SZGR2

Summary ?

GeneID	7414
Symbol	VCL
Synonyms	CMD1W\|CMH15\|HEL114\|MV\|MVCL
Description	vinculin
Reference	MIM:193065\|HGNC:HGNC:12665\|Ensembl:ENSG00000035403\|HPRD:01900\|Vega:OTTHUMG00000018498
Gene type	protein-coding
Map location	10q22.2
Pascal p-value	0.3
Sherlock p-value	3.539E-5
Fetal beta	0.282
eGene	Myers' cis & trans Meta
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
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.169

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs10128354	chr10	75470044	VCL	7414		0.12		cis
rs7901055	chr10	76415028	VCL	7414		0.14		cis

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	IDA		7816144
GO:0005198	structural molecule activity	IEA		-
GO:0016491	oxidoreductase activity	ISS		-
GO:0045294	alpha-catenin binding	IPI		9700171
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007155	cell adhesion	TAS		15501673
GO:0006928	cell motion	TAS		16130169
GO:0030336	negative regulation of cell migration	TAS		15494027
GO:0043297	apical junction assembly	IMP		9700171
GO:0030032	lamellipodium biogenesis	ISS		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005737	cytoplasm	IEA		-
GO:0005925	focal adhesion	ISS		-
GO:0005916	fascia adherens	IEA		-
GO:0005912	adherens junction	ISS		-
GO:0005911	cell-cell junction	ISS		-
GO:0005886	plasma membrane	IEA		-
GO:0015629	actin cytoskeleton	IEA		-
GO:0030055	cell-substrate junction	NAS		2116004
GO:0043234	protein complex	IDA		9700171
GO:0043034	costamere	ISS		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ABI2	ABI-2 \| ABI2B \| AIP-1 \| AblBP3 \| SSH3BP2 \| argBPIA \| argBPIB	abl interactor 2	Two-hybrid	BioGRID	16189514
ACTA1	ACTA \| ASMA \| CFTD \| CFTD1 \| CFTDM \| MPFD \| NEM1 \| NEM2 \| NEM3	actin, alpha 1, skeletal muscle	-	HPRD	7816144
BCAR1	CAS \| CAS1 \| CASS1 \| CRKAS \| P130Cas	breast cancer anti-estrogen resistance 1	Affinity Capture-Western	BioGRID	11577104
C19orf57	MGC11271 \| MGC149720	chromosome 19 open reading frame 57	Two-hybrid	BioGRID	16189514
CDH1	Arc-1 \| CD324 \| CDHE \| ECAD \| LCAM \| UVO	cadherin 1, type 1, E-cadherin (epithelial)	Affinity Capture-Western	BioGRID	9405455 \|9535896
CLTC	CHC \| CHC17 \| CLH-17 \| CLTCL2 \| Hc \| KIAA0034	clathrin, heavy chain (Hc)	-	HPRD,BioGRID	8276759
CORO2B	CLIPINC \| KIAA0925	coronin, actin binding protein, 2B	-	HPRD,BioGRID	10224093
CTNNA1	CAP102 \| FLJ36832	catenin (cadherin-associated protein), alpha 1, 102kDa	-	HPRD,BioGRID	9700171
CTNNB1	CTNNB \| DKFZp686D02253 \| FLJ25606 \| FLJ37923	catenin (cadherin-associated protein), beta 1, 88kDa	Affinity Capture-Western	BioGRID	9405455
GSN	DKFZp313L0718	gelsolin (amyloidosis, Finnish type)	-	HPRD,BioGRID	11577104
NRAP	-	nebulin-related anchoring protein	-	HPRD,BioGRID	10320340
PSME1	IFI5111 \| MGC8628 \| PA28A \| PA28alpha \| REGalpha	proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)	Two-hybrid	BioGRID	16169070
PXN	FLJ16691	paxillin	-	HPRD,BioGRID	9054445
PXN	FLJ16691	paxillin	-	HPRD	7525621 \|7534286\|9054445
RAVER1	KIAA1978	ribonucleoprotein, PTB-binding 1	-	HPRD	11724819
SELE	CD62E \| ELAM \| ELAM1 \| ESEL \| LECAM2	selectin E	-	HPRD	8609175
SORBS1	CAP \| DKFZp451C066 \| DKFZp586P1422 \| FLAF2 \| FLJ12406 \| KIAA1296 \| R85FL \| SH3D5 \| SH3P12 \| SORB1	sorbin and SH3 domain containing 1	-	HPRD,BioGRID	10085297
SORBS2	ARGBP2 \| FLJ93447 \| KIAA0777 \| PRO0618	sorbin and SH3 domain containing 2	-	HPRD,BioGRID	10521485
TGFB1I1	ARA55 \| HIC-5 \| HIC5 \| TSC-5	transforming growth factor beta 1 induced transcript 1	Reconstituted Complex	BioGRID	9858471
TRIP6	MGC10556 \| MGC10558 \| MGC29959 \| MGC3837 \| MGC4423 \| OIP1 \| ZRP-1	thyroid hormone receptor interactor 6	Two-hybrid	BioGRID	16189514
VASP	-	vasodilator-stimulated phosphoprotein	-	HPRD,BioGRID	10882740

