R-HSA-446353	Cell-extracellular matrix interactions	3.788352	0.0006473	0.0180193	7/11
R-HSA-912526	Interleukin receptor SHC signaling	3.788352	0.0006473	0.0180193	7/11
R-HSA-1236382	Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants	3.663461	0.0003549	0.0121197	8/13
R-HSA-1643713	Signaling by EGFR in Cancer	3.663461	0.0003549	0.0121197	8/13
R-HSA-5637815	Signaling by Ligand-Responsive EGFR Variants in Cancer	3.663461	0.0003549	0.0121197	8/13
R-HSA-2172127	DAP12 interactions	3.571875	0.0001934	0.0074665	9/15
R-HSA-2424491	DAP12 signaling	3.571875	0.0001934	0.0074665	9/15
R-HSA-909733	Interferon alpha/beta signaling	3.534668	0.0000001	0.0000131	19/32
R-HSA-73728	RNA Polymerase I Promoter Opening	3.472656	0.0013295	0.0310692	7/12
R-HSA-5218921	VEGFR2 mediated cell proliferation	3.472656	0.0013295	0.0310692	7/12
R-HSA-451927	Interleukin-2 family signaling	3.401786	0.0000308	0.0016103	12/21
R-HSA-202430	Translocation of ZAP-70 to Immunological synapse	3.401786	0.0007069	0.0190225	8/14
R-HSA-977225	Amyloid fiber formation	3.333750	0.0000090	0.0006017	14/25
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	3.307292	0.0000001	0.0000216	20/36
R-HSA-5627123	RHO GTPases activate PAKs	3.175000	0.0012938	0.0310692	8/15
R-HSA-389948	PD-1 signaling	3.175000	0.0012938	0.0310692	8/15
R-HSA-202733	Cell surface interactions at the vascular wall	3.049162	0.0000004	0.0000550	21/41
R-HSA-983170	Antigen Presentation: Folding, assembly and peptide loading of class I MHC	2.976562	0.0006149	0.0180193	10/20
R-HSA-212300	PRC2 methylates histones and DNA	2.976562	0.0006149	0.0180193	10/20
R-HSA-202427	Phosphorylation of CD3 and TCR zeta chains	2.976562	0.0022110	0.0478864	8/16
R-HSA-397014	Muscle contraction	2.758765	0.0000091	0.0006017	19/41
R-HSA-202433	Generation of second messenger molecules	2.728516	0.0008343	0.0217906	11/24
R-HSA-877300	Interferon gamma signaling	2.717731	0.0000041	0.0003665	21/46
R-HSA-1474244	Extracellular matrix organization	2.574324	0.0001317	0.0055693	16/37
R-HSA-201722	Formation of the beta-catenin:TCF transactivating complex	2.518630	0.0018690	0.0414926	11/26
R-HSA-114608	Platelet degranulation	2.480469	0.0000370	0.0018240	20/48
R-HSA-5625740	RHO GTPases activate PKNs	2.463362	0.0014729	0.0335377	12/29
R-HSA-76005	Response to elevated platelet cytosolic Ca2+	2.404147	0.0000416	0.0019420	21/52
R-HSA-76002	Platelet activation, signaling and aggregation	2.175180	0.0000007	0.0000897	38/104
R-HSA-372790	Signaling by GPCR	2.000640	0.0000032	0.0003160	41/122

Factor 14 : 57 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-191273	Cholesterol biosynthesis	5.255172	0.0000000	0.0000000	16/20
R-HSA-5625886	Activated PKN1 stimulates transcription of AR (androgen receptor) regulated genes KLK2 and KLK3	4.777430	0.0000297	0.0009693	8/11
R-HSA-2514853	Condensation of Prometaphase Chromosomes	4.598276	0.0001444	0.0034655	7/10
R-HSA-2299718	Condensation of Prophase Chromosomes	4.379310	0.0000001	0.0000063	14/21
R-HSA-427359	SIRT1 negatively regulates rRNA expression	4.379310	0.0000773	0.0019607	8/12
R-HSA-5334118	DNA methylation	4.379310	0.0000773	0.0019607	8/12
R-HSA-73728	RNA Polymerase I Promoter Opening	4.379310	0.0000773	0.0019607	8/12
R-HSA-389977	Post-chaperonin tubulin folding pathway	3.941379	0.0014730	0.0198190	6/10
R-HSA-156711	Polo-like kinase mediated events	3.941379	0.0014730	0.0198190	6/10
R-HSA-171306	Packaging Of Telomere Ends	3.831897	0.0007200	0.0133204	7/12
R-HSA-983189	Kinesins	3.712894	0.0000054	0.0002096	13/23
R-HSA-912446	Meiotic recombination	3.284483	0.0000317	0.0009693	13/26
R-HSA-1221632	Meiotic synapsis	3.284483	0.0000317	0.0009693	13/26
R-HSA-606279	Deposition of new CENPA-containing nucleosomes at the centromere	3.184953	0.0000063	0.0002246	16/33
R-HSA-774815	Nucleosome assembly	3.184953	0.0000063	0.0002246	16/33
R-HSA-2500257	Resolution of Sister Chromatid Cohesion	3.037264	0.0000000	0.0000000	43/93
R-HSA-2426168	Activation of gene expression by SREBF (SREBP)	3.010776	0.0003476	0.0071782	11/24
R-HSA-8957322	Metabolism of steroids	2.996370	0.0000000	0.0000020	26/57
R-HSA-1500620	Meiosis	2.985893	0.0000016	0.0000670	20/44
R-HSA-2559586	DNA Damage/Telomere Stress Induced Senescence	2.985893	0.0000328	0.0009708	15/33
R-HSA-141424	Amplification of signal from the kinetochores	2.977931	0.0000000	0.0000000	34/75
R-HSA-141444	Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal	2.977931	0.0000000	0.0000000	34/75
R-HSA-212300	PRC2 methylates histones and DNA	2.956034	0.0014331	0.0198190	9/20
R-HSA-69273	Cyclin A/B1/B2 associated events during G2/M transition	2.919540	0.0029193	0.0355112	8/18
R-HSA-5663220	RHO GTPases Activate Formins	2.865187	0.0000000	0.0000000	41/94
R-HSA-1474165	Reproduction	2.856072	0.0000037	0.0001493	20/46
R-HSA-179409	APC-Cdc20 mediated degradation of Nek2A	2.856072	0.0010800	0.0174372	10/23
R-HSA-201722	Formation of the beta-catenin:TCF transactivating complex	2.779178	0.0008043	0.0140046	11/26
R-HSA-1655829	Regulation of cholesterol biosynthesis by SREBP (SREBF)	2.754727	0.0003002	0.0066640	13/31
R-HSA-69618	Mitotic Spindle Checkpoint	2.730918	0.0000000	0.0000001	37/89
R-HSA-5625740	RHO GTPases activate PKNs	2.718193	0.0005942	0.0112259	12/29
R-HSA-977225	Amyloid fiber formation	2.627586	0.0023142	0.0302825	10/25
R-HSA-68877	Mitotic Prometaphase	2.591837	0.0000000	0.0000000	58/147
R-HSA-1912408	Pre-NOTCH Transcription and Translation	2.526525	0.0032579	0.0385731	10/26
R-HSA-195258	RHO GTPase Effectors	2.493041	0.0000000	0.0000000	63/166
R-HSA-2565942	Regulation of PLK1 Activity at G2/M Transition	2.425464	0.0000126	0.0004290	24/65
R-HSA-8854518	AURKA Activation by TPX2	2.388715	0.0000859	0.0021191	20/55
R-HSA-2559582	Senescence-Associated Secretory Phenotype (SASP)	2.376009	0.0003134	0.0067871	17/47
R-HSA-8950505	Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation	2.330923	0.0042751	0.0486698	11/31
R-HSA-194315	Signaling by Rho GTPases	2.284858	0.0000000	0.0000000	72/207
R-HSA-9020591	Interleukin-12 signaling	2.252217	0.0039865	0.0465792	12/35
R-HSA-5620912	Anchoring of the basal body to the plasma membrane	2.226768	0.0002607	0.0059358	20/59
R-HSA-380320	Recruitment of NuMA to mitotic centrosomes	2.224972	0.0001860	0.0043459	21/62
R-HSA-2467813	Separation of Sister Chromatids	2.218657	0.0000000	0.0000003	51/151
R-HSA-2555396	Mitotic Metaphase and Anaphase	2.217026	0.0000000	0.0000001	54/160
R-HSA-68882	Mitotic Anaphase	2.189655	0.0000000	0.0000003	53/159
R-HSA-174143	APC/C-mediated degradation of cell cycle proteins	2.189655	0.0000444	0.0012329	26/78
R-HSA-453276	Regulation of mitotic cell cycle	2.189655	0.0000444	0.0012329	26/78
R-HSA-73886	Chromosome Maintenance	2.189655	0.0003366	0.0071159	20/60
R-HSA-380259	Loss of Nlp from mitotic centrosomes	2.147546	0.0011919	0.0182232	17/52
R-HSA-380284	Loss of proteins required for interphase microtubule organization from the centrosome	2.147546	0.0011919	0.0182232	17/52
R-HSA-380270	Recruitment of mitotic centrosome proteins and complexes	2.046071	0.0012108	0.0182232	19/61
R-HSA-380287	Centrosome maturation	2.046071	0.0012108	0.0182232	19/61
R-HSA-69275	G2/M Transition	2.035454	0.0000010	0.0000483	44/142
R-HSA-68886	M Phase	2.025019	0.0000000	0.0000000	82/266
R-HSA-453274	Mitotic G2-G2/M phases	2.007184	0.0000016	0.0000670	44/144
R-HSA-69620	Cell Cycle Checkpoints	2.001970	0.0000000	0.0000003	64/210

