SZGR2

Summary ?

GeneID	6323
Symbol	SCN1A
Synonyms	EIEE6\|FEB3\|FEB3A\|FHM3\|GEFSP2\|HBSCI\|NAC1\|Nav1.1\|SCN1\|SMEI
Description	sodium voltage-gated channel alpha subunit 1
Reference	MIM:182389\|HGNC:HGNC:10585\|Ensembl:ENSG00000144285\|HPRD:01669\|Vega:OTTHUMG00000044173
Gene type	protein-coding
Map location	2q24.3
Pascal p-value	6.973E-4
Sherlock p-value	0.091
Fetal beta	-1.752
eGene	Cortex Nucleus accumbens basal ganglia Myers' cis & trans
Support	EXCITABILITY

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
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_IIA	Genome scan meta-analysis (All samples)	Psr: 0.02395
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs1523756	chr3	77596678	SCN1A	6323	0.12	trans
rs1324669	chr13	107872446	SCN1A	6323	0.03	trans
rs17686192	chr17	60992355	SCN1A	6323	0.01	trans
rs17759603	chr17	60999051	SCN1A	6323	0.04	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:0005244	voltage-gated ion channel activity	IEA		-
GO:0005248	voltage-gated sodium channel activity	NAS		10742094
GO:0031402	sodium ion binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0006814	sodium ion transport	NAS		10742094
GO:0006811	ion transport	IEA		-
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	NAS		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
CHESLER BRAIN HIGHEST EXPRESSION	40	29	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
MCCLUNG DELTA FOSB TARGETS 2WK	48	36	All SZGR 2.0 genes in this pathway
RIGGINS TAMOXIFEN RESISTANCE DN	220	147	All SZGR 2.0 genes in this pathway
MIKKELSEN MEF ICP WITH H3K27ME3	206	108	All SZGR 2.0 genes in this pathway
MIKKELSEN ES ICP WITH H3K4ME3	718	401	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	1426	1432	1A	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-132/212	101	107	m8	hsa-miR-212^SZ	UAACAGUCUCCAGUCACGGCC
miR-132/212	101	107	m8	hsa-miR-132^brain	UAACAGUCUACAGCCAUGGUCG
miR-137	1271	1278	1A,m8	hsa-miR-137	UAUUGCUUAAGAAUACGCGUAG
miR-142-5p	882	888	1A	hsa-miR-142-5p	CAUAAAGUAGAAAGCACUAC
miR-144	1425	1432	1A,m8	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-149	1343	1349	1A	hsa-miR-149^brain	UCUGGCUCCGUGUCUUCACUCC
miR-17-5p/20/93.mr/106/519.d	326	332	1A	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
				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	92	98	1A	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-200bc/429	1036	1042	m8	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-214	233	239	1A	hsa-miR-214^brain	ACAGCAGGCACAGACAGGCAG
miR-218	1031	1037	m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-223	97	103	m8	hsa-miR-223	UGUCAGUUUGUCAAAUACCCC
miR-27	44	50	1A	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	44	50	1A	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-30-5p	34	41	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
miR-34/449	365	371	1A	hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
miR-363	751	757	1A	hsa-miR-363	AUUGCACGGUAUCCAUCUGUAA
miR-363	751	757	1A	hsa-miR-363	AUUGCACGGUAUCCAUCUGUAA
miR-452	1013	1019	1A	hsa-miR-452	UGUUUGCAGAGGAAACUGAGAC
miR-452	1013	1019	1A	hsa-miR-452	UGUUUGCAGAGGAAACUGAGAC
miR-493-5p	1463	1469	m8	hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU
miR-500	749	756	1A,m8	hsa-miR-500	AUGCACCUGGGCAAGGAUUCUG
miR-96	92	98	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: SCN1A