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG FOCAL ADHESION	201	138	All SZGR 2.0 genes in this pathway
KEGG ADHERENS JUNCTION	75	53	All SZGR 2.0 genes in this pathway
KEGG LEUKOCYTE TRANSENDOTHELIAL MIGRATION	118	78	All SZGR 2.0 genes in this pathway
KEGG REGULATION OF ACTIN CYTOSKELETON	216	144	All SZGR 2.0 genes in this pathway
BIOCARTA CELL2CELL PATHWAY	14	11	All SZGR 2.0 genes in this pathway
BIOCARTA INTEGRIN PATHWAY	38	29	All SZGR 2.0 genes in this pathway
BIOCARTA RHO PATHWAY	32	23	All SZGR 2.0 genes in this pathway
PID RHOA PATHWAY	45	33	All SZGR 2.0 genes in this pathway
PID AVB3 INTEGRIN PATHWAY	75	53	All SZGR 2.0 genes in this pathway
PID ECADHERIN STABILIZATION PATHWAY	42	34	All SZGR 2.0 genes in this pathway
PID VEGFR1 2 PATHWAY	69	57	All SZGR 2.0 genes in this pathway
PID FAK PATHWAY	59	45	All SZGR 2.0 genes in this pathway
REACTOME RESPONSE TO ELEVATED PLATELET CYTOSOLIC CA2	89	56	All SZGR 2.0 genes in this pathway
REACTOME MUSCLE CONTRACTION	48	24	All SZGR 2.0 genes in this pathway
REACTOME SMOOTH MUSCLE CONTRACTION	25	14	All SZGR 2.0 genes in this pathway
REACTOME HEMOSTASIS	466	331	All SZGR 2.0 genes in this pathway
REACTOME PLATELET ACTIVATION SIGNALING AND AGGREGATION	208	138	All SZGR 2.0 genes in this pathway
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL UP	285	181	All SZGR 2.0 genes in this pathway
LIU PROSTATE CANCER DN	481	290	All SZGR 2.0 genes in this pathway
FULCHER INFLAMMATORY RESPONSE LECTIN VS LPS UP	579	346	All SZGR 2.0 genes in this pathway
CASORELLI ACUTE PROMYELOCYTIC LEUKEMIA DN	663	425	All SZGR 2.0 genes in this pathway
DIAZ CHRONIC MEYLOGENOUS LEUKEMIA UP	1382	904	All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL DN	460	312	All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION DN	329	219	All SZGR 2.0 genes in this pathway
NAGASHIMA NRG1 SIGNALING UP	176	123	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS UP	214	155	All SZGR 2.0 genes in this pathway
PROVENZANI METASTASIS UP	194	112	All SZGR 2.0 genes in this pathway
BERENJENO ROCK SIGNALING NOT VIA RHOA DN	48	34	All SZGR 2.0 genes in this pathway
BARIS THYROID CANCER DN	59	45	All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN	855	609	All SZGR 2.0 genes in this pathway
MARTORIATI MDM4 TARGETS FETAL LIVER DN	514	319	All SZGR 2.0 genes in this pathway
TOMLINS PROSTATE CANCER DN	40	33	All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN	848	527	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN	637	377	All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS	957	597	All SZGR 2.0 genes in this pathway
GUENTHER GROWTH SPHERICAL VS ADHERENT DN	26	19	All SZGR 2.0 genes in this pathway
BENPORATH CYCLING GENES	648	385	All SZGR 2.0 genes in this pathway
LU IL4 SIGNALING	94	56	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	All SZGR 2.0 genes in this pathway
LEI MYB TARGETS	318	215	All SZGR 2.0 genes in this pathway
HASLINGER B CLL WITH CHROMOSOME 12 TRISOMY	24	12	All SZGR 2.0 genes in this pathway
TAVOR CEBPA TARGETS UP	48	36	All SZGR 2.0 genes in this pathway
YAGI AML FAB MARKERS	191	131	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 10	30	17	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN	830	547	All SZGR 2.0 genes in this pathway
