SZGR2

Summary ?

GeneID	785
Symbol	CACNB4
Synonyms	CAB4\|CACNLB4\|EA5\|EIG9\|EJM\|EJM4\|EJM6
Description	calcium voltage-gated channel auxiliary subunit beta 4
Reference	MIM:601949\|HGNC:HGNC:1404\|Ensembl:ENSG00000182389\|HPRD:09057\|Vega:OTTHUMG00000155091
Gene type	protein-coding
Map location	2q23.3
Pascal p-value	0.058
Sherlock p-value	0.984
Fetal beta	-1.242
DMG	1 (# studies)
eGene	Myers' cis & trans
Support	CANABINOID DOPAMINE EXCITABILITY METABOTROPIC GLUTAMATE RECEPTOR SEROTONIN CompositeSet

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
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).	2
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.02395

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg05105477	2	152906698	CACNB4	2.2E-5	0.606	0.017	DMG:Wockner_2014
cg22159341	2	152893963	CACNB4	4.786E-4	0.7	0.046	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs16829545	chr2	151977407	CACNB4	785	0	cis
rs12463708	chr2	149073943	CACNB4	785	0.09	trans
rs16829545	chr2	151977407	CACNB4	785	0.17	trans
rs6813178	chr4	71575238	CACNB4	785	0.11	trans
rs6032295	chr20	44178138	CACNB4	785	0.01	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.

No co-expressed genes in brain regions

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005509	calcium ion binding	IEA		-
GO:0005515	protein binding	IPI		16525042
GO:0005244	voltage-gated ion channel activity	IEA		-
GO:0005245	voltage-gated calcium channel activity	IDA		16525042
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006816	calcium ion transport	IEA		-
GO:0006811	ion transport	IEA		-
GO:0051925	regulation of calcium ion transport via voltage-gated calcium channel	IDA		11880487
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005829	cytosol	EXP		8825650
GO:0009898	internal side of plasma membrane	TAS		16385006
GO:0005891	voltage-gated calcium channel complex	IDA		16525042

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG MAPK SIGNALING PATHWAY	267	205	All SZGR 2.0 genes in this pathway
KEGG CARDIAC MUSCLE CONTRACTION	80	51	All SZGR 2.0 genes in this pathway
KEGG HYPERTROPHIC CARDIOMYOPATHY HCM	85	65	All SZGR 2.0 genes in this pathway
KEGG ARRHYTHMOGENIC RIGHT VENTRICULAR CARDIOMYOPATHY ARVC	76	59	All SZGR 2.0 genes in this pathway
KEGG DILATED CARDIOMYOPATHY	92	68	All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY	396	292	All SZGR 2.0 genes in this pathway
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES	186	155	All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM	279	221	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
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
CHEBOTAEV GR TARGETS DN	120	73	All SZGR 2.0 genes in this pathway
ODONNELL METASTASIS UP	82	58	All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS	1038	678	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
SAKAI TUMOR INFILTRATING MONOCYTES UP	27	19	All SZGR 2.0 genes in this pathway
MATSUDA NATURAL KILLER DIFFERENTIATION	475	313	All SZGR 2.0 genes in this pathway
ZHENG BOUND BY FOXP3	491	310	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP	489	314	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	614	620	1A	hsa-miR-129^brain	CUUUUUGCGGUCUGGGCUUGC
miR-129-5p	614	620	1A	hsa-miR-129-5p	CUUUUUGCGGUCUGGGCUUGCU
miR-132/212	736	742	1A	hsa-miR-212^SZ	UAACAGUCUCCAGUCACGGCC
miR-132/212	736	742	1A	hsa-miR-132^brain	UAACAGUCUACAGCCAUGGUCG
miR-151	168	175	1A,m8	hsa-miR-151^brain	ACUAGACUGAAGCUCCUUGAGG
miR-182	611	617	1A	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-183	38	44	1A	hsa-miR-183	UAUGGCACUGGUAGAAUUCACUG
miR-299-5p	360	366	1A	hsa-miR-299-5p	UGGUUUACCGUCCCACAUACAU
miR-338	509	515	1A	hsa-miR-338^brain	UCCAGCAUCAGUGAUUUUGUUGA
miR-455	294	301	1A,m8	hsa-miR-455	UAUGUGCCUUUGGACUACAUCG
miR-96	610	617	1A,m8	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: CACNB4