Factor 15 : 32 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-389960	Formation of tubulin folding intermediates by CCT/TriC	3.278265	0.0000684	0.0015566	10/13
R-HSA-156902	Peptide chain elongation	3.058429	0.0000000	0.0000000	61/85
R-HSA-192823	Viral mRNA Translation	3.058429	0.0000000	0.0000000	61/85
R-HSA-156842	Eukaryotic Translation Elongation	3.037106	0.0000000	0.0000000	62/87
R-HSA-163210	Formation of ATP by chemiosmotic coupling	3.008291	0.0000489	0.0011436	12/17
R-HSA-389958	Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding	2.983221	0.0000128	0.0003153	14/20
R-HSA-2408557	Selenocysteine synthesis	2.958152	0.0000000	0.0000000	59/85
R-HSA-72764	Eukaryotic Translation Termination	2.954164	0.0000000	0.0000000	61/88
R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	2.935869	0.0000000	0.0000000	62/90
R-HSA-72689	Formation of a pool of free 40S subunits	2.929950	0.0000000	0.0000000	66/96
R-HSA-389957	Prefoldin mediated transfer of substrate to CCT/TriC	2.915931	0.0000389	0.0009328	13/19
R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	2.814360	0.0000000	0.0000000	70/106
R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane	2.788057	0.0000000	0.0000000	70/107
R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	2.748228	0.0000000	0.0000000	69/107
R-HSA-2408522	Selenoamino acid metabolism	2.668972	0.0000000	0.0000000	62/99
R-HSA-72613	Eukaryotic Translation Initiation	2.616861	0.0000000	0.0000000	70/114
R-HSA-72737	Cap-dependent Translation Initiation	2.616861	0.0000000	0.0000000	70/114
R-HSA-927802	Nonsense-Mediated Decay (NMD)	2.604400	0.0000000	0.0000000	66/108
R-HSA-975957	Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)	2.604400	0.0000000	0.0000000	66/108
R-HSA-72695	Formation of the ternary complex, and subsequently, the 43S complex	2.574804	0.0000000	0.0000012	29/48
R-HSA-72649	Translation initiation complex formation	2.479561	0.0000000	0.0000009	32/55
R-HSA-8949613	Cristae formation	2.458699	0.0001744	0.0038724	15/26
R-HSA-168273	Influenza Viral RNA Transcription and Replication	2.445263	0.0000000	0.0000000	70/122
R-HSA-72662	Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	2.435283	0.0000001	0.0000014	32/56
R-HSA-72702	Ribosomal scanning and start codon recognition	2.402074	0.0000001	0.0000034	31/55
R-HSA-168255	Influenza Life Cycle	2.374865	0.0000000	0.0000000	73/131
R-HSA-168254	Influenza Infection	2.283078	0.0000000	0.0000000	75/140
R-HSA-9010553	Regulation of expression of SLITs and ROBOs	2.274850	0.0000000	0.0000000	79/148
R-HSA-376176	Signaling by ROBO receptors	2.130873	0.0000000	0.0000000	84/168
R-HSA-909733	Interferon alpha/beta signaling	2.130873	0.0009251	0.0195598	16/32
R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	2.073281	0.0000000	0.0000001	54/111
R-HSA-8950505	Gene and protein expression by JAK-STAT signaling after Interleukin-12 stimulation	2.062135	0.0020340	0.0410491	15/31

Factor 16 : 53 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-389957	Prefoldin mediated transfer of substrate to CCT/TriC	4.148820	0.0000000	0.0000010	15/19
R-HSA-389958	Cooperation of Prefoldin and TriC/CCT in actin and tubulin folding	3.941379	0.0000001	0.0000029	15/20
R-HSA-389960	Formation of tubulin folding intermediates by CCT/TriC	3.638196	0.0001071	0.0022643	9/13
R-HSA-6814122	Cooperation of PDCL (PhLP1) and TRiC/CCT in G-protein beta folding	3.319056	0.0000280	0.0006534	12/19
R-HSA-8876725	Protein methylation	3.233952	0.0008608	0.0136496	8/13
R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	2.919540	0.0000010	0.0000301	20/36
R-HSA-983170	Antigen Presentation: Folding, assembly and peptide loading of class I MHC	2.890345	0.0003445	0.0065369	11/20
R-HSA-3299685	Detoxification of Reactive Oxygen Species	2.741829	0.0003533	0.0065369	12/23
R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane	2.701257	0.0000000	0.0000000	55/107
R-HSA-156902	Peptide chain elongation	2.658499	0.0000000	0.0000000	43/85
R-HSA-156842	Eukaryotic Translation Elongation	2.657788	0.0000000	0.0000000	44/87
R-HSA-5339562	Uptake and actions of bacterial toxins	2.627586	0.0050094	0.0383474	8/16
R-HSA-5626467	RHO GTPases activate IQGAPs	2.627586	0.0050094	0.0383474	8/16
R-HSA-192823	Viral mRNA Translation	2.596673	0.0000000	0.0000000	42/85
R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	2.569195	0.0000000	0.0000000	44/90
R-HSA-72764	Eukaryotic Translation Termination	2.567868	0.0000000	0.0000000	43/88
R-HSA-1236975	Antigen processing-Cross presentation	2.554598	0.0000000	0.0000004	35/72
R-HSA-2408557	Selenocysteine synthesis	2.534848	0.0000000	0.0000001	41/85
R-HSA-1236974	ER-Phagosome pathway	2.473022	0.0000001	0.0000036	32/68
R-HSA-72689	Formation of a pool of free 40S subunits	2.463362	0.0000000	0.0000000	45/96
R-HSA-2408522	Selenoamino acid metabolism	2.388715	0.0000000	0.0000001	45/99
R-HSA-191273	Cholesterol biosynthesis	2.364828	0.0069954	0.0463931	9/20
R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	2.330124	0.0000000	0.0000001	47/106
R-HSA-114608	Platelet degranulation	2.299138	0.0000681	0.0015501	21/48
R-HSA-2173789	TGF-beta receptor signaling activates SMADs	2.284858	0.0060708	0.0445525	10/23
R-HSA-9010553	Regulation of expression of SLITs and ROBOs	2.272507	0.0000000	0.0000000	64/148
R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	2.259233	0.0000000	0.0000003	46/107
R-HSA-927802	Nonsense-Mediated Decay (NMD)	2.238314	0.0000000	0.0000004	46/108
R-HSA-975957	Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)	2.238314	0.0000000	0.0000004	46/108
R-HSA-76005	Response to elevated platelet cytosolic Ca2+	2.223342	0.0000850	0.0018870	22/52
R-HSA-72613	Eukaryotic Translation Initiation	2.212704	0.0000000	0.0000003	48/114
R-HSA-72737	Cap-dependent Translation Initiation	2.212704	0.0000000	0.0000003	48/114
R-HSA-390466	Chaperonin-mediated protein folding	2.189655	0.0002288	0.0046174	20/48
R-HSA-391251	Protein folding	2.181392	0.0001198	0.0024730	22/53
R-HSA-163200	Respiratory electron transport, ATP synthesis by chemiosmotic coupling, and heat production by uncoupling proteins.	2.130475	0.0000001	0.0000029	45/111
R-HSA-1474244	Extracellular matrix organization	2.130475	0.0019252	0.0216385	15/37
R-HSA-8854050	FBXL7 down-regulates AURKA during mitotic entry and in early mitosis	2.102069	0.0004384	0.0077857	20/50
R-HSA-611105	Respiratory electron transport	2.090768	0.0000021	0.0000577	37/93
R-HSA-5658442	Regulation of RAS by GAPs	2.082238	0.0003694	0.0066951	21/53
R-HSA-376176	Signaling by ROBO receptors	2.064532	0.0000000	0.0000000	66/168
R-HSA-168255	Influenza Life Cycle	2.045907	0.0000001	0.0000021	51/131
R-HSA-4641258	Degradation of DVL	2.037720	0.0009556	0.0146308	19/49
R-HSA-168273	Influenza Viral RNA Transcription and Replication	2.024534	0.0000003	0.0000084	47/122
R-HSA-450408	AUF1 (hnRNP D0) binds and destabilizes mRNA	2.021220	0.0007979	0.0128817	20/52
R-HSA-5358346	Hedgehog ligand biogenesis	2.021220	0.0007979	0.0128817	20/52
R-HSA-5610783	Degradation of GLI2 by the proteasome	2.021220	0.0007979	0.0128817	20/52
R-HSA-5610785	GLI3 is processed to GLI3R by the proteasome	2.021220	0.0007979	0.0128817	20/52
R-HSA-9604323	Negative regulation of NOTCH4 signaling	2.021220	0.0007979	0.0128817	20/52
R-HSA-5619115	Disorders of transmembrane transporters	2.014483	0.0003482	0.0065369	23/60
R-HSA-8852276	The role of GTSE1 in G2/M progression after G2 checkpoint	2.014483	0.0003482	0.0065369	23/60
R-HSA-180534	Vpu mediated degradation of CD4	2.012619	0.0015298	0.0209000	18/47
R-HSA-211733	Regulation of activated PAK-2p34 by proteasome mediated degradation	2.012619	0.0015298	0.0209000	18/47
R-HSA-1236978	Cross-presentation of soluble exogenous antigens (endosomes)	2.001970	0.0029422	0.0266596	16/42

