SZGR2

Summary ?

GeneID	3675
Symbol	ITGA3
Synonyms	CD49C\|FRP-2\|GAP-B3\|GAPB3\|ILNEB\|MSK18\|VCA-2\|VL3A\|VLA3a
Description	integrin subunit alpha 3
Reference	MIM:605025\|HGNC:HGNC:6139\|Ensembl:ENSG00000005884\|HPRD:05431\|Vega:OTTHUMG00000161890
Gene type	protein-coding
Map location	17q21.33
Pascal p-value	0.581
Sherlock p-value	0.127
Fetal beta	-0.374
eGene	Cerebellar Hemisphere Cerebellum Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DNM:Gulsuner_2013	Whole Exome Sequencing analysis	155 DNMs identified by exome sequencing of quads or trios of schizophrenia individuals and their parents.
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 2

Section I. Genetics and epigenetics annotation

DNM table

Gene	Chromosome	Position	Ref	Alt	Transcript	AA change	Mutation type	Sift	CG46	Trait	Study
ITGA3	chr17	48154453	C	G	NM_002204 NM_005501	p.680P>A p.680P>A	missense missense			Schizophrenia	DNM:Gulsuner_2013

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs1570589	chr9	116874354	ITGA3	3675		0.15		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.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
ATHL1	0.72	0.78
ADAM33	0.72	0.77
ACADVL	0.72	0.73
MYO15B	0.69	0.81
CATSPER2	0.69	0.70
DNAH1	0.69	0.77
AL117190.3	0.68	0.81
DCDC2B	0.67	0.69
CES8	0.67	0.64
MALAT1	0.65	0.69

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MOBKL3	-0.47	-0.56
HSPA13	-0.45	-0.49
DNAJA1	-0.44	-0.51
METTL9	-0.44	-0.50
ARF4	-0.44	-0.48
SERP1	-0.44	-0.50
UBE2N	-0.44	-0.56
RBMXL1	-0.44	-0.45
MARCKS	-0.44	-0.43
IPMK	-0.44	-0.47

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004872	receptor activity	IEA		-
GO:0005509	calcium ion binding	IEA		-
GO:0005515	protein binding	IEA		-
GO:0005515	protein binding	IPI		14676841
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0001764	neuron migration	IEA	neuron (GO term level: 8)	-
GO:0007160	cell-matrix adhesion	TAS		1655803
GO:0007155	cell adhesion	IEA		-
GO:0007229	integrin-mediated signaling pathway	IEA		-
GO:0007613	memory	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0019717	synaptosome	IEA	Synap, Brain (GO term level: 7)	-
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	IEA		-
GO:0005886	plasma membrane	IEA		-
GO:0008305	integrin complex	IEA		-
GO:0008305	integrin complex	TAS		1655803
GO:0016323	basolateral plasma membrane	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
BIN1	AMPH2 \| AMPHL \| DKFZp547F068 \| MGC10367 \| SH3P9	bridging integrator 1	-	HPRD,BioGRID	10094488
CALR	CRT \| FLJ26680 \| RO \| SSA \| cC1qR	calreticulin	-	HPRD	8006073\|11327697
CALR	CRT \| FLJ26680 \| RO \| SSA \| cC1qR	calreticulin	-	HPRD	11327697
CD151	GP27 \| MER2 \| PETA-3 \| RAPH \| SFA1 \| TSPAN24	CD151 molecule (Raph blood group)	Reconstituted Complex	BioGRID	10734060
CD82	4F9 \| C33 \| GR15 \| IA4 \| KAI1 \| R2 \| SAR2 \| ST6 \| TSPAN27	CD82 molecule	-	HPRD	8757325
CD9	5H9 \| BA2 \| BTCC-1 \| DRAP-27 \| GIG2 \| MIC3 \| MRP-1 \| P24 \| TSPAN29	CD9 molecule	-	HPRD,BioGRID	10065872 \|10694273
FHL2	AAG11 \| DRAL \| SLIM3	four and a half LIM domains 2	-	HPRD,BioGRID	10906324
FN1	CIG \| DKFZp686F10164 \| DKFZp686H0342 \| DKFZp686I1370 \| DKFZp686O13149 \| ED-B \| FINC \| FN \| FNZ \| GFND \| GFND2 \| LETS \| MSF	fibronectin 1	-	HPRD	9733622
ITGB1	CD29 \| FNRB \| GPIIA \| MDF2 \| MSK12 \| VLA-BETA \| VLAB	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	VLA3-alpha3 interacts with VLA3-beta.	BIND	1690718 \|1693624 \|3546305
ITGB1	CD29 \| FNRB \| GPIIA \| MDF2 \| MSK12 \| VLA-BETA \| VLAB	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	VLA3-alpha3 interacts with VLA3-beta	BIND	3546305
ITGB1	CD29 \| FNRB \| GPIIA \| MDF2 \| MSK12 \| VLA-BETA \| VLAB	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	-	HPRD,BioGRID	15254262
LAMA3	BM600 \| E170 \| LAMNA \| LOCS \| lama3a	laminin, alpha 3	-	HPRD	9950675 \|11278628
LGALS8	Gal-8 \| PCTA-1 \| PCTA1 \| Po66-CBP	lectin, galactoside-binding, soluble, 8	-	HPRD,BioGRID	10852818
RABIF	MSS4 \| RASGFR3 \| RASGRF3	RAB interacting factor	-	HPRD,BioGRID	10094488
TIMP2	CSC-21K	TIMP metallopeptidase inhibitor 2	TIMP2 interacts with ITGA3 (alpha3).	BIND	12887919
TSPAN4	NAG-2 \| NAG2 \| TETRASPAN \| TM4SF7 \| TSPAN-4	tetraspanin 4	-	HPRD,BioGRID	9360996 \|10734060

