SZGR2

Summary ?

GeneID	4684
Symbol	NCAM1
Synonyms	CD56\|MSK39\|NCAM
Description	neural cell adhesion molecule 1
Reference	MIM:116930\|HGNC:HGNC:7656\|Ensembl:ENSG00000149294\|HPRD:00301\|Vega:OTTHUMG00000167196
Gene type	protein-coding
Map location	11q23.1
Pascal p-value	1.166E-4
Sherlock p-value	0.919
Fetal beta	0.625
eGene	Myers' cis & trans
Support	CELL ADHESION AND TRANSSYNAPTIC SIGNALING G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS G2Cdb.human_clathrin G2Cdb.human_Synaptosome CompositeSet Darnell FMRP targets Potential synaptic genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGCnp	Genome-wide Association Study	GWAS
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
GSMA_I	Genome scan meta-analysis	Psr: 0.006
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenics,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0233

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs6733654	chr2	1963270	NCAM1	4684	0.12	trans
rs17029291	chr3	32402138	NCAM1	4684	6.899E-6	trans
rs1553189	chr3	112939422	NCAM1	4684	0.18	trans
rs10992675	chr9	95963315	NCAM1	4684	0.2	trans
rs4607971	chr10	19407890	NCAM1	4684	0.07	trans
rs7111397	chr11	20133985	NCAM1	4684	0.12	trans
rs1761450	chr19	54818034	NCAM1	4684	0.07	trans
rs6040268	chr20	10956100	NCAM1	4684	0.14	trans
rs6040269	chr20	10956136	NCAM1	4684	0.14	trans
rs11906936	chr20	10957136	NCAM1	4684	0.14	trans
rs1327232	chr20	10958909	NCAM1	4684	0.12	trans
rs12157904	chr22	37982011	NCAM1	4684	0.06	trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MRPL21	0.89	0.82
JTB	0.89	0.77
C14orf2	0.87	0.74
MRPL33	0.86	0.65
UQCRQ	0.86	0.71
C17orf61	0.86	0.70
COX5A	0.86	0.72
NDUFA2	0.85	0.72
HAX1	0.85	0.73
AC009171.1	0.85	0.73

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MYH9	-0.47	-0.42
BAT2D1	-0.43	-0.37
MMRN2	-0.42	-0.40
PLEC1	-0.41	-0.44
PRX	-0.39	-0.45
ITIH5	-0.39	-0.42
Z83840.4	-0.39	-0.45
AC010300.1	-0.38	-0.57
KIF16B	-0.38	-0.38
RRBP1	-0.38	-0.45

