Neuropsychiatric De novo Mutations Database

KEGG

Other pathways: Gene Ontology Transcription Factor Target MicroRNA Target KEGG Wikipathways Pathway Commons

Including 64 KEGG pathways in ASD, 26 in ID, 17 in EE and 34 in SCZ.

KEGG pathway

KEGG accession	KEGG pathway name	Number of reference genes	Number of genes	Expected number	Ratio of entrichment	Raw P_Value	Adjusted P_Value	Other disease
04810	Regulation of actin cytoskeleton	213	13	1.63	7.98	1.27e-08	1.23e-06	SCZ
ABI2 \| PAK2 \| PIK3R2 \| ITGB3 \| FGD3 \| PDGFD \| ITGA5 \| MYH9 \| ROCK1 \| NCKAP1 \| MYH10 \| CHRM3
04510	Focal adhesion	200	12	1.53	7.84	5.59e-08	2.71e-06	EE SCZ
PTEN \| PAK2 \| PIK3R2 \| ITGB3 \| PDGFD \| ITGA5 \| LAMC3 \| RELN \| ROCK1 \| THBS3 \| PRKCA
04972	Pancreatic secretion	101	8	0.77	10.35	1.18e-06	3.82e-05	EE
GNAS \| AMY2B \| ADCY5 \| ITPR1 \| KCNMA1 \| SLC4A2 \| PRKCA
04971	Gastric acid secretion	74	7	0.57	12.36	1.67e-06	4.05e-05	SCZ
GNAS \| SLC4A2 \| PRKCA \| ADCY5 \| ITPR1 \| CHRM3
04270	Vascular smooth muscle contraction	116	8	0.89	9.01	3.35e-06	6.50e-05	SCZ
GNAS \| ADCY5 \| ITPR1 \| KCNMA1 \| CACNA1S \| ROCK1 \| CACNA1D
04970	Salivary secretion	89	7	0.68	10.28	5.80e-06	6.75e-05	EE SCZ
GNAS \| SLC4A2 \| PRKCA \| ADCY5 \| ITPR1 \| KCNMA1
05010	Alzheimer's disease	167	9	1.28	7.04	6.26e-06	6.75e-05	ID
APH1A \| ITPR1 \| LRP1 \| CACNA1S \| CACNA1D \| APAF1 \| PSEN1 \| SDHA
05414	Dilated cardiomyopathy	90	7	0.69	10.16	6.25e-06	6.75e-05	EE SCZ
GNAS \| ITGA5 \| CACNA1D \| CACNA1S \| CACNA2D3 \| ADCY5
04512	ECM-receptor interaction	85	7	0.65	10.76	4.27e-06	6.75e-05	SCZ
ITGA5 \| LAMC3 \| RELN \| SV2B \| THBS3 \| ITGB3
04020	Calcium signaling pathway	177	9	1.35	6.65	1.00e-05	9.70e-05	EE SCZ
GNAS \| CACNA1E \| PLCD4 \| ITPR1 \| CACNA1S \| CACNA1D \| PRKCA \| HRH2
04912	GnRH signaling pathway	101	7	0.77	9.06	1.34e-05	0.0001	ID SCZ
GNAS \| MAPK13 \| CACNA1D \| CACNA1S \| PRKCA \| ADCY5
04070	Phosphatidylinositol signaling system	78	6	0.60	10.05	3.10e-05	0.0002	-
PRKCA \| PTEN \| PLCD4 \| ITPR1 \| PIK3R2
05412	Arrhythmogenic right ventricular cardiomyopathy (ARVC)	74	6	0.57	10.60	2.29e-05	0.0002	ID SCZ
ITGA5 \| TCF7L1 \| CACNA1D \| CACNA1S \| CACNA2D3
04540	Gap junction	90	6	0.69	8.71	6.96e-05	0.0005	SCZ
PDGFD \| GNAS \| TUBA1A \| PRKCA \| ADCY5
04145	Phagosome	153	7	1.17	5.98	0.0002	0.0012	-
ITGA5 \| C3 \| COLEC12 \| THBS3 \| TUBA1A \| SFTPD
04010	MAPK signaling pathway	268	9	2.05	4.39	0.0002	0.0012	-
CACNA1E \| PAK2 \| MAPK13 \| CACNA1S \| CACNA1D \| PRKCA \| CACNA2D3 \| RPS6KA3
04360	Axon guidance	129	6	0.99	6.08	0.0005	0.0023	-
ROCK1 \| EPHB2 \| NTNG1 \| PAK2 \| PLXNB1
04973	Carbohydrate digestion and absorption	44	4	0.34	11.88	0.0004	0.0023	-
CACNA1D \| AMY2B \| SLC5A1
05222	Small cell lung cancer	85	5	0.65	7.69	0.0005	0.0023	EE
LAMC3 \| APAF1 \| PTEN \| PIK3R2
05410	Hypertrophic cardiomyopathy (HCM)	83	5	0.64	7.87	0.0005	0.0023	EE
ITGA5 \| CACNA1D \| CACNA1S \| CACNA2D3
04330	Notch signaling pathway	47	4	0.36	11.12	0.0005	0.0023	-
NOTCH3 \| DLL1 \| PSEN1
04530	Tight junction	132	6	1.01	5.94	0.0006	0.0026	ID SCZ
MYH9 \| MPDZ \| CASK \| PRKCA \| PTEN
04310	Wnt signaling pathway	150	6	1.15	5.23	0.0011	0.0046	-
TCF7L1 \| ROCK1 \| PRKCA \| TBL1XR1 \| PSEN1
05146	Amoebiasis	106	5	0.81	6.16	0.0014	0.0057	EE SCZ
GNAS \| LAMC3 \| PRKCA \| PIK3R2
04114	Oocyte meiosis	112	5	0.86	5.83	0.0018	0.0070	ID
SMC3 \| ADCY5 \| SLK \| RPS6KA3