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 ECM RECEPTOR INTERACTION	84	53	All SZGR 2.0 genes in this pathway
KEGG HEMATOPOIETIC CELL LINEAGE	88	60	All SZGR 2.0 genes in this pathway
KEGG REGULATION OF ACTIN CYTOSKELETON	216	144	All SZGR 2.0 genes in this pathway
KEGG PATHWAYS IN CANCER	328	259	All SZGR 2.0 genes in this pathway
KEGG SMALL CELL LUNG CANCER	84	67	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
ST INTEGRIN SIGNALING PATHWAY	82	62	All SZGR 2.0 genes in this pathway
PID INTEGRIN1 PATHWAY	66	44	All SZGR 2.0 genes in this pathway
PID INTEGRIN CS PATHWAY	26	16	All SZGR 2.0 genes in this pathway
PID ARF6 TRAFFICKING PATHWAY	49	34	All SZGR 2.0 genes in this pathway
PID REELIN PATHWAY	29	29	All SZGR 2.0 genes in this pathway
PID CXCR4 PATHWAY	102	78	All SZGR 2.0 genes in this pathway
PID UPA UPAR PATHWAY	42	30	All SZGR 2.0 genes in this pathway
PID IL23 PATHWAY	37	30	All SZGR 2.0 genes in this pathway
PID DELTA NP63 PATHWAY	47	34	All SZGR 2.0 genes in this pathway
PID TAP63 PATHWAY	54	40	All SZGR 2.0 genes in this pathway
REACTOME CELL SURFACE INTERACTIONS AT THE VASCULAR WALL	91	65	All SZGR 2.0 genes in this pathway
REACTOME BASIGIN INTERACTIONS	30	23	All SZGR 2.0 genes in this pathway
REACTOME INTEGRIN CELL SURFACE INTERACTIONS	79	48	All SZGR 2.0 genes in this pathway
REACTOME HEMOSTASIS	466	331	All SZGR 2.0 genes in this pathway
CORRE MULTIPLE MYELOMA UP	74	45	All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS BASAL DN	455	304	All SZGR 2.0 genes in this pathway
RODRIGUES NTN1 TARGETS DN	158	102	All SZGR 2.0 genes in this pathway
ENK UV RESPONSE EPIDERMIS UP	293	179	All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP	443	294	All SZGR 2.0 genes in this pathway
WANG BARRETTS ESOPHAGUS UP	51	27	All SZGR 2.0 genes in this pathway
BEGUM TARGETS OF PAX3 FOXO1 FUSION DN	45	34	All SZGR 2.0 genes in this pathway
MAHADEVAN GIST MORPHOLOGICAL SWITCH	15	11	All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER UP	358	245	All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN	848	527	All SZGR 2.0 genes in this pathway
COLIN PILOCYTIC ASTROCYTOMA VS GLIOBLASTOMA UP	35	32	All SZGR 2.0 genes in this pathway
NIKOLSKY BREAST CANCER 17Q21 Q25 AMPLICON	335	181	All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS PLASMABLAST UP	398	262	All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS DN	366	238	All SZGR 2.0 genes in this pathway
KANG IMMORTALIZED BY TERT UP	89	61	All SZGR 2.0 genes in this pathway
CROMER METASTASIS DN	81	58	All SZGR 2.0 genes in this pathway
SESTO RESPONSE TO UV C8	72	56	All SZGR 2.0 genes in this pathway
HENDRICKS SMARCA4 TARGETS UP	56	35	All SZGR 2.0 genes in this pathway