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005515	protein binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007155	cell adhesion	IEA		-
GO:0007155	cell adhesion	NAS		10770948
GO:0007166	cell surface receptor linked signal transduction	IEA		-
GO:0034109	homotypic cell-cell adhesion	IEA		-
GO:0050850	positive regulation of calcium-mediated signaling	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0030424	axon	IEA	neuron, axon, Neurotransmitter (GO term level: 6)	-
GO:0005576	extracellular region	IEA		-
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	TAS		3576199
GO:0009897	external side of plasma membrane	IEA		-
GO:0005886	plasma membrane	TAS		3576199
GO:0031225	anchored to membrane	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG CELL ADHESION MOLECULES CAMS	134	93	All SZGR 2.0 genes in this pathway
KEGG PRION DISEASES	35	28	All SZGR 2.0 genes in this pathway
PID FGF PATHWAY	55	37	All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY	396	292	All SZGR 2.0 genes in this pathway
REACTOME AXON GUIDANCE	251	188	All SZGR 2.0 genes in this pathway
REACTOME NCAM1 INTERACTIONS	39	27	All SZGR 2.0 genes in this pathway
REACTOME NCAM SIGNALING FOR NEURITE OUT GROWTH	64	49	All SZGR 2.0 genes in this pathway
REACTOME L1CAM INTERACTIONS	86	62	All SZGR 2.0 genes in this pathway
REACTOME SIGNAL TRANSDUCTION BY L1	34	25	All SZGR 2.0 genes in this pathway
REACTOME INTERFERON GAMMA SIGNALING	63	48	All SZGR 2.0 genes in this pathway
REACTOME INTERFERON SIGNALING	159	116	All SZGR 2.0 genes in this pathway
REACTOME IMMUNE SYSTEM	933	616	All SZGR 2.0 genes in this pathway
REACTOME CYTOKINE SIGNALING IN IMMUNE SYSTEM	270	204	All SZGR 2.0 genes in this pathway
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL UP	285	181	All SZGR 2.0 genes in this pathway
LIU PROSTATE CANCER DN	481	290	All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY DN	367	220	All SZGR 2.0 genes in this pathway
JAEGER METASTASIS UP	44	23	All SZGR 2.0 genes in this pathway
ODONNELL TFRC TARGETS UP	456	228	All SZGR 2.0 genes in this pathway
HAHTOLA SEZARY SYNDROM DN	42	26	All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER DN	232	154	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION KRAS UP	126	72	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION CDC25 UP	120	73	All SZGR 2.0 genes in this pathway
CASTELLANO NRAS TARGETS DN	14	14	All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS A UP	191	128	All SZGR 2.0 genes in this pathway
SILIGAN TARGETS OF EWS FLI1 FUSION UP	15	12	All SZGR 2.0 genes in this pathway
EBAUER TARGETS OF PAX3 FOXO1 FUSION UP	207	128	All SZGR 2.0 genes in this pathway
DAWSON METHYLATED IN LYMPHOMA TCL1	59	45	All SZGR 2.0 genes in this pathway
LI WILMS TUMOR VS FETAL KIDNEY 2 UP	30	24	All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM5	94	59	All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS	957	597	All SZGR 2.0 genes in this pathway
WOTTON RUNX TARGETS UP	21	14	All SZGR 2.0 genes in this pathway
GOTZMANN EPITHELIAL TO MESENCHYMAL TRANSITION UP	69	55	All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS	1038	678	All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS	1062	725	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS	652	441	All SZGR 2.0 genes in this pathway
LEE TARGETS OF PTCH1 AND SUFU DN	83	69	All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS UP	266	171	All SZGR 2.0 genes in this pathway
LEI HOXC8 TARGETS DN	17	13	All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST UP	398	262	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	All SZGR 2.0 genes in this pathway
YAO HOXA10 TARGETS VIA PROGESTERONE UP	79	58	All SZGR 2.0 genes in this pathway
WANG TARGETS OF MLL CBP FUSION UP	44	26	All SZGR 2.0 genes in this pathway
VERHAAK AML WITH NPM1 MUTATED DN	246	180	All SZGR 2.0 genes in this pathway
YAGI AML FAB MARKERS	191	131	All SZGR 2.0 genes in this pathway
REN ALVEOLAR RHABDOMYOSARCOMA UP	98	64	All SZGR 2.0 genes in this pathway
RAMALHO STEMNESS DN	74	55	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS UP	37	27	All SZGR 2.0 genes in this pathway