Factor 17 : 36 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-202427	Phosphorylation of CD3 and TCR zeta chains	6.559917	0.0000003	0.0000384	10/16
R-HSA-389948	PD-1 signaling	6.297521	0.0000018	0.0001296	9/15
R-HSA-6783783	Interleukin-10 signaling	6.297521	0.0001083	0.0048067	6/10
R-HSA-202430	Translocation of ZAP-70 to Immunological synapse	5.997639	0.0000113	0.0007177	8/14
R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	5.831038	0.0000000	0.0000000	20/36
R-HSA-373076	Class A/1 (Rhodopsin-like receptors)	5.247934	0.0000014	0.0001099	11/22
R-HSA-216083	Integrin cell surface interactions	5.247934	0.0001279	0.0054066	7/14
R-HSA-375276	Peptide ligand-binding receptors	5.247934	0.0004033	0.0127908	6/12
R-HSA-500792	GPCR ligand binding	4.591942	0.0000004	0.0000401	14/32
R-HSA-2172127	DAP12 interactions	4.198347	0.0017040	0.0423655	6/15
R-HSA-2424491	DAP12 signaling	4.198347	0.0017040	0.0423655	6/15
R-HSA-3299685	Detoxification of Reactive Oxygen Species	4.107079	0.0001427	0.0057579	9/23
R-HSA-983695	Antigen activates B Cell Receptor (BCR) leading to generation of second messengers	3.998426	0.0004204	0.0128720	8/21
R-HSA-202433	Generation of second messenger molecules	3.935950	0.0002093	0.0080815	9/24
R-HSA-877300	Interferon gamma signaling	3.878908	0.0000004	0.0000401	17/46
R-HSA-191273	Cholesterol biosynthesis	3.673554	0.0017409	0.0423655	7/20
R-HSA-416476	G alpha (q) signalling events	3.417259	0.0000236	0.0014000	14/43
R-HSA-388841	Costimulation by the CD28 family	3.327958	0.0000636	0.0029736	13/41
R-HSA-202733	Cell surface interactions at the vascular wall	3.327958	0.0000636	0.0029736	13/41
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	3.207071	0.0003384	0.0120111	11/36
R-HSA-1500931	Cell-Cell communication	3.047187	0.0017652	0.0423655	9/31
R-HSA-114608	Platelet degranulation	2.842631	0.0003749	0.0123308	13/48
R-HSA-76005	Response to elevated platelet cytosolic Ca2+	2.825811	0.0002398	0.0088723	14/52
R-HSA-76002	Platelet activation, signaling and aggregation	2.724889	0.0000007	0.0000627	27/104
R-HSA-372790	Signaling by GPCR	2.666983	0.0000002	0.0000307	31/122
R-HSA-388396	GPCR downstream signalling	2.623967	0.0000004	0.0000401	30/120
R-HSA-418594	G alpha (i) signalling events	2.623967	0.0003517	0.0120111	15/60
R-HSA-109582	Hemostasis	2.354213	0.0000000	0.0000023	48/214
R-HSA-156842	Eukaryotic Translation Elongation	2.171559	0.0011070	0.0307183	18/87
R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	2.099174	0.0016682	0.0423655	18/90
R-HSA-156902	Peptide chain elongation	2.099174	0.0022293	0.0494909	17/85
R-HSA-192823	Viral mRNA Translation	2.099174	0.0022293	0.0494909	17/85
R-HSA-2408557	Selenocysteine synthesis	2.099174	0.0022293	0.0494909	17/85
R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane	2.059937	0.0009077	0.0268681	21/107
R-HSA-913531	Interferon Signaling	2.040863	0.0010301	0.0295071	21/108
R-HSA-1280215	Cytokine Signaling in Immune system	2.039949	0.0000000	0.0000030	62/319

Factor 18 : 47 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-156842	Eukaryotic Translation Elongation	10.124868	0.0000000	0.0000000	83/87
R-HSA-156902	Peptide chain elongation	10.113387	0.0000000	0.0000000	81/85
R-HSA-192823	Viral mRNA Translation	9.863674	0.0000000	0.0000000	79/85
R-HSA-2408557	Selenocysteine synthesis	9.863674	0.0000000	0.0000000	79/85
R-HSA-72764	Eukaryotic Translation Termination	9.527412	0.0000000	0.0000000	79/88
R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	9.433612	0.0000000	0.0000000	80/90
R-HSA-72689	Formation of a pool of free 40S subunits	9.396762	0.0000000	0.0000000	85/96
R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	8.710517	0.0000000	0.0000000	87/106
R-HSA-2408522	Selenoamino acid metabolism	8.683211	0.0000000	0.0000000	81/99
R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	8.529925	0.0000000	0.0000000	86/107
R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane	8.331554	0.0000000	0.0000000	84/107
R-HSA-72695	Formation of the ternary complex, and subsequently, the 43S complex	8.180710	0.0000000	0.0000000	37/48
R-HSA-72613	Eukaryotic Translation Initiation	8.099252	0.0000000	0.0000000	87/114
R-HSA-72737	Cap-dependent Translation Initiation	8.099252	0.0000000	0.0000000	87/114
R-HSA-927802	Nonsense-Mediated Decay (NMD)	7.861343	0.0000000	0.0000000	80/108
R-HSA-975957	Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)	7.861343	0.0000000	0.0000000	80/108
R-HSA-72649	Translation initiation complex formation	7.525449	0.0000000	0.0000000	39/55
R-HSA-72662	Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	7.391066	0.0000000	0.0000000	39/56
R-HSA-72702	Ribosomal scanning and start codon recognition	7.332489	0.0000000	0.0000000	38/55
R-HSA-168273	Influenza Viral RNA Transcription and Replication	7.046212	0.0000000	0.0000000	81/122
R-HSA-168255	Influenza Life Cycle	6.562121	0.0000000	0.0000000	81/131
R-HSA-168254	Influenza Infection	6.216076	0.0000000	0.0000000	82/140
R-HSA-9010553	Regulation of expression of SLITs and ROBOs	5.951780	0.0000000	0.0000000	83/148
R-HSA-376176	Signaling by ROBO receptors	5.369578	0.0000000	0.0000000	85/168
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol	5.339780	0.0000000	0.0000000	80/159
R-HSA-70263	Gluconeogenesis	5.306407	0.0000120	0.0003121	9/18
R-HSA-2979096	NOTCH2 Activation and Transmission of Signal to the Nucleus	5.306407	0.0012213	0.0258212	5/10
R-HSA-8868773	rRNA processing in the nucleus and cytosol	5.023817	0.0000000	0.0000000	80/169
R-HSA-1236382	Constitutive Signaling by Ligand-Responsive EGFR Cancer Variants	4.898222	0.0006491	0.0147798	6/13
R-HSA-1643713	Signaling by EGFR in Cancer	4.898222	0.0006491	0.0147798	6/13
R-HSA-5637815	Signaling by Ligand-Responsive EGFR Variants in Cancer	4.898222	0.0006491	0.0147798	6/13
R-HSA-72312	rRNA processing	4.824006	0.0000000	0.0000000	80/176
R-HSA-2122948	Activated NOTCH1 Transmits Signal to the Nucleus	4.824006	0.0020674	0.0407963	5/11
R-HSA-9013507	NOTCH3 Activation and Transmission of Signal to the Nucleus	4.824006	0.0020674	0.0407963	5/11
R-HSA-1980145	Signaling by NOTCH2	4.548349	0.0010466	0.0226688	6/14
R-HSA-6804760	Regulation of TP53 Activity through Methylation	4.548349	0.0010466	0.0226688	6/14
R-HSA-71291	Metabolism of amino acids and derivatives	4.314555	0.0000000	0.0000000	87/214
R-HSA-917937	Iron uptake and transport	4.245125	0.0000074	0.0001982	12/30
R-HSA-8982491	Glycogen metabolism	4.245125	0.0016075	0.0331973	6/15
R-HSA-72766	Translation	4.069575	0.0000000	0.0000000	102/266
R-HSA-2672351	Stimuli-sensing channels	3.979805	0.0023706	0.0447891	6/16
R-HSA-422475	Axon guidance	3.918577	0.0000000	0.0000000	96/260
R-HSA-5663205	Infectious disease	3.204518	0.0000000	0.0000000	93/308
R-HSA-70171	Glycolysis	3.032232	0.0003305	0.0081521	12/42
R-HSA-1266738	Developmental Biology	2.994118	0.0000000	0.0000000	101/358
R-HSA-70326	Glucose metabolism	2.497133	0.0021737	0.0419617	12/51
R-HSA-71387	Metabolism of carbohydrates	2.266815	0.0001668	0.0042326	22/103

