SZGR2

Summary ?

GeneID	152330
Symbol	CNTN4
Synonyms	AXCAM\|BIG-2
Description	contactin 4
Reference	MIM:607280\|HGNC:HGNC:2174\|Ensembl:ENSG00000144619\|HPRD:16239\|Vega:OTTHUMG00000119031
Gene type	protein-coding
Map location	3p26.3
Fetal beta	1.652
eGene	Anterior cingulate cortex BA24 Myers' cis & trans
Support	CELL ADHESION AND TRANSSYNAPTIC SIGNALING Potential synaptic genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:GWAScat	Genome-wide Association Studies	This data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGC128	Genome-wide Association Study	A multi-stage schizophrenia GWAS of up to 36,989 cases and 113,075 controls. Reported by the Schizophrenia Working Group of PGC. 128 independent associations spanning 108 loci
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.
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 9

Section I. Genetics and epigenetics annotation

CV:PGC128

SNP ID	Chromosome	Position	Allele	P	Function	Gene	Up/Down Distance
rs17194490	chr3	2547786	TG	4.865E-11	intronic	CNTN4

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs7370564		0	CNTN4	152330		0.09		trans
rs13068096	3	2518282	CNTN4	ENSG00000144619.10	1.20428E-6	0.04	377785	gtex_brain_ba24
rs34163547	3	2519380	CNTN4	ENSG00000144619.10	1.22317E-6	0.04	378883	gtex_brain_ba24
rs11706456	3	2522747	CNTN4	ENSG00000144619.10	7.67373E-7	0.04	382250	gtex_brain_ba24

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.

No co-expressed genes in brain regions

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:0007420	brain development	ISS	Brain (GO term level: 7)	-
GO:0007413	axonal fasciculation	TAS	neuron, axon (GO term level: 13)	15106122
GO:0007411	axon guidance	TAS	axon (GO term level: 13)	15106122
GO:0031175	neurite development	ISS	neuron, axon, neurite, dendrite (GO term level: 10)	-
GO:0048167	regulation of synaptic plasticity	TAS	Synap (GO term level: 8)	15106122
GO:0007158	neuron adhesion	TAS	neuron (GO term level: 5)	14571131
GO:0045665	negative regulation of neuron differentiation	IMP	neuron (GO term level: 10)	14571131
GO:0007399	nervous system development	IMP	neurite (GO term level: 5)	15106122
GO:0007155	cell adhesion	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0030424	axon	NAS	neuron, axon, Neurotransmitter (GO term level: 6)	14571131
GO:0005576	extracellular region	IEA		-
GO:0005886	plasma membrane	NAS		15106122
GO:0031225	anchored to membrane	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
CHEMNITZ RESPONSE TO PROSTAGLANDIN E2 DN	391	222	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE FIMA UP	544	308	All SZGR 2.0 genes in this pathway
SABATES COLORECTAL ADENOMA DN	291	176	All SZGR 2.0 genes in this pathway
LASTOWSKA NEUROBLASTOMA COPY NUMBER DN	800	473	All SZGR 2.0 genes in this pathway
ROVERSI GLIOMA LOH REGIONS	44	30	All SZGR 2.0 genes in this pathway
GRADE COLON CANCER UP	871	505	All SZGR 2.0 genes in this pathway
TAYLOR METHYLATED IN ACUTE LYMPHOBLASTIC LEUKEMIA	77	52	All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA CD1 DN	45	30	All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3	590	403	All SZGR 2.0 genes in this pathway
PURBEY TARGETS OF CTBP1 AND SATB1 DN	180	116	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-129-5p	1590	1597	1A,m8	hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
miR-129-5p	1590	1597	1A,m8	hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
miR-142-5p	1168	1174	1A	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-145	107	113	1A	hsa-miR-145	GUCCAGUUUUCCCAGGAAUCCCUU
miR-148/152	208	215	1A,m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-155	785	791	m8	hsa-miR-155	UUAAUGCUAAUCGUGAUAGGGG
miR-181	913	920	1A,m8	hsa-miR-181a^brain	AACAUUCAACGCUGUCGGUGAGU
				hsa-miR-181b^SZ	AACAUUCAUUGCUGUCGGUGGG
				hsa-miR-181c^brain	AACAUUCAACCUGUCGGUGAGU
				hsa-miR-181d^brain	AACAUUCAUUGUUGUCGGUGGGUU
miR-200bc/429	1516	1522	m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-25/32/92/363/367	703	710	1A,m8	hsa-miR-25^brain	CAUUGCACUUGUCUCGGUCUGA
				hsa-miR-32	UAUUGCACAUUACUAAGUUGC
				hsa-miR-92	UAUUGCACUUGUCCCGGCCUG
				hsa-miR-367	AAUUGCACUUUAGCAAUGGUGA
				hsa-miR-92b^SZ	UAUUGCACUCGUCCCGGCCUC
miR-30-5p	246	252	1A	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-33	205	211	m8	hsa-miR-33	GUGCAUUGUAGUUGCAUUG
miR-33	205	211	m8	hsa-miR-33b	GUGCAUUGCUGUUGCAUUGCA
miR-362	463	469	m8	hsa-miR-362	AAUCCUUGGAACCUAGGUGUGAGU
miR-365	142	148	1A	hsa-miR-365	UAAUGCCCCUAAAAAUCCUUAU
miR-369-3p	276	282	1A	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	276	282	m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-376c	1560	1566	m8	hsa-miR-376c	AACAUAGAGGAAAUUCCACG
miR-410	278	284	1A	hsa-miR-410	AAUAUAACACAGAUGGCCUGU
miR-448	262	268	m8	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-9	237	243	m8	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA

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: CNTN4