SZGR2

Summary ?

GeneID	253559
Symbol	CADM2
Synonyms	IGSF4D\|NECL3\|Necl-3\|SynCAM 2\|synCAM2
Description	cell adhesion molecule 2
Reference	MIM:609938\|HGNC:HGNC:29849\|Ensembl:ENSG00000175161\|HPRD:11046\|Vega:OTTHUMG00000158990
Gene type	protein-coding
Map location	3p12.1
Pascal p-value	0.146
DMG	1 (# studies)
eGene	Cortex Myers' cis & trans
Support	CELL ADHESION AND TRANSSYNAPTIC SIGNALING

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
DMG:Wockner_2014	Genome-wide DNA methylation analysis	This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24).	1
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_IIE	Genome scan meta-analysis (European-ancestry samples)	Psr: 0.04359
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.04047
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg04416247	3	85213671	CADM2	2.455E-4	0.511	0.037	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs16894557	chr6	28999825	CADM2	253559		0.18		trans

Section II. Transcriptome annotation

General gene expression (GTEx)

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

Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
REACTOME CELL CELL COMMUNICATION	120	77	All SZGR 2.0 genes in this pathway
REACTOME ADHERENS JUNCTIONS INTERACTIONS	27	20	All SZGR 2.0 genes in this pathway
REACTOME CELL CELL JUNCTION ORGANIZATION	56	31	All SZGR 2.0 genes in this pathway
REACTOME CELL JUNCTION ORGANIZATION	78	43	All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS DN	120	81	All SZGR 2.0 genes in this pathway
ZHENG GLIOBLASTOMA PLASTICITY UP	250	168	All SZGR 2.0 genes in this pathway
YAUCH HEDGEHOG SIGNALING PARACRINE UP	149	85	All SZGR 2.0 genes in this pathway
YAUCH HEDGEHOG SIGNALING PARACRINE DN	264	159	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	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-101	176	182	1A	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-124.1	261	267	1A	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-140	1180	1186	1A	hsa-miR-140^brain	AGUGGUUUUACCCUAUGGUAG
miR-141/200a	1974	1980	1A	hsa-miR-141	UAACACUGUCUGGUAAAGAUGG
miR-141/200a	1974	1980	1A	hsa-miR-200a	UAACACUGUCUGGUAACGAUGU
miR-143	277	283	m8	hsa-miR-143^brain	UGAGAUGAAGCACUGUAGCUCA
miR-144	176	182	1A	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-153	1345	1351	m8	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-17-5p/20/93.mr/106/519.d	1929	1935	m8	hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
miR-182	1276	1283	1A,m8	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-186	166	173	1A,m8	hsa-miR-186	CAAAGAAUUCUCCUUUUGGGCUU
miR-186	166	173	1A,m8	hsa-miR-186	CAAAGAAUUCUCCUUUUGGGCUU
miR-203.1	199	205	m8	hsa-miR-203	UGAAAUGUUUAGGACCACUAG
miR-21	1140	1146	1A	hsa-miR-21^brain	UAGCUUAUCAGACUGAUGUUGA
miR-21	1140	1146	1A	hsa-miR-590	GAGCUUAUUCAUAAAAGUGCAG
miR-218	1111	1118	1A,m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-30-5p	457	463	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-338	39	46	1A,m8	hsa-miR-338^brain	UCCAGCAUCAGUGAUUUUGUUGA
miR-34b	816	822	1A	hsa-miR-34b	UAGGCAGUGUCAUUAGCUGAUUG
miR-369-3p	1006	1012	1A	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	1006	1013	1A,m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-485-5p	1159	1166	1A,m8	hsa-miR-485-5p	AGAGGCUGGCCGUGAUGAAUUC
miR-495	1096	1102	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-543	565	571	m8	hsa-miR-543	AAACAUUCGCGGUGCACUUCU
				hsa-miR-543	AAACAUUCGCGGUGCACUUCU
				hsa-miR-543	AAACAUUCGCGGUGCACUUCU
miR-93.hd/291-3p/294/295/302/372/373/520	1928	1934	m8	hsa-miR-93^brain	AAAGUGCUGUUCGUGCAGGUAG
				hsa-miR-302a	UAAGUGCUUCCAUGUUUUGGUGA
				hsa-miR-302b	UAAGUGCUUCCAUGUUUUAGUAG
				hsa-miR-302c	UAAGUGCUUCCAUGUUUCAGUGG
				hsa-miR-302d	UAAGUGCUUCCAUGUUUGAGUGU
				hsa-miR-372	AAAGUGCUGCGACAUUUGAGCGU
				hsa-miR-373	GAAGUGCUUCGAUUUUGGGGUGU
				hsa-miR-520e	AAAGUGCUUCCUUUUUGAGGG
				hsa-miR-520a	AAAGUGCUUCCCUUUGGACUGU
				hsa-miR-520b	AAAGUGCUUCCUUUUAGAGGG
				hsa-miR-520c	AAAGUGCUUCCUUUUAGAGGGUU
				hsa-miR-520d	AAAGUGCUUCUCUUUGGUGGGUU
miR-96	1277	1283	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: CADM2