04115	p53 signaling pathway	68	4	0.52	7.69	0.0019	0.0071	-
APAF1 \| TSC2 \| PTEN
04720	Long-term potentiation	70	4	0.54	7.47	0.0021	0.0075	EE ID SCZ
PRKCA \| RPS6KA3 \| ITPR1
04976	Bile secretion	71	4	0.54	7.36	0.0022	0.0076	SCZ
GNAS \| SLC4A2 \| SLC5A1
05016	Huntington's disease	183	6	1.40	4.28	0.0030	0.0100	ID
DNAH2 \| APAF1 \| REST \| SDHA \| ITPR1
05322	Systemic lupus erythematosus	136	5	1.04	4.80	0.0041	0.0128	-
C3 \| HIST1H2AE \| H2AFV \| TROVE2
04960	Aldosterone-regulated sodium reabsorption	42	3	0.32	9.33	0.0041	0.0128	-
PRKCA \| NR3C2
04914	Progesterone-mediated oocyte maturation	86	4	0.66	6.08	0.0044	0.0133	SCZ
MAPK13 \| ADCY5 \| RPS6KA3
05215	Prostate cancer	89	4	0.68	5.87	0.0049	0.0144	EE ID
PDGFD \| TCF7L1 \| PTEN
04930	Type II diabetes mellitus	48	3	0.37	8.17	0.0060	0.0171	EE
CACNA1D \| CACNA1E
05213	Endometrial cancer	52	3	0.40	7.54	0.0074	0.0199	-
TCF7L1 \| PTEN
04916	Melanogenesis	101	4	0.77	5.18	0.0077	0.0199	ID
GNAS \| TCF7L1 \| PRKCA
04150	mTOR signaling pathway	52	3	0.40	7.54	0.0074	0.0199	-
TSC2 \| RPS6KA3
05014	Amyotrophic lateral sclerosis (ALS)	53	3	0.41	7.40	0.0078	0.0199	EE ID
MAPK13 \| APAF1
05142	Chagas disease (American trypanosomiasis)	104	4	0.80	5.03	0.0085	0.0211	-
GNAS \| C3 \| MAPK13
05130	Pathogenic Escherichia coli infection	56	3	0.43	7.00	0.0091	0.0221	ID
ROCK1 \| TUBA1A
04660	T cell receptor signaling pathway	108	4	0.83	4.84	0.0097	0.0229	-
PDCD1 \| MAPK13 \| PAK2
05131	Shigellosis	61	3	0.47	6.43	0.0115	0.0266	-
ITGA5 \| MAPK13
04670	Leukocyte transendothelial migration	116	4	0.89	4.51	0.0123	0.0277	SCZ
MAPK13 \| ROCK1 \| PRKCA
05200	Pathways in cancer	326	7	2.49	2.81	0.0133	0.0293	SCZ
LAMC3 \| STK36 \| TCF7L1 \| PRKCA \| PTEN \| PIK3R2
05214	Glioma	65	3	0.50	6.03	0.0137	0.0295	EE ID
PRKCA \| PTEN
04320	Dorso-ventral axis formation	24	2	0.18	10.89	0.0144	0.0297	-
NOTCH3
01100	Metabolic pathways	1130	16	8.65	1.85	0.0143	0.0297	ID SCZ
SUCLA2 \| CAD \| ACACB \| DNMT3A \| AMY2B \| PLCD4 \| DGKA \| SCP2 \| WBSCR17 \| PAFAH1B2 \| ASAH2 \| ST3GAL6 \| SDHA \| CYP4F3 \| ST3GAL3
00601	Glycosphingolipid biosynthesis - lacto and neolacto series	26	2	0.20	10.05	0.0168	0.0323	-
ST3GAL6
03018	RNA degradation	71	3	0.54	5.52	0.0173	0.0323	-
CNOT6 \| CNOT4
04722	Neurotrophin signaling pathway	127	4	0.97	4.12	0.0167	0.0323	ID
MAPK13 \| PSEN1 \| RPS6KA3
04730	Long-term depression	70	3	0.54	5.60	0.0167	0.0323	EE SCZ
GNAS \| PRKCA
05218	Melanoma	71	3	0.54	5.52	0.0173	0.0323	-
PDGFD \| PTEN
05145	Toxoplasmosis	132	4	1.01	3.96	0.0189	0.0340	SCZ
LAMC3 \| MAPK13 \| PIK3R2
04080	Neuroactive ligand-receptor interaction	272	6	2.08	2.88	0.0189	0.0340	EE ID
OPRL1 \| GABRB3 \| GRM7 \| CHRM3 \| HRH2
04514	Cell adhesion molecules (CAMs)	133	4	1.02	3.93	0.0194	0.0342	SCZ
PDCD1 \| NRXN1 \| NRXN2
04370	VEGF signaling pathway	76	3	0.58	5.16	0.0207	0.0359	-
MAPK13 \| PRKCA
04260	Cardiac muscle contraction	77	3	0.59	5.09	0.0214	0.0364	EE
CACNA1D \| CACNA1S
00020	Citrate cycle (TCA cycle)	30	2	0.23	8.71	0.0221	0.0370	-
SUCLA2
04664	Fc epsilon RI signaling pathway	79	3	0.60	4.96	0.0229	0.0376	-
MAPK13 \| PRKCA
00640	Propanoate metabolism	32	2	0.24	8.17	0.0249	0.0403	-
SUCLA2
04350	TGF-beta signaling pathway	84	3	0.64	4.67	0.0268	0.0426	ID
LTBP1 \| THBS3
04012	ErbB signaling pathway	87	3	0.67	4.51	0.0294	0.0460	-
PRKCA \| PAK2
00565	Ether lipid metabolism	36	2	0.28	7.26	0.0310	0.0477	-
PAFAH1B2 \| ENPP2