Factor 19 : 17 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-216083	Integrin cell surface interactions	7.246407	0.0000004	0.0000523	9/14
R-HSA-375276	Peptide ligand-binding receptors	6.575444	0.0000218	0.0021501	7/12
R-HSA-373076	Class A/1 (Rhodopsin-like receptors)	6.148467	0.0000001	0.0000167	12/22
R-HSA-6783783	Interleukin-10 signaling	5.636095	0.0009244	0.0432035	5/10
R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	5.322978	0.0000000	0.0000007	17/36
R-HSA-909733	Interferon alpha/beta signaling	4.931583	0.0000002	0.0000229	14/32
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	4.696746	0.0000001	0.0000215	15/36
R-HSA-500792	GPCR ligand binding	4.579327	0.0000012	0.0001366	13/32
R-HSA-1474244	Extracellular matrix organization	3.655845	0.0000471	0.0029855	12/37
R-HSA-202733	Cell surface interactions at the vascular wall	3.574109	0.0000298	0.0024029	13/41
R-HSA-877300	Interferon gamma signaling	3.430666	0.0000247	0.0021975	14/46
R-HSA-114608	Platelet degranulation	2.818047	0.0007215	0.0376872	12/48
R-HSA-76005	Response to elevated platelet cytosolic Ca2+	2.818047	0.0004353	0.0241607	13/52
R-HSA-449147	Signaling by Interleukins	2.297176	0.0000001	0.0000179	43/211
R-HSA-913531	Interferon Signaling	2.191815	0.0003968	0.0234904	21/108
R-HSA-1280215	Cytokine Signaling in Immune system	2.190833	0.0000000	0.0000005	62/319
R-HSA-372790	Signaling by GPCR	2.032690	0.0008603	0.0424409	22/122

Factor 20 : 56 significant Reactome pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
R-HSA-202430	Translocation of ZAP-70 to Immunological synapse	8.123667	0.0000011	0.0000276	8/14
R-HSA-389948	PD-1 signaling	7.582090	0.0000023	0.0000541	8/15
R-HSA-198933	Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell	7.503109	0.0000000	0.0000000	19/36
R-HSA-202427	Phosphorylation of CD3 and TCR zeta chains	7.108209	0.0000042	0.0000965	8/16
R-HSA-5213460	RIPK1-mediated regulated necrosis	7.108209	0.0000176	0.0003641	7/14
R-HSA-5218859	Regulated Necrosis	7.108209	0.0000176	0.0003641	7/14
R-HSA-5675482	Regulation of necroptotic cell death	7.108209	0.0000176	0.0003641	7/14
R-HSA-983170	Antigen Presentation: Folding, assembly and peptide loading of class I MHC	6.397388	0.0000031	0.0000728	9/20
R-HSA-375276	Peptide ligand-binding receptors	5.923508	0.0008712	0.0151698	5/12
R-HSA-156902	Peptide chain elongation	5.352063	0.0000000	0.0000000	32/85
R-HSA-192823	Viral mRNA Translation	5.352063	0.0000000	0.0000000	32/85
R-HSA-2408557	Selenocysteine synthesis	5.352063	0.0000000	0.0000000	32/85
R-HSA-202433	Generation of second messenger molecules	5.331157	0.0000189	0.0003806	9/24
R-HSA-72764	Eukaryotic Translation Termination	5.331157	0.0000000	0.0000000	33/88
R-HSA-877300	Interferon gamma signaling	5.253894	0.0000000	0.0000002	17/46
R-HSA-156842	Eukaryotic Translation Elongation	5.229027	0.0000000	0.0000000	32/87
R-HSA-1489509	DAG and IP3 signaling	5.077292	0.0019588	0.0305156	5/14
R-HSA-216083	Integrin cell surface interactions	5.077292	0.0019588	0.0305156	5/14
R-HSA-975956	Nonsense Mediated Decay (NMD) independent of the Exon Junction Complex (EJC)	5.054726	0.0000000	0.0000000	32/90
R-HSA-72689	Formation of a pool of free 40S subunits	5.034981	0.0000000	0.0000000	34/96
R-HSA-909733	Interferon alpha/beta signaling	4.886894	0.0000058	0.0001288	11/32
R-HSA-72695	Formation of the ternary complex, and subsequently, the 43S complex	4.738806	0.0000001	0.0000021	16/48
R-HSA-2408522	Selenoamino acid metabolism	4.595206	0.0000000	0.0000000	32/99
R-HSA-156827	L13a-mediated translational silencing of Ceruloplasmin expression	4.559983	0.0000000	0.0000000	34/106
R-HSA-373076	Class A/1 (Rhodopsin-like receptors)	4.523406	0.0005363	0.0097187	7/22
R-HSA-72706	GTP hydrolysis and joining of the 60S ribosomal subunit	4.517366	0.0000000	0.0000000	34/107
R-HSA-1799339	SRP-dependent cotranslational protein targeting to membrane	4.384503	0.0000000	0.0000000	33/107
R-HSA-72613	Eukaryotic Translation Initiation	4.239984	0.0000000	0.0000000	34/114
R-HSA-72737	Cap-dependent Translation Initiation	4.239984	0.0000000	0.0000000	34/114
R-HSA-927802	Nonsense-Mediated Decay (NMD)	4.212272	0.0000000	0.0000000	32/108
R-HSA-975957	Nonsense Mediated Decay (NMD) enhanced by the Exon Junction Complex (EJC)	4.212272	0.0000000	0.0000000	32/108
R-HSA-72649	Translation initiation complex formation	4.135685	0.0000006	0.0000152	16/55
R-HSA-72702	Ribosomal scanning and start codon recognition	4.135685	0.0000006	0.0000152	16/55
R-HSA-72662	Activation of the mRNA upon binding of the cap-binding complex and eIFs, and subsequent binding to 43S	4.061834	0.0000007	0.0000193	16/56
R-HSA-168273	Influenza Viral RNA Transcription and Replication	3.728896	0.0000000	0.0000000	32/122
R-HSA-168255	Influenza Life Cycle	3.581235	0.0000000	0.0000000	33/131
R-HSA-500792	GPCR ligand binding	3.554105	0.0012834	0.0211051	8/32
R-HSA-9010553	Regulation of expression of SLITs and ROBOs	3.458048	0.0000000	0.0000000	36/148
R-HSA-168254	Influenza Infection	3.351013	0.0000000	0.0000000	33/140
R-HSA-76005	Response to elevated platelet cytosolic Ca2+	3.280712	0.0001857	0.0035086	12/52
R-HSA-114608	Platelet degranulation	3.257929	0.0003681	0.0068090	11/48
R-HSA-376176	Signaling by ROBO receptors	3.215618	0.0000000	0.0000000	38/168
R-HSA-913531	Interferon Signaling	3.159204	0.0000002	0.0000067	24/108
R-HSA-6785807	Interleukin-4 and Interleukin-13 signaling	3.159204	0.0028864	0.0427187	8/36
R-HSA-6791226	Major pathway of rRNA processing in the nucleolus and cytosol	2.861166	0.0000000	0.0000008	32/159
R-HSA-418594	G alpha (i) signalling events	2.843284	0.0007574	0.0134513	12/60
R-HSA-8868773	rRNA processing in the nucleus and cytosol	2.775987	0.0000000	0.0000011	33/169
R-HSA-71291	Metabolism of amino acids and derivatives	2.723706	0.0000000	0.0000000	41/214
R-HSA-72312	rRNA processing	2.665578	0.0000001	0.0000028	33/176
R-HSA-1236975	Antigen processing-Cross presentation	2.566853	0.0012678	0.0211051	13/72
R-HSA-1236974	ER-Phagosome pathway	2.508780	0.0023746	0.0363552	12/68
R-HSA-202424	Downstream TCR signaling	2.487873	0.0011440	0.0195364	14/80
R-HSA-422475	Axon guidance	2.460534	0.0000000	0.0000002	45/260
R-HSA-1280215	Cytokine Signaling in Immune system	2.361975	0.0000000	0.0000000	53/319
R-HSA-5663205	Infectious disease	2.261703	0.0000000	0.0000005	49/308
R-HSA-202403	TCR signaling	2.221315	0.0025167	0.0378791	15/96

Summary:
Factor	1	2	3	4	5	6	7	8	9	10
Signif_GO_terms	0	0	0	8	1	21	34	58	40	2
Factor	11	12	13	14	15	16	17	18	19	20
Signif_GO_terms	33	36	33	57	32	53	36	47	17	56

5.3 KEGG Pathway Over-Representation Analysis

Gene sets: The KEGG pathway database.

