SZGR2

Summary ?

GeneID	6331
Symbol	SCN5A
Synonyms	CDCD2\|CMD1E\|CMPD2\|HB1\|HB2\|HBBD\|HH1\|ICCD\|IVF\|LQT3\|Nav1.5\|PFHB1\|SSS1\|VF1
Description	sodium voltage-gated channel alpha subunit 5
Reference	MIM:600163\|HGNC:HGNC:10593\|Ensembl:ENSG00000183873\|HPRD:02543\|Vega:OTTHUMG00000156166
Gene type	protein-coding
Map location	3p21
Pascal p-value	5.935E-6
Fetal beta	-0.099
DMG	1 (# studies)
eGene	Meta
Support	EXCITABILITY

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).	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_I	Genome scan meta-analysis	Psr: 0.006
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0369

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg12926589	3	38691364	SCN5A	1.83E-5	-0.284	0.016	DMG:Wockner_2014

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:0005244	voltage-gated ion channel activity	IEA		-
GO:0005248	voltage-gated sodium channel activity	IEA		-
GO:0005248	voltage-gated sodium channel activity	TAS		7651517
GO:0005216	ion channel activity	IEA		-
GO:0031402	sodium ion binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0008015	blood circulation	NAS		7889574
GO:0008016	regulation of heart contraction	TAS		9521325
GO:0006814	sodium ion transport	IEA		-
GO:0006814	sodium ion transport	TAS		7651517
GO:0006811	ion transport	IEA		-
GO:0006936	muscle contraction	TAS		7889574
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0001518	voltage-gated sodium channel complex	IEA		-
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 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 L1CAM INTERACTIONS	86	62	All SZGR 2.0 genes in this pathway
REACTOME INTERACTION BETWEEN L1 AND ANKYRINS	23	19	All SZGR 2.0 genes in this pathway
LIN APC TARGETS	77	55	All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY NO BLOOD UP	222	139	All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY UP	487	303	All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3	1069	729	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 AND H3K27ME3	349	234	All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3	435	318	All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K27ME3	341	243	All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3	590	403	All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP	857	456	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
let-7/98	1614	1620	m8	hsa-let-7a^brain	UGAGGUAGUAGGUUGUAUAGUU
				hsa-let-7b^brain	UGAGGUAGUAGGUUGUGUGGUU
				hsa-let-7c^brain	UGAGGUAGUAGGUUGUAUGGUU
				hsa-let-7d^brain	AGAGGUAGUAGGUUGCAUAGU
				hsa-let-7e^brain	UGAGGUAGGAGGUUGUAUAGU
				hsa-let-7f^brain	UGAGGUAGUAGAUUGUAUAGUU
				hsa-miR-98^brain	UGAGGUAGUAAGUUGUAUUGUU
				hsa-let-7g^SZ	UGAGGUAGUAGUUUGUACAGU
				hsa-let-7i^brain	UGAGGUAGUAGUUUGUGCUGU
miR-125/351	1364	1370	1A	hsa-miR-125b^brain	UCCCUGAGACCCUAACUUGUGA
miR-125/351	1364	1370	1A	hsa-miR-125a^brain	UCCCUGAGACCCUUUAACCUGUG
miR-153	1434	1440	1A	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-200bc/429	1683	1689	1A	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
				hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-214	1412	1418	1A	hsa-miR-214^brain	ACAGCAGGCACAGACAGGCAG
miR-219	1417	1423	m8	hsa-miR-219^brain	UGAUUGUCCAAACGCAAUUCU
miR-369-3p	326	332	1A	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	326	332	m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-378*	1384	1390	1A	hsa-miR-422b	CUGGACUUGGAGUCAGAAGGCC
miR-378*	1384	1390	1A	hsa-miR-422a	CUGGACUUAGGGUCAGAAGGCC
miR-448	1433	1440	1A,m8	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU

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: SCN5A