KEGG pathway

KEGG accession	KEGG pathway name	Number of reference genes	Number of genes	Expected number	Ratio of entrichment	Raw P_Value	Adjusted P_Value	Other disease
04720	Long-term potentiation	70	4	0.17	23.25	2.79e-05	0.0008	EE ASD SCZ
GRIA1 \| GRIN2A \| CAMK2G
04110	Cell cycle	124	4	0.30	13.12	0.0003	0.0022	-
RB1 \| STAG1 \| RBL2
05014	Amyotrophic lateral sclerosis (ALS)	53	3	0.13	23.03	0.0003	0.0022	EE ASD
GRIA1 \| GRIN2A
04722	Neurotrophin signaling pathway	127	4	0.31	12.81	0.0003	0.0022	ASD
RAPGEF1 \| NGFR \| CAMK2G
05010	Alzheimer's disease	167	4	0.41	9.75	0.0008	0.0048	ASD
GRIN2A \| NDUFA10 \| GRIN2B
04530	Tight junction	132	3	0.32	9.25	0.0043	0.0215	ASD SCZ
MYH9 \| CTNNB1
00510	N-Glycan biosynthesis	49	2	0.12	16.61	0.0065	0.0255	-
TUSC3
00561	Glycerolipid metabolism	50	2	0.12	16.27	0.0068	0.0255	-
DGKH
05130	Pathogenic Escherichia coli infection	56	2	0.14	14.53	0.0085	0.0283	ASD
TUBA1A
05016	Huntington's disease	183	3	0.45	6.67	0.0105	0.0307	ASD
DLG4 \| NDUFA10
05214	Glioma	65	2	0.16	12.52	0.0113	0.0307	EE ASD
RB1
05211	Renal cell carcinoma	70	2	0.17	11.62	0.0130	0.0307	-
RAPGEF1
04622	RIG-I-like receptor signaling pathway	71	2	0.17	11.46	0.0133	0.0307	-
DDX3X
05412	Arrhythmogenic right ventricular cardiomyopathy (ARVC)	74	2	0.18	11.00	0.0144	0.0309	ASD SCZ
CTNNB1
04350	TGF-beta signaling pathway	84	2	0.21	9.69	0.0183	0.0366	ASD
SMAD6
05215	Prostate cancer	89	2	0.22	9.14	0.0204	0.0382	EE ASD
RB1
01100	Metabolic pathways	1130	7	2.78	2.52	0.0217	0.0383	ASD SCZ
DGKH \| MAT1A \| TUSC3 \| PNLIPRP1 \| GFPT2 \| MGAT5B
04912	GnRH signaling pathway	101	2	0.25	8.06	0.0258	0.0407	ASD SCZ
CAMK2G
04916	Melanogenesis	101	2	0.25	8.06	0.0258	0.0407	ASD
CTNNB1
04080	Neuroactive ligand-receptor interaction	272	3	0.67	4.49	0.0298	0.0446	EE ASD
GRIA1 \| GRIN2A
04114	Oocyte meiosis	112	2	0.28	7.27	0.0312	0.0446	ASD
CAMK2G \| SMC1A