Factor 4 : 4 significant KEGG pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
hsa04080	Neuroactive ligand-receptor interaction	2.092017	0.0002068	0.0044982	13/14
hsa05332	Graft-versus-host disease	2.027647	0.0000269	0.0023412	18/20
hsa05320	Autoimmune thyroid disease	2.015789	0.0000552	0.0025215	17/19
hsa05330	Allograft rejection	2.015789	0.0000552	0.0025215	17/19

Factor 7 : 15 significant KEGG pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
hsa04640	Hematopoietic cell lineage	2.904417	0.0000000	0.0000000	26/30
hsa04080	Neuroactive ligand-receptor interaction	2.633125	0.0002250	0.0036711	11/14
hsa05150	Staphylococcus aureus infection	2.577885	0.0006031	0.0082843	10/13
hsa05332	Graft-versus-host disease	2.513438	0.0000374	0.0011087	15/20
hsa05320	Autoimmune thyroid disease	2.469342	0.0000958	0.0020845	14/19
hsa05330	Allograft rejection	2.469342	0.0000958	0.0020845	14/19
hsa04940	Type I diabetes mellitus	2.393750	0.0000949	0.0020845	15/21
hsa04060	Cytokine-cytokine receptor interaction	2.345875	0.0000002	0.0000197	28/40
hsa05322	Systemic lupus erythematosus	2.345875	0.0000058	0.0003052	21/30
hsa04672	Intestinal immune network for IgA production	2.303984	0.0014447	0.0157116	11/16
hsa04514	Cell adhesion molecules (CAMs)	2.292960	0.0000009	0.0000752	26/38
hsa05416	Viral myocarditis	2.234167	0.0000304	0.0011087	20/30
hsa04970	Salivary secretion	2.234167	0.0013084	0.0148476	12/18
hsa04612	Antigen processing and presentation	2.182209	0.0000015	0.0000994	28/43
hsa05321	Inflammatory bowel disease (IBD)	2.062308	0.0007524	0.0097953	16/26

Factor 8 : 19 significant KEGG pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
hsa05330	Allograft rejection	4.283128	0.0000000	0.0000000	18/19
hsa04940	Type I diabetes mellitus	4.090500	0.0000000	0.0000000	19/21
hsa05332	Graft-versus-host disease	4.068971	0.0000000	0.0000000	18/20
hsa05320	Autoimmune thyroid disease	4.045176	0.0000000	0.0000000	17/19
hsa04672	Intestinal immune network for IgA production	3.673377	0.0000008	0.0000185	13/16
hsa05150	Staphylococcus aureus infection	3.477753	0.0000389	0.0006777	10/13
hsa04514	Cell adhesion molecules (CAMs)	3.450297	0.0000000	0.0000000	29/38
hsa04640	Hematopoietic cell lineage	3.164756	0.0000000	0.0000007	21/30
hsa05322	Systemic lupus erythematosus	3.164756	0.0000000	0.0000007	21/30
hsa03010	Ribosome	3.097117	0.0000000	0.0000000	87/127
hsa04612	Antigen processing and presentation	3.049100	0.0000000	0.0000000	29/43
hsa05416	Viral myocarditis	2.863350	0.0000012	0.0000250	19/30
hsa05323	Rheumatoid arthritis	2.712648	0.0000012	0.0000250	21/35
hsa05321	Inflammatory bowel disease (IBD)	2.608315	0.0000828	0.0013502	15/26
hsa05140	Leishmaniasis	2.511711	0.0000114	0.0002132	20/36
hsa05340	Primary immunodeficiency	2.466043	0.0008749	0.0108738	12/22
hsa03060	Protein export	2.368184	0.0022272	0.0242208	11/21
hsa04145	Phagosome	2.260540	0.0000002	0.0000049	35/70
hsa04260	Cardiac muscle contraction	2.182590	0.0015841	0.0187933	14/29

Factor 9 : 31 significant KEGG pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
hsa04640	Hematopoietic cell lineage	5.140561	0.0000000	0.0000000	26/30
hsa05332	Graft-versus-host disease	5.041703	0.0000000	0.0000000	17/20
hsa05150	Staphylococcus aureus infection	5.018890	0.0000002	0.0000032	11/13
hsa05330	Allograft rejection	4.994877	0.0000000	0.0000000	16/19
hsa04514	Cell adhesion molecules (CAMs)	4.682697	0.0000000	0.0000000	30/38
hsa05320	Autoimmune thyroid disease	4.682697	0.0000000	0.0000001	15/19
hsa04940	Type I diabetes mellitus	4.519174	0.0000000	0.0000001	16/21
hsa04672	Intestinal immune network for IgA production	4.448562	0.0000004	0.0000082	12/16
hsa05416	Viral myocarditis	3.954277	0.0000000	0.0000001	20/30
hsa04060	Cytokine-cytokine receptor interaction	3.558850	0.0000000	0.0000000	24/40
hsa05340	Primary immunodeficiency	3.504928	0.0000086	0.0001252	13/22
hsa05412	Arrhythmogenic right ventricular cardiomyopathy (ARVC)	3.459993	0.0013485	0.0103514	7/12
hsa05321	Inflammatory bowel disease (IBD)	3.421971	0.0000026	0.0000395	15/26
hsa04612	Antigen processing and presentation	3.310558	0.0000000	0.0000002	24/43
hsa05410	Hypertrophic cardiomyopathy (HCM)	3.163422	0.0013127	0.0103514	8/15
hsa05414	Dilated cardiomyopathy (DCM)	3.163422	0.0013127	0.0103514	8/15
hsa05140	Leishmaniasis	3.130469	0.0000007	0.0000128	19/36
hsa05323	Rheumatoid arthritis	3.050442	0.0000024	0.0000391	18/35
hsa05322	Systemic lupus erythematosus	2.965708	0.0000266	0.0003307	15/30
hsa04080	Neuroactive ligand-receptor interaction	2.965708	0.0042861	0.0294384	7/14
hsa04658	Th1 and Th2 cell differentiation	2.909751	0.0000000	0.0000011	26/53
hsa04650	Natural killer cell mediated cytotoxicity	2.851642	0.0000001	0.0000030	25/52
hsa04659	Th17 cell differentiation	2.730334	0.0000000	0.0000011	29/63
hsa04670	Leukocyte transendothelial migration	2.636185	0.0000116	0.0001587	20/45
hsa05146	Amoebiasis	2.372566	0.0049560	0.0323378	10/25
hsa04630	JAK-STAT signaling pathway	2.178888	0.0005936	0.0053426	18/49
hsa05145	Toxoplasmosis	2.118363	0.0004565	0.0045822	20/56
hsa04662	B cell receptor signaling pathway	2.118363	0.0023411	0.0167631	15/42
hsa04660	T cell receptor signaling pathway	2.063101	0.0001993	0.0023647	24/69
hsa05206	MicroRNAs in cancer	2.036158	0.0003376	0.0035244	23/67
hsa04145	Phagosome	2.033628	0.0002565	0.0027899	24/70

Factor 11 : 16 significant KEGG pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
hsa04672	Intestinal immune network for IgA production	3.051635	0.0000993	0.0024845	11/16
hsa04940	Type I diabetes mellitus	2.959161	0.0000179	0.0018841	14/21
hsa05332	Graft-versus-host disease	2.885182	0.0000542	0.0018841	13/20
hsa05320	Autoimmune thyroid disease	2.803416	0.0001602	0.0029869	12/19
hsa05330	Allograft rejection	2.803416	0.0001602	0.0029869	12/19
hsa05150	Staphylococcus aureus infection	2.731533	0.0027496	0.0299014	8/13
hsa04640	Hematopoietic cell lineage	2.515287	0.0000485	0.0018841	17/30
hsa05416	Viral myocarditis	2.515287	0.0000485	0.0018841	17/30
hsa04666	Fc gamma R-mediated phagocytosis	2.441308	0.0000071	0.0018543	22/40
hsa05130	Pathogenic Escherichia coli infection	2.421132	0.0000577	0.0018841	18/33
hsa04514	Cell adhesion molecules (CAMs)	2.336180	0.0000443	0.0018841	20/38
hsa04060	Cytokine-cytokine receptor interaction	2.219371	0.0001142	0.0024845	20/40
hsa05140	Leishmaniasis	2.219371	0.0002523	0.0043650	18/36
hsa04650	Natural killer cell mediated cytotoxicity	2.134010	0.0000375	0.0018841	25/52
hsa05132	Salmonella infection	2.113687	0.0002676	0.0043650	20/42
hsa05323	Rheumatoid arthritis	2.029139	0.0018977	0.0227493	16/35