PAL PRMT5 TARGETS UP	203	135	All SZGR 2.0 genes in this pathway
MODY HIPPOCAMPUS NEONATAL	35	25	All SZGR 2.0 genes in this pathway
KAYO AGING MUSCLE UP	244	165	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
KIM GASTRIC CANCER CHEMOSENSITIVITY	103	64	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 8	86	57	All SZGR 2.0 genes in this pathway
TAKAO RESPONSE TO UVB RADIATION DN	98	67	All SZGR 2.0 genes in this pathway
KUNINGER IGF1 VS PDGFB TARGETS UP	82	51	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 UP	428	266	All SZGR 2.0 genes in this pathway
SIMBULAN PARP1 TARGETS DN	17	10	All SZGR 2.0 genes in this pathway
JI CARCINOGENESIS BY KRAS AND STK11 DN	17	12	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS UP	317	208	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION UP	461	298	All SZGR 2.0 genes in this pathway
DAIRKEE CANCER PRONE RESPONSE BPA E2	118	65	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP	648	398	All SZGR 2.0 genes in this pathway
RAY TUMORIGENESIS BY ERBB2 CDC25A UP	104	57	All SZGR 2.0 genes in this pathway
MOOTHA PGC	420	269	All SZGR 2.0 genes in this pathway
NUTT GBM VS AO GLIOMA DN	45	22	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS DN	668	419	All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC DN	253	192	All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE	721	492	All SZGR 2.0 genes in this pathway
NAKAYAMA SOFT TISSUE TUMORS PCA2 UP	87	50	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 0	76	54	All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA PRONEURAL	177	132	All SZGR 2.0 genes in this pathway
IKEDA MIR30 TARGETS UP	116	87	All SZGR 2.0 genes in this pathway
IKEDA MIR30 TARGETS DN	27	24	All SZGR 2.0 genes in this pathway
ABDELMOHSEN ELAVL4 TARGETS	16	13	All SZGR 2.0 genes in this pathway
ACEVEDO FGFR1 TARGETS IN PROSTATE CANCER MODEL DN	308	187	All SZGR 2.0 genes in this pathway
DURAND STROMA S UP	297	194	All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family	Target position			miRNA ID	miRNA seq
miRNA family	UTR start	UTR end	Match method	miRNA ID	miRNA seq
miR-125/351	1262	1268	1A	hsa-miR-125b^brain	UCCCUGAGACCCUAACUUGUGA
miR-125/351	1262	1268	1A	hsa-miR-125a^brain	UCCCUGAGACCCUUUAACCUGUG
miR-128	1902	1908	1A	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
				hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
				hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
				hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-136	1976	1982	m8	hsa-miR-136	ACUCCAUUUGUUUUGAUGAUGGA
miR-148/152	1532	1538	m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-182	611	617	1A	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-204/211	1459	1465	1A	hsa-miR-204^brain	UUCCCUUUGUCAUCCUAUGCCU
miR-204/211	1459	1465	1A	hsa-miR-211	UUCCCUUUGUCAUCCUUCGCCU
miR-205	1083	1089	1A	hsa-miR-205	UCCUUCAUUCCACCGGAGUCUG
miR-27	1902	1909	1A,m8	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	1902	1909	1A,m8	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-30-5p	721	728	1A,m8	hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
				hsa-miR-30a-5p	UGUAAACAUCCUCGACUGGAAG
				hsa-miR-30c^brain	UGUAAACAUCCUACACUCUCAGC
				hsa-miR-30d^SZ	UGUAAACAUCCCCGACUGGAAG
				hsa-miR-30b^SZ	UGUAAACAUCCUACACUCAGCU
				hsa-miR-30e-5p	UGUAAACAUCCUUGACUGGA
miR-377	1558	1564	1A	hsa-miR-377	AUCACACAAAGGCAACUUUUGU
miR-378	1647	1653	1A	hsa-miR-378	CUCCUGACUCCAGGUCCUGUGU
miR-381	1123	1129	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-381	1123	1129	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-384	333	339	m8	hsa-miR-384	AUUCCUAGAAAUUGUUCAUA
miR-505	1102	1108	1A	hsa-miR-505	GUCAACACUUGCUGGUUUCCUC
miR-539	1954	1960	1A	hsa-miR-539	GGAGAAAUUAUCCUUGGUGUGU
miR-96	611	617	1A	hsa-miR-96^brain	UUUGGCACUAGCACAUUUUUGC

SZ: miRNAs which differentially expressed in brain cortex of schizophrenia patients comparing with control samples using microarray. Click here to see the list of SZ related miRNAs.
Brain: miRNAs which are expressed in brain based on miRNA microarray expression studies. Click here to see the list of brain related miRNAs.

Gene Page: NCAM1