KEGG pathway

KEGG accession	KEGG pathway name	Number of reference genes	Number of genes	Expected number	Ratio of entrichment	Raw P_Value	Adjusted P_Value	Other disease
04080	Neuroactive ligand-receptor interaction	272	7	0.69	10.18	6.33e-06	0.0002	ID ASD
GABRA1 \| GABRB1 \| GABRB3 \| RXFP1 \| TAAR2 \| GRIN2B
05014	Amyotrophic lateral sclerosis (ALS)	53	3	0.13	22.40	0.0003	0.0026	ID ASD
GRIN2B \| GRIN1
04144	Endocytosis	201	5	0.51	9.84	0.0002	0.0026	SCZ
VPS37A \| IQSEC2 \| SMURF1 \| RAB5C
04020	Calcium signaling pathway	177	4	0.45	8.94	0.0011	0.0062	ASD SCZ
RYR2 \| ATP2B4 \| CACNA1A
05410	Hypertrophic cardiomyopathy (HCM)	83	3	0.21	14.30	0.0012	0.0062	ASD
RYR2 \| TTN
05414	Dilated cardiomyopathy	90	3	0.23	13.19	0.0016	0.0069	ASD SCZ
RYR2 \| TTN
04930	Type II diabetes mellitus	48	2	0.12	16.49	0.0066	0.0245	ASD
MTOR
04742	Taste transduction	52	2	0.13	15.22	0.0077	0.0250	-
KCNB1
04730	Long-term depression	70	2	0.18	11.30	0.0137	0.0312	ASD SCZ
GNAO1
04510	Focal adhesion	200	3	0.51	5.93	0.0144	0.0312	ASD SCZ
FLNA \| PTEN
04720	Long-term potentiation	70	2	0.18	11.30	0.0137	0.0312	ID ASD SCZ
GRIN2B
05214	Glioma	65	2	0.16	12.17	0.0119	0.0312	ID ASD
PTEN
04260	Cardiac muscle contraction	77	2	0.19	10.28	0.0164	0.0328	ASD
RYR2
05222	Small cell lung cancer	85	2	0.21	9.31	0.0197	0.0349	ASD
PTEN
05215	Prostate cancer	89	2	0.22	8.89	0.0215	0.0349	ID ASD
PTEN
04970	Salivary secretion	89	2	0.22	8.89	0.0215	0.0349	ASD SCZ
BEST2
04972	Pancreatic secretion	101	2	0.26	7.83	0.0272	0.0416	ASD
RYR2
05146	Amoebiasis	106	2	0.27	7.47	0.0297	0.0429	ASD SCZ
RAB5C \| COL4A4