Factor 12 : 7 significant KEGG pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
hsa05320	Autoimmune thyroid disease	3.176003	4.10e-06	0.0001792	14/19
hsa05330	Allograft rejection	3.176003	4.10e-06	0.0001792	14/19
hsa04940	Type I diabetes mellitus	3.078778	3.40e-06	0.0001792	15/21
hsa05332	Graft-versus-host disease	3.017203	1.08e-05	0.0004035	14/20
hsa05322	Systemic lupus erythematosus	2.729850	2.70e-06	0.0001792	19/30
hsa05416	Viral myocarditis	2.729850	2.70e-06	0.0001792	19/30
hsa04612	Antigen processing and presentation	2.505982	7.00e-07	0.0001792	25/43

Factor 13 : 33 significant KEGG pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
hsa05410	Hypertrophic cardiomyopathy (HCM)	4.622414	0.0000002	0.0000092	12/15
hsa05414	Dilated cardiomyopathy (DCM)	4.237213	0.0000026	0.0001143	11/15
hsa05412	Arrhythmogenic right ventricular cardiomyopathy (ARVC)	3.852012	0.0001967	0.0030198	8/12
hsa04640	Hematopoietic cell lineage	3.659411	0.0000000	0.0000018	19/30
hsa05330	Allograft rejection	3.345168	0.0000743	0.0017625	11/19
hsa04060	Cytokine-cytokine receptor interaction	3.322360	0.0000000	0.0000012	23/40
hsa04940	Type I diabetes mellitus	3.301724	0.0000410	0.0011904	12/21
hsa04514	Cell adhesion molecules (CAMs)	3.193115	0.0000001	0.0000068	21/38
hsa05332	Graft-versus-host disease	3.177910	0.0001396	0.0024784	11/20
hsa05150	Staphylococcus aureus infection	3.111240	0.0029282	0.0191064	7/13
hsa05320	Autoimmune thyroid disease	3.041062	0.0004574	0.0053027	10/19
hsa04650	Natural killer cell mediated cytotoxicity	3.000124	0.0000000	0.0000012	27/52
hsa04970	Salivary secretion	2.889009	0.0014358	0.0124914	9/18
hsa05140	Leishmaniasis	2.728508	0.0000287	0.0009364	17/36
hsa05416	Viral myocarditis	2.696408	0.0001744	0.0028441	14/30
hsa04918	Thyroid hormone synthesis	2.512181	0.0029256	0.0191064	10/23
hsa04971	Gastric acid secretion	2.432849	0.0096779	0.0451060	8/19
hsa04612	Antigen processing and presentation	2.418705	0.0001209	0.0024275	18/43
hsa05340	Primary immunodeficiency	2.363734	0.0076529	0.0407633	9/22
hsa04015	Rap1 signaling pathway	2.329846	0.0000127	0.0004742	25/62
hsa04658	Th1 and Th2 cell differentiation	2.289403	0.0000867	0.0018862	21/53
hsa05321	Inflammatory bowel disease (IBD)	2.222314	0.0083033	0.0423392	10/26
hsa04659	Th17 cell differentiation	2.201149	0.0000579	0.0015106	24/63
hsa04064	NF-kappa B signaling pathway	2.182806	0.0007911	0.0086035	17/45
hsa05323	Rheumatoid arthritis	2.146121	0.0038740	0.0236763	13/35
hsa04921	Oxytocin signaling pathway	2.135354	0.0010584	0.0101044	17/46
hsa05322	Systemic lupus erythematosus	2.118606	0.0086268	0.0423392	11/30
hsa04915	Estrogen signaling pathway	2.101097	0.0018045	0.0144093	16/44
hsa04912	GnRH signaling pathway	2.086506	0.0051305	0.0297570	13/36
hsa04625	C-type lectin receptor signaling pathway	2.080086	0.0010840	0.0101044	18/50
hsa05132	Salmonella infection	2.063578	0.0030589	0.0194727	15/42
hsa04670	Leukocyte transendothelial migration	2.054406	0.0023636	0.0166731	16/45
hsa04380	Osteoclast differentiation	2.000083	0.0018219	0.0144093	18/52

Factor 14 : 5 significant KEGG pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
hsa00100	Steroid biosynthesis	5.070449	0.0000121	0.0010564	8/10
hsa00900	Terpenoid backbone biosynthesis	3.380299	0.0008310	0.0433802	8/15
hsa04114	Oocyte meiosis	2.453443	0.0000084	0.0010564	24/62
hsa05034	Alcoholism	2.281702	0.0003406	0.0222238	18/50
hsa04110	Cell cycle	2.180838	0.0000052	0.0010564	32/93

Factor 15 : 8 significant KEGG pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
hsa05330	Allograft rejection	2.309759	0.0022587	0.0491263	11/19
hsa04940	Type I diabetes mellitus	2.279762	0.0016576	0.0393293	12/21
hsa03010	Ribosome	2.261811	0.0000000	0.0000000	72/127
hsa05322	Systemic lupus erythematosus	2.260764	0.0002048	0.0066813	17/30
hsa04260	Cardiac muscle contraction	2.201149	0.0004772	0.0138387	16/29
hsa00190	Oxidative phosphorylation	2.139867	0.0000000	0.0000000	59/110
hsa05012	Parkinson disease	2.068673	0.0000000	0.0000001	56/108
hsa05130	Pathogenic Escherichia coli infection	2.055240	0.0009123	0.0238111	17/33

Factor 16 : 10 significant KEGG pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
hsa04971	Gastric acid secretion	2.718315	0.0005240	0.0136759	11/19
hsa03060	Protein export	2.683012	0.0003414	0.0111368	12/21
hsa05416	Viral myocarditis	2.347636	0.0004396	0.0127483	15/30
hsa04260	Cardiac muscle contraction	2.266683	0.0010682	0.0199136	14/29
hsa05010	Alzheimer disease	2.100516	0.0000000	0.0000011	51/114
hsa04514	Cell adhesion molecules (CAMs)	2.100516	0.0009471	0.0190140	17/38
hsa05012	Parkinson disease	2.086787	0.0000000	0.0000027	48/108
hsa04612	Antigen processing and presentation	2.074655	0.0005788	0.0137341	19/43
hsa03010	Ribosome	2.070356	0.0000000	0.0000007	56/127
hsa05034	Alcoholism	2.065919	0.0002313	0.0086250	22/50