CHIBA RESPONSE TO TSA UP	52	33	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 14HR DN	298	200	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 20HR DN	101	70	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL	254	164	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 48HR DN	504	323	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 8HR DN	47	31	All SZGR 2.0 genes in this pathway
VERRECCHIA RESPONSE TO TGFB1 C1	19	15	All SZGR 2.0 genes in this pathway
VERRECCHIA EARLY RESPONSE TO TGFB1	58	43	All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN WITHOUT MGMT 48HR DN	32	25	All SZGR 2.0 genes in this pathway
BAELDE DIABETIC NEPHROPATHY DN	434	302	All SZGR 2.0 genes in this pathway
BANDRES RESPONSE TO CARMUSTIN MGMT 48HR DN	161	105	All SZGR 2.0 genes in this pathway
HELLEBREKERS SILENCED DURING TUMOR ANGIOGENESIS	80	56	All SZGR 2.0 genes in this pathway
GU PDEF TARGETS UP	71	49	All SZGR 2.0 genes in this pathway
AGUIRRE PANCREATIC CANCER COPY NUMBER UP	298	174	All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS UP	395	249	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
POOLA INVASIVE BREAST CANCER DN	134	83	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
FOURNIER ACINAR DEVELOPMENT LATE 2	277	172	All SZGR 2.0 genes in this pathway
MIKKELSEN NPC HCP WITH H3K4ME3 AND H3K27ME3	210	148	All SZGR 2.0 genes in this pathway
NAKAMURA ADIPOGENESIS EARLY DN	38	27	All SZGR 2.0 genes in this pathway
NAKAMURA ADIPOGENESIS LATE DN	38	25	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
BROWNE HCMV INFECTION 2HR DN	49	33	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 UP	430	288	All SZGR 2.0 genes in this pathway
PASINI SUZ12 TARGETS DN	315	215	All SZGR 2.0 genes in this pathway
VANDESLUIS COMMD1 TARGETS GROUP 3 UP	89	50	All SZGR 2.0 genes in this pathway
WIEDERSCHAIN TARGETS OF BMI1 AND PCGF2	57	39	All SZGR 2.0 genes in this pathway
FEVR CTNNB1 TARGETS UP	682	433	All SZGR 2.0 genes in this pathway
KOINUMA TARGETS OF SMAD2 OR SMAD3	824	528	All SZGR 2.0 genes in this pathway
KATSANOU ELAVL1 TARGETS UP	169	105	All SZGR 2.0 genes in this pathway
PEDERSEN METASTASIS BY ERBB2 ISOFORM 7	403	240	All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A	770	480	All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN	784	464	All SZGR 2.0 genes in this pathway
FOSTER KDM1A TARGETS DN	211	119	All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM B	517	302	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-124/506	1160	1166	m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	1160	1166	m8	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-181	883	890	1A,m8	hsa-miR-181a^brain	AACAUUCAACGCUGUCGGUGAGU
				hsa-miR-181b^SZ	AACAUUCAUUGCUGUCGGUGGG
				hsa-miR-181c^brain	AACAUUCAACCUGUCGGUGAGU
				hsa-miR-181d^brain	AACAUUCAUUGUUGUCGGUGGGUU
miR-24	410	416	1A	hsa-miR-24^SZ	UGGCUCAGUUCAGCAGGAACAG
miR-381	1169	1175	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU

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: ITGA3