KEGG pathway

KEGG accession	KEGG pathway name	Number of reference genes	Number of genes	Expected number	Ratio of entrichment	Raw P_Value	Adjusted P_Value	Other disease
04020	Calcium signaling pathway	177	10	1.14	8.76	2.63e-07	1.81e-05	ASD EE
ITPR1 \| RYR3 \| ADCY9 \| PTK2B \| CAMK4 \| GRIN2A \| HTR2A \| CACNA1I \| NOS3
05416	Viral myocarditis	70	6	0.45	13.30	6.31e-06	0.0002	-
MYH9 \| LAMA2 \| MYH10 \| MYH7B \| ICAM1
04270	Vascular smooth muscle contraction	116	6	0.75	8.02	0.0001	0.0017	ASD
ACTA2 \| KCNU1 \| ITPR1 \| ADCY9 \| MYH11
04670	Leukocyte transendothelial migration	116	6	0.75	8.02	0.0001	0.0017	ASD
PTK2B \| RASSF5 \| ACTN1 \| ESAM \| ICAM1
04530	Tight junction	132	6	0.85	7.05	0.0002	0.0028	ID ASD
MYH9 \| ACTN1 \| MYH10 \| MYH7B \| CTNNA2
01100	Metabolic pathways	1130	18	7.28	2.47	0.0004	0.0034	ID ASD
PRDX6 \| DPM1 \| BCAT1 \| CHSY1 \| ST3GAL6 \| FLAD1 \| GLS \| LCT \| AOX1 \| ALAS1 \| SQLE \| PIK3C2B \| DPYD \| ACSL4 \| STT3B \| DNMT1 \| NOS3
05200	Pathways in cancer	326	9	2.10	4.28	0.0003	0.0034	ASD
RASSF5 \| MAPK8 \| TPR \| HSP90AA1 \| GLI3 \| LAMA2 \| HIF1A \| CTNNA2
04144	Endocytosis	201	7	1.30	5.40	0.0004	0.0034	EE
CHMP2A \| ASAP2 \| CLTCL1 \| ASAP1 \| HSPA8 \| PML
04912	GnRH signaling pathway	101	5	0.65	7.68	0.0005	0.0038	ID ASD
PTK2B \| MAPK8 \| ITPR1 \| ADCY9
04141	Protein processing in endoplasmic reticulum	165	6	1.06	5.64	0.0007	0.0048	-
MAPK8 \| STT3B \| HSP90AA1 \| MBTPS1 \| UBQLN1
04540	Gap junction	90	4	0.58	6.89	0.0028	0.0114	ASD
HTR2A \| ITPR1 \| ADCY9
04510	Focal adhesion	200	6	1.29	4.65	0.0020	0.0114	ASD EE
MAPK8 \| RELN \| ACTN1 \| LAMA2 \| COL6A2
04810	Regulation of actin cytoskeleton	213	6	1.37	4.37	0.0027	0.0114	ASD
MYH9 \| SSH2 \| ACTN1 \| CD14 \| MYH10
04970	Salivary secretion	89	4	0.57	6.97	0.0027	0.0114	ASD EE
ITPR1 \| RYR3 \| ADCY9
04512	ECM-receptor interaction	85	4	0.55	7.30	0.0023	0.0114	ASD
RELN \| LAMA2 \| COL6A2
04914	Progesterone-mediated oocyte maturation	86	4	0.55	7.22	0.0024	0.0114	ASD
MAPK8 \| HSP90AA1 \| ADCY9
04120	Ubiquitin mediated proteolysis	135	5	0.87	5.75	0.0019	0.0114	-
BIRC6 \| HUWE1 \| UBR5 \| PML
00770	Pantothenate and CoA biosynthesis	16	2	0.10	19.39	0.0047	0.0180	-
BCAT1
05146	Amoebiasis	106	4	0.68	5.85	0.0050	0.0182	ASD EE
ACTN1 \| LAMA2 \| CD14
00360	Phenylalanine metabolism	17	2	0.11	18.25	0.0053	0.0183	-
MIF
04621	NOD-like receptor signaling pathway	58	3	0.37	8.02	0.0063	0.0207	-
MAPK8 \| HSP90AA1
04514	Cell adhesion molecules (CAMs)	133	4	0.86	4.67	0.0110	0.0292	ASD
ESAM \| NFASC \| NRXN1
04730	Long-term depression	70	3	0.45	6.65	0.0106	0.0292	ASD EE
GNAO1 \| GRID2
05145	Toxoplasmosis	132	4	0.85	4.70	0.0107	0.0292	ASD
MAPK8 \| LAMA2 \| GNAO1
04976	Bile secretion	71	3	0.46	6.55	0.0110	0.0292	ASD
ADCY9 \| HMGCR
04720	Long-term potentiation	70	3	0.45	6.65	0.0106	0.0292	ID ASD EE
CAMK4 \| GRIN2A
05412	Arrhythmogenic right ventricular cardiomyopathy (ARVC)	74	3	0.48	6.29	0.0123	0.0303	ID ASD
ACTN1 \| LAMA2
04971	Gastric acid secretion	74	3	0.48	6.29	0.0123	0.0303	ASD
ITPR1 \| ADCY9
05414	Dilated cardiomyopathy	90	3	0.58	5.17	0.0206	0.0490	ASD EE
LAMA2 \| ADCY9
05340	Primary immunodeficiency	35	2	0.23	8.86	0.0214	0.0492	-
TNFRSF13C \| BLNK