Factor 17 : 53 significant KEGG pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
hsa05150	Staphylococcus aureus infection	7.365385	0.0000000	0.0000008	10/13
hsa05332	Graft-versus-host disease	7.181250	0.0000000	0.0000000	15/20
hsa05330	Allograft rejection	7.055263	0.0000000	0.0000000	14/19
hsa04940	Type I diabetes mellitus	6.839286	0.0000000	0.0000000	15/21
hsa05320	Autoimmune thyroid disease	6.551316	0.0000000	0.0000001	13/19
hsa04640	Hematopoietic cell lineage	6.383333	0.0000000	0.0000000	20/30
hsa04672	Intestinal immune network for IgA production	5.984375	0.0000006	0.0000136	10/16
hsa04514	Cell adhesion molecules (CAMs)	5.795395	0.0000000	0.0000000	23/38
hsa05416	Viral myocarditis	5.745000	0.0000000	0.0000000	18/30
hsa05412	Arrhythmogenic right ventricular cardiomyopathy (ARVC)	5.585417	0.0000629	0.0007818	7/12
hsa04060	Cytokine-cytokine receptor interaction	5.026875	0.0000000	0.0000000	21/40
hsa05414	Dilated cardiomyopathy (DCM)	4.468333	0.0003869	0.0037398	7/15
hsa05322	Systemic lupus erythematosus	4.149167	0.0000031	0.0000543	13/30
hsa05323	Rheumatoid arthritis	4.103571	0.0000006	0.0000136	15/35
hsa04080	Neuroactive ligand-receptor interaction	4.103571	0.0017887	0.0141467	6/14
hsa05321	Inflammatory bowel disease (IBD)	4.050961	0.0000245	0.0003193	11/26
hsa04612	Antigen processing and presentation	4.008140	0.0000001	0.0000018	18/43
hsa05140	Leishmaniasis	3.989583	0.0000010	0.0000196	15/36
hsa05410	Hypertrophic cardiomyopathy (HCM)	3.830000	0.0027232	0.0193311	6/15
hsa04970	Salivary secretion	3.723611	0.0014501	0.0122091	7/18
hsa01040	Biosynthesis of unsaturated fatty acids	3.682692	0.0076150	0.0414065	5/13
hsa04750	Inflammatory mediator regulation of TRP channels	3.546296	0.0002204	0.0022124	10/27
hsa04971	Gastric acid secretion	3.527632	0.0020940	0.0156155	7/19
hsa05020	Prion diseases	3.419643	0.0108518	0.0472055	5/14
hsa05145	Toxoplasmosis	3.248661	0.0000015	0.0000276	19/56
hsa04650	Natural killer cell mediated cytotoxicity	3.130288	0.0000096	0.0001563	17/52
hsa04658	Th1 and Th2 cell differentiation	3.071226	0.0000128	0.0001854	17/53
hsa05340	Primary immunodeficiency	3.046591	0.0053817	0.0326655	7/22
hsa04924	Renin secretion	3.023684	0.0102994	0.0455706	6/19
hsa04925	Aldosterone synthesis and secretion	2.971552	0.0019722	0.0151393	9/29
hsa04713	Circadian entrainment	2.914130	0.0070600	0.0392058	7/23
hsa04270	Vascular smooth muscle contraction	2.779839	0.0032899	0.0216530	9/31
hsa04611	Platelet activation	2.766111	0.0004453	0.0041506	13/45
hsa04145	Phagosome	2.735714	0.0000155	0.0002128	20/70
hsa05146	Amoebiasis	2.681000	0.0115351	0.0493551	7/25
hsa04015	Rap1 signaling pathway	2.625403	0.0001216	0.0013219	17/62
hsa04659	Th17 cell differentiation	2.583730	0.0001510	0.0015764	17/63
hsa05164	Influenza A	2.560756	0.0000118	0.0001816	23/86
hsa04720	Long-term potentiation	2.534559	0.0064626	0.0374830	9/34
hsa05418	Fluid shear stress and atherosclerosis	2.489500	0.0013364	0.0116267	13/50
hsa04928	Parathyroid hormone synthesis, secretion and action	2.462143	0.0079236	0.0416293	9/35
hsa04810	Regulation of actin cytoskeleton	2.424051	0.0001051	0.0011926	20/79
hsa04912	GnRH signaling pathway	2.393750	0.0096235	0.0440867	9/36
hsa04630	JAK-STAT signaling pathway	2.344898	0.0035193	0.0224033	12/49
hsa04921	Oxytocin signaling pathway	2.289674	0.0062443	0.0370398	11/46
hsa04020	Calcium signaling pathway	2.279762	0.0092818	0.0440462	10/42
hsa05132	Salmonella infection	2.279762	0.0092818	0.0440462	10/42
hsa05168	Herpes simplex infection	2.231068	0.0000907	0.0010756	24/103
hsa05152	Tuberculosis	2.191867	0.0006340	0.0057061	19/83
hsa05205	Proteoglycans in cancer	2.098630	0.0027404	0.0193311	16/73
hsa04510	Focal adhesion	2.051786	0.0046395	0.0288311	15/70
hsa04910	Insulin signaling pathway	2.040574	0.0086038	0.0440310	13/61
hsa04210	Apoptosis	2.009568	0.0033185	0.0216530	17/81

Factor 18 : 3 significant KEGG pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
hsa03010	Ribosome	5.656991	0.0e+00	0.0000000	82/127
hsa00010	Glycolysis / Gluconeogenesis	3.796623	8.6e-06	0.0007457	13/30
hsa04060	Cytokine-cytokine receptor interaction	3.723611	5.0e-07	0.0000611	17/40

Factor 19 : 20 significant KEGG pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
hsa05412	Arrhythmogenic right ventricular cardiomyopathy (ARVC)	4.839350	0.0006221	0.0147614	6/12
hsa04080	Neuroactive ligand-receptor interaction	4.839350	0.0002113	0.0068945	7/14
hsa00100	Steroid biosynthesis	4.839350	0.0018490	0.0320560	5/10
hsa04672	Intestinal immune network for IgA production	4.234431	0.0005866	0.0147614	7/16
hsa04514	Cell adhesion molecules (CAMs)	4.075242	0.0000003	0.0000785	16/38
hsa04060	Cytokine-cytokine receptor interaction	3.871480	0.0000007	0.0000914	16/40
hsa05332	Graft-versus-host disease	3.871480	0.0004879	0.0141487	8/20
hsa05410	Hypertrophic cardiomyopathy (HCM)	3.871480	0.0025751	0.0353740	6/15
hsa05414	Dilated cardiomyopathy (DCM)	3.871480	0.0025751	0.0353740	6/15
hsa05320	Autoimmune thyroid disease	3.565837	0.0019651	0.0320560	7/19
hsa05330	Allograft rejection	3.565837	0.0019651	0.0320560	7/19
hsa04640	Hematopoietic cell lineage	3.548857	0.0001066	0.0046390	11/30
hsa05140	Leishmaniasis	3.226234	0.0001498	0.0055843	12/36
hsa04940	Type I diabetes mellitus	3.226234	0.0037816	0.0469997	7/21
hsa04650	Natural killer cell mediated cytotoxicity	3.164191	0.0000083	0.0005391	17/52
hsa05206	MicroRNAs in cancer	3.033622	0.0000015	0.0001307	21/67
hsa05416	Viral myocarditis	2.903610	0.0023780	0.0353740	9/30
hsa04630	JAK-STAT signaling pathway	2.370294	0.0032144	0.0419479	12/49
hsa04659	Th17 cell differentiation	2.304453	0.0013830	0.0277671	15/63
hsa04621	NOD-like receptor signaling pathway	2.124593	0.0013057	0.0277671	18/82

Factor 20 : 24 significant KEGG pathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
hsa05332	Graft-versus-host disease	9.532444	0.0000000	0.0000000	16/20
hsa05320	Autoimmune thyroid disease	9.407018	0.0000000	0.0000000	15/19
hsa05330	Allograft rejection	9.407018	0.0000000	0.0000000	15/19
hsa04940	Type I diabetes mellitus	9.078518	0.0000000	0.0000000	16/21
hsa05150	Staphylococcus aureus infection	8.249231	0.0000001	0.0000022	9/13
hsa04672	Intestinal immune network for IgA production	7.447222	0.0000001	0.0000019	10/16
hsa04640	Hematopoietic cell lineage	7.149333	0.0000000	0.0000000	18/30
hsa04612	Antigen processing and presentation	6.650543	0.0000000	0.0000000	24/43
hsa04514	Cell adhesion molecules (CAMs)	6.271345	0.0000000	0.0000000	20/38
hsa05416	Viral myocarditis	5.957778	0.0000000	0.0000001	15/30
hsa05321	Inflammatory bowel disease (IBD)	5.041197	0.0000029	0.0000512	11/26
hsa05322	Systemic lupus erythematosus	4.369037	0.0000149	0.0002287	11/30
hsa05140	Leishmaniasis	4.302840	0.0000029	0.0000512	13/36
hsa04060	Cytokine-cytokine receptor interaction	4.170444	0.0000019	0.0000405	14/40
hsa05323	Rheumatoid arthritis	3.744889	0.0000779	0.0011289	11/35
hsa04145	Phagosome	3.234222	0.0000022	0.0000447	19/70
hsa03010	Ribosome	3.189991	0.0000000	0.0000000	34/127
hsa05145	Toxoplasmosis	2.978889	0.0001369	0.0018801	14/56
hsa05168	Herpes simplex infection	2.660755	0.0000073	0.0001196	23/103
hsa04659	Th17 cell differentiation	2.647901	0.0005166	0.0064205	14/63
hsa04658	Th1 and Th2 cell differentiation	2.473040	0.0036579	0.0381888	11/53
hsa05169	Epstein-Barr virus infection	2.183003	0.0001479	0.0019307	24/131
hsa05152	Tuberculosis	2.153414	0.0030987	0.0336983	15/83
hsa05163	Human cytomegalovirus infection	2.021389	0.0019548	0.0221830	19/112

Summary:
Factor	1	2	3	4	5	6	7	8	9	10
Signif_GO_terms	0	0	0	4	0	0	15	19	31	0
Factor	11	12	13	14	15	16	17	18	19	20
Signif_GO_terms	16	7	33	5	8	10	53	3	20	24

5.4 Wikipathway Over-Representation Analysis

Gene sets: The Wikipathway database.