WU HBX TARGETS 3 UP	18	11	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR DN	101	70	All SZGR 2.0 genes in this pathway
CHEN LVAD SUPPORT OF FAILING HEART UP	103	69	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 8	86	57	All SZGR 2.0 genes in this pathway
ZHONG SECRETOME OF LUNG CANCER AND ENDOTHELIUM	66	47	All SZGR 2.0 genes in this pathway
ZHONG SECRETOME OF LUNG CANCER AND FIBROBLAST	132	93	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS UP	317	208	All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS PTEN DN	353	226	All SZGR 2.0 genes in this pathway
IZADPANAH STEM CELL ADIPOSE VS BONE DN	108	68	All SZGR 2.0 genes in this pathway
CHUNG BLISTER CYTOTOXICITY DN	44	29	All SZGR 2.0 genes in this pathway
WANG TUMOR INVASIVENESS UP	374	247	All SZGR 2.0 genes in this pathway
LEE LIVER CANCER SURVIVAL DN	175	103	All SZGR 2.0 genes in this pathway
DAVIES MULTIPLE MYELOMA VS MGUS DN	28	18	All SZGR 2.0 genes in this pathway
BOHN PRIMARY IMMUNODEFICIENCY SYNDROM DN	40	31	All SZGR 2.0 genes in this pathway
GOLDRATH ANTIGEN RESPONSE	346	192	All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS DN	435	289	All SZGR 2.0 genes in this pathway
TAVAZOIE METASTASIS	108	68	All SZGR 2.0 genes in this pathway
ZHAN EARLY DIFFERENTIATION GENES DN	42	29	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS DN	457	302	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS DN	668	419	All SZGR 2.0 genes in this pathway
ROME INSULIN TARGETS IN MUSCLE UP	442	263	All SZGR 2.0 genes in this pathway
VALK AML CLUSTER 12	30	20	All SZGR 2.0 genes in this pathway
FONTAINE PAPILLARY THYROID CARCINOMA UP	66	38	All SZGR 2.0 genes in this pathway
FOURNIER ACINAR DEVELOPMENT LATE 2	277	172	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 14	143	86	All SZGR 2.0 genes in this pathway
SASSON RESPONSE TO GONADOTROPHINS DN	87	66	All SZGR 2.0 genes in this pathway
SASSON RESPONSE TO FORSKOLIN DN	88	68	All SZGR 2.0 genes in this pathway
WHITFIELD CELL CYCLE M G1	148	95	All SZGR 2.0 genes in this pathway
RAGHAVACHARI PLATELET SPECIFIC GENES	70	46	All SZGR 2.0 genes in this pathway
LU EZH2 TARGETS DN	414	237	All SZGR 2.0 genes in this pathway
PASINI SUZ12 TARGETS DN	315	215	All SZGR 2.0 genes in this pathway
BAKKER FOXO3 TARGETS UP	61	41	All SZGR 2.0 genes in this pathway
KOINUMA TARGETS OF SMAD2 OR SMAD3	824	528	All SZGR 2.0 genes in this pathway
ALFANO MYC TARGETS	239	156	All SZGR 2.0 genes in this pathway
ZWANG CLASS 1 TRANSIENTLY INDUCED BY EGF	516	308	All SZGR 2.0 genes in this pathway
CHEMELLO SOLEUS VS EDL MYOFIBERS DN	19	10	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-103/107	954	961	1A,m8	hsa-miR-103^brain	AGCAGCAUUGUACAGGGCUAUGA
miR-103/107	954	961	1A,m8	hsa-miR-107^brain	AGCAGCAUUGUACAGGGCUAUCA
miR-182	1678	1684	1A	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-29	792	798	m8	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
miR-34/449	882	888	m8	hsa-miR-34a^brain	UGGCAGUGUCUUAGCUGGUUGUU
				hsa-miR-34c	AGGCAGUGUAGUUAGCUGAUUGC
				hsa-miR-449	UGGCAGUGUAUUGUUAGCUGGU
				hsa-miR-449b	AGGCAGUGUAUUGUUAGCUGGC
miR-485-3p	1667	1673	1A	hsa-miR-485-3p	GUCAUACACGGCUCUCCUCUCU
miR-9	1680	1686	1A	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-96	1678	1684	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: VCL