SZGR2

Summary ?

GeneID	57731
Symbol	SPTBN4
Synonyms	QV\|SPNB4\|SPTBN3
Description	spectrin beta, non-erythrocytic 4
Reference	MIM:606214\|HGNC:HGNC:14896\|Ensembl:ENSG00000160460\|HPRD:09372\|Vega:OTTHUMG00000182592
Gene type	protein-coding
Map location	19q13.13
Pascal p-value	0.415
Sherlock p-value	0.495
Fetal beta	-0.887
DMG	1 (# studies)
eGene	Cerebellar Hemisphere Cerebellum
Support	G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-CONSENSUS 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).	1

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg08871964	19	41025863	SPTBN4	1.608E-4	0.345	0.032	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:0003779	actin binding	TAS		11086001
GO:0005515	protein binding	IPI		12812986
GO:0005200	structural constituent of cytoskeleton	TAS		11294830
GO:0030506	ankyrin binding	IDA		11294830
GO:0030506	ankyrin binding	ISS		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007016	cytoskeletal anchoring at plasma membrane	TAS		11086001
GO:0016192	vesicle-mediated transport	TAS		11294830
GO:0051016	barbed-end actin filament capping	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005856	cytoskeleton	IEA		-
GO:0005737	cytoplasm	IDA		11294830
GO:0005737	cytoplasm	ISS		-
GO:0008091	spectrin	IDA		11086001
GO:0008091	spectrin	ISS		-
GO:0016605	PML body	IDA		11294830
GO:0016605	PML body	ISS		-
GO:0016363	nuclear matrix	IDA		11294830
GO:0016363	nuclear matrix	ISS		-

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 NCAM SIGNALING FOR NEURITE OUT GROWTH	64	49	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
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
AFFAR YY1 TARGETS DN	234	137	All SZGR 2.0 genes in this pathway
URS ADIPOCYTE DIFFERENTIATION UP	74	51	All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN UP	439	257	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3 UNMETHYLATED	536	296	All SZGR 2.0 genes in this pathway
ASGHARZADEH NEUROBLASTOMA POOR SURVIVAL DN	46	30	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	468	474	1A	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-103/107	481	487	m8	hsa-miR-103^brain	AGCAGCAUUGUACAGGGCUAUGA
miR-103/107	481	487	m8	hsa-miR-107^brain	AGCAGCAUUGUACAGGGCUAUCA
miR-128	47	53	m8	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
miR-128	47	53	m8	hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-135	190	196	1A	hsa-miR-135a	UAUGGCUUUUUAUUCCUAUGUGA
miR-135	190	196	1A	hsa-miR-135b	UAUGGCUUUUCAUUCCUAUGUG
miR-153	253	259	1A	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-224	569	575	1A	hsa-miR-224	CAAGUCACUAGUGGUUCCGUUUA
miR-24	295	301	1A	hsa-miR-24^SZ	UGGCUCAGUUCAGCAGGAACAG
miR-25/32/92/363/367	255	261	1A	hsa-miR-25^brain	CAUUGCACUUGUCUCGGUCUGA
				hsa-miR-32	UAUUGCACAUUACUAAGUUGC
				hsa-miR-92	UAUUGCACUUGUCCCGGCCUG
				hsa-miR-367	AAUUGCACUUUAGCAAUGGUGA
				hsa-miR-92b^SZ	UAUUGCACUCGUCCCGGCCUC
miR-29	428	434	1A	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
miR-330	884	890	1A	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA
miR-448	253	259	1A	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: SPTBN4