Factor 6 : 1 significant Wikipathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
WP531	DNA Mismatch Repair	2.019353	8.69e-05	0.0043144	15/16

Factor 7 : 5 significant Wikipathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
WP455	GPCRs, Class A Rhodopsin-like	2.667831	0.0000520	0.0038769	12/14
WP3613	Photodynamic therapy-induced unfolded protein response	2.334352	0.0005217	0.0233026	12/16
WP2840	Hair Follicle Development: Cytodifferentiation (Part 3 of 3)	2.247895	0.0005474	0.0233026	13/18
WP2328	Allograft Rejection	2.208849	0.0000094	0.0009314	22/31
WP2877	Vitamin D Receptor Pathway	2.100917	0.0000040	0.0006007	27/40

Factor 8 : 5 significant Wikipathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
WP477	Cytoplasmic Ribosomal Proteins	4.400657	0.0000000	0.0000000	80/84
WP2328	Allograft Rejection	3.279199	0.0000000	0.0000007	22/31
WP4585	Cancer immunotherapy by PD-1 blockade	2.675136	0.0006052	0.0360720	11/19
WP4217	Ebola Virus Pathway on Host	2.152102	0.0000013	0.0001328	34/73
WP2431	Spinal Cord Injury	2.123020	0.0007863	0.0390541	17/37

Factor 9 : 8 significant Wikipathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
WP455	GPCRs, Class A Rhodopsin-like	4.256231	0.0000016	0.0001617	11/14
WP2328	Allograft Rejection	4.193823	0.0000000	0.0000000	24/31
WP4494	Selective expression of chemokine receptors during T-cell polarization	3.791915	0.0005025	0.0213921	7/10
WP4585	Cancer immunotherapy by PD-1 blockade	3.706383	0.0000023	0.0001700	13/19
WP2118	Arrhythmogenic Right Ventricular Cardiomyopathy	3.095441	0.0013460	0.0445663	8/14
WP4538	Regulatory circuits of the STAT3 signaling pathway	2.527943	0.0003537	0.0175688	14/30
WP4217	Ebola Virus Pathway on Host	2.300379	0.0000012	0.0001617	31/73
WP4298	Viral Acute Myocarditis	2.141613	0.0009225	0.0343614	17/43

Factor 11 : 5 significant Wikipathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
WP3945	TYROBP Causal Network	2.662484	0.0000230	0.0034332	16/25
WP2877	Vitamin D Receptor Pathway	2.600082	0.0000002	0.0000612	25/40
WP2328	Allograft Rejection	2.415560	0.0000468	0.0046499	18/31
WP4718	Cholesterol metabolism (includes both Bloch and Kandutsch-Russell pathways)	2.377218	0.0001628	0.0097041	16/28
WP2272	Pathogenic Escherichia coli infection	2.269162	0.0001429	0.0097041	18/33

Factor 12 : 5 significant Wikipathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
WP4240	Regulation of sister chromatid separation at the metaphase-anaphase transition	2.847521	0.0007687	0.0381795	9/13
WP2328	Allograft Rejection	2.653604	0.0000021	0.0006250	20/31
WP3613	Photodynamic therapy-induced unfolded protein response	2.570679	0.0012584	0.0468759	10/16
WP466	DNA Replication	2.442145	0.0000219	0.0021771	19/32
WP2864	Apoptosis-related network due to altered Notch3 in ovarian cancer	2.127458	0.0012346	0.0468759	15/29

Factor 13 : 7 significant Wikipathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
WP98	Prostaglandin Synthesis and Regulation	3.514148	0.0003836	0.0267002	8/12
WP2118	Arrhythmogenic Right Ventricular Cardiomyopathy	3.012127	0.0016238	0.0450632	8/14
WP2328	Allograft Rejection	2.890670	0.0000078	0.0023185	17/31
WP4585	Cancer immunotherapy by PD-1 blockade	2.774327	0.0009815	0.0388446	10/19
WP2877	Vitamin D Receptor Pathway	2.503830	0.0000340	0.0050675	19/40
WP4541	Hippo-Merlin Signaling Dysregulation	2.306159	0.0010608	0.0388446	14/32
WP4217	Ebola Virus Pathway on Host	2.021838	0.0000692	0.0068772	28/73

Factor 14 : 3 significant Wikipathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
WP197	Cholesterol Biosynthesis Pathway	4.922661	8.00e-07	0.0001256	10/12
WP4240	Regulation of sister chromatid separation at the metaphase-anaphase transition	4.089595	3.99e-05	0.0039587	9/13
WP4718	Cholesterol metabolism (includes both Bloch and Kandutsch-Russell pathways)	3.797481	0.00e+00	0.0000070	18/28

Factor 15 : 4 significant Wikipathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
WP477	Cytoplasmic Ribosomal Proteins	2.829528	0.0000000	0.0000000	59/84
WP111	Electron Transport Chain (OXPHOS system in mitochondria)	2.332279	0.0000000	0.0000000	55/95
WP623	Oxidative phosphorylation	2.184939	0.0000009	0.0000926	32/59
WP2272	Pathogenic Escherichia coli infection	2.075278	0.0008059	0.0480303	17/33

Factor 16 : 6 significant Wikipathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
WP4629	Computational Model of Aerobic Glycolysis	4.331569	0.0000056	0.0004566	9/10
WP1946	Cori Cycle	4.010712	0.0000061	0.0004566	10/12
WP534	Glycolysis and Gluconeogenesis	2.776647	0.0000378	0.0018773	15/26
WP477	Cytoplasmic Ribosomal Proteins	2.234540	0.0000001	0.0000221	39/84
WP111	Electron Transport Chain (OXPHOS system in mitochondria)	2.077127	0.0000004	0.0000619	41/95
WP183	Proteasome Degradation	2.062652	0.0001307	0.0055652	24/56

Factor 17 : 7 significant Wikipathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
WP2328	Allograft Rejection	5.513963	0.0000000	0.0000000	19/31
WP455	GPCRs, Class A Rhodopsin-like	4.498233	0.0003354	0.0199926	7/14
WP2118	Arrhythmogenic Right Ventricular Cardiomyopathy	4.498233	0.0003354	0.0199926	7/14
WP2806	Human Complement System	4.048410	0.0001266	0.0125757	9/20
WP4718	Cholesterol metabolism (includes both Bloch and Kandutsch-Russell pathways)	3.213024	0.0005183	0.0220667	10/28
WP4298	Viral Acute Myocarditis	2.719862	0.0005012	0.0220667	13/43
WP4217	Ebola Virus Pathway on Host	2.588025	0.0000220	0.0032847	21/73

Factor 18 : 10 significant Wikipathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
WP477	Cytoplasmic Ribosomal Proteins	7.776786	0.0000000	0.0000000	78/84
WP4629	Computational Model of Aerobic Glycolysis	7.537500	0.0000000	0.0000059	9/10
WP1946	Cori Cycle	6.281250	0.0000007	0.0000522	9/12
WP1742	TP53 Network	4.568182	0.0007561	0.0321884	6/11
WP534	Glycolysis and Gluconeogenesis	4.509615	0.0000002	0.0000227	14/26
WP3982	miRNA regulation of p53 pathway in prostate cancer	3.908333	0.0008872	0.0330470	7/15
WP3614	Photodynamic therapy-induced HIF-1 survival signaling	3.806818	0.0000882	0.0052565	10/22
WP4286	Genotoxicity pathway	2.887931	0.0012647	0.0394404	10/29
WP4018	Pathways in clear cell renal cell carcinoma	2.726744	0.0002737	0.0135956	14/43
WP4290	Metabolic reprogramming in colon cancer	2.576923	0.0013235	0.0394404	12/39

Factor 19 : 8 significant Wikipathways
GeneSet	description	enrichmentRatio	pValue	FDR	GeneRatio
WP4494	Selective expression of chemokine receptors during T-cell polarization	6.881081	0.0000011	0.0001663	8/10
WP619	Type II interferon signaling (IFNG)	5.913429	0.0000001	0.0000336	11/16
WP455	GPCRs, Class A Rhodopsin-like	4.300676	0.0004453	0.0265410	7/14
WP98	Prostaglandin Synthesis and Regulation	4.300676	0.0011796	0.0497529	6/12
WP3624	Lung fibrosis	4.300676	0.0011796	0.0497529	6/12
WP2328	Allograft Rejection	3.884481	0.0000026	0.0002556	14/31
WP236	Adipogenesis	2.736794	0.0002701	0.0201234	14/44
WP2877	Vitamin D Receptor Pathway	2.580405	0.0013356	0.0497529	12/40

Factor 20 : 3 significant Wikipathways
GeneSet	description	enrichmentRatio	FDR	GeneRatio
WP2328	Allograft Rejection	6.750331	0e+00	18/31
WP477	Cytoplasmic Ribosomal Proteins	4.428789	0e+00	32/84
WP4217	Ebola Virus Pathway on Host	3.822106	2e-07	24/73

Summary:
Factor	1	2	3	4	5	6	7	8	9	10
Signif_GO_terms	0	0	0	0	0	1	5	5	8	0
Factor	11	12	13	14	15	16	17	18	19	20
Signif_GO_terms	5	5	7	3	4	6	7	10	8	3

Guided Factor Analysis on Stimulated T Cell CROP-seq Data

– 2 donors pooled, batch effect and 3 other covariates corrected

Yifan Zhou (zhouyf@uchicago.edu)

2021-04-01