SZGR2

Summary ?

GeneID	3678
Symbol	ITGA5
Synonyms	CD49e\|FNRA\|VLA-5\|VLA5A
Description	integrin subunit alpha 5
Reference	MIM:135620\|HGNC:HGNC:6141\|Ensembl:ENSG00000161638\|HPRD:00627\|Vega:OTTHUMG00000169841
Gene type	protein-coding
Map location	12q13.13
Pascal p-value	0.451
Fetal beta	-0.035
DMG	1 (# studies)
eGene	Myers' cis & trans Meta
Support	Ascano FMRP targets

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
DMG:vanEijk_2014	Genome-wide DNA methylation analysis	This dataset includes 432 differentially methylated CpG sites corresponding to 391 unique transcripts between schizophrenia patients (n=260) and unaffected controls (n=250).	1
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1
Network	Shortest path distance of core genes in the Human protein-protein interaction network	Contribution to shortest path in PPI network: 0.0066

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg09303642	12	54690818	ITGA5	5.18E-5	-4.226		DMG:vanEijk_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs10994209	chr10	61877705	ITGA5	3678		0.12		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
RAB8A	0.92	0.92
GANAB	0.91	0.91
HEATR6	0.91	0.94
NAT10	0.91	0.94
DET1	0.91	0.92
GEMIN5	0.91	0.94
TH1L	0.91	0.94
RPN2	0.91	0.90
RNPEP	0.91	0.93
DDB1	0.91	0.92

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
MT-CO2	-0.77	-0.87
AF347015.31	-0.77	-0.86
AF347015.27	-0.74	-0.84
FXYD1	-0.73	-0.83
IFI27	-0.73	-0.84
AF347015.33	-0.73	-0.82
AF347015.8	-0.72	-0.84
AF347015.21	-0.72	-0.88
MT-CYB	-0.72	-0.82
CXCL14	-0.70	-0.81

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004872	receptor activity	IEA		-
GO:0005178	integrin binding	IEA		-
GO:0005509	calcium ion binding	IEA		-
GO:0005515	protein binding	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007155	cell adhesion	TAS		2454952
GO:0007157	heterophilic cell adhesion	IEA		-
GO:0007229	integrin-mediated signaling pathway	IEA		-
GO:0007613	memory	IEA		-
GO:0007044	cell-substrate junction assembly	IEA		-
GO:0007159	leukocyte adhesion	IEA		-
GO:0033631	cell-cell adhesion mediated by integrin	IEA		-
GO:0044419	interspecies interaction between organisms	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0019717	synaptosome	IEA	Synap, Brain (GO term level: 7)	-
GO:0001726	ruffle	TAS		11919189
GO:0005794	Golgi apparatus	IDA		18029348
GO:0005634	nucleus	IDA		18029348
GO:0005737	cytoplasm	IDA		18029348
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	IEA		-
GO:0009897	external side of plasma membrane	IEA		-
GO:0008305	integrin complex	TAS		2454952

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ANGPTL3	ANGPT5	angiopoietin-like 3	-	HPRD	11877390
ARHGAP5	GFI2 \| RhoGAP5 \| p190-B	Rho GTPase activating protein 5	-	HPRD	8537347
AUP1	-	ancient ubiquitous protein 1	-	HPRD,BioGRID	12042322
CD9	5H9 \| BA2 \| BTCC-1 \| DRAP-27 \| GIG2 \| MIC3 \| MRP-1 \| P24 \| TSPAN29	CD9 molecule	-	HPRD,BioGRID	10065872
COL18A1	FLJ27325 \| FLJ34914 \| KNO \| KNO1 \| MGC74745	collagen, type XVIII, alpha 1	-	HPRD	11158588
COL1A1	OI4	collagen, type I, alpha 1	-	HPRD	1693626
EGFR	ERBB \| ERBB1 \| HER1 \| PIG61 \| mENA	epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)	-	HPRD	10888683
F2	PT	coagulation factor II (thrombin)	-	HPRD	9864377
FN1	CIG \| DKFZp686F10164 \| DKFZp686H0342 \| DKFZp686I1370 \| DKFZp686O13149 \| ED-B \| FINC \| FN \| FNZ \| GFND \| GFND2 \| LETS \| MSF	fibronectin 1	Reconstituted Complex	BioGRID	1532572
FN1	CIG \| DKFZp686F10164 \| DKFZp686H0342 \| DKFZp686I1370 \| DKFZp686O13149 \| ED-B \| FINC \| FN \| FNZ \| GFND \| GFND2 \| LETS \| MSF	fibronectin 1	-	HPRD	9211865 \|11801679
GIPC1	C19orf3 \| GIPC \| GLUT1CBP \| Hs.6454 \| IIP-1 \| MGC15889 \| MGC3774 \| NIP \| RGS19IP1 \| SEMCAP \| SYNECTIIN \| SYNECTIN \| TIP-2	GIPC PDZ domain containing family, member 1	-	HPRD,BioGRID	11479315
ILK	DKFZp686F1765 \| P59	integrin-linked kinase	Affinity Capture-Western	BioGRID	8538749
ITGB1	CD29 \| FNRB \| GPIIA \| MDF2 \| MSK12 \| VLA-BETA \| VLAB	integrin, beta 1 (fibronectin receptor, beta polypeptide, antigen CD29 includes MDF2, MSK12)	VLA5-alpha5 interacts with VLA5-beta.	BIND	1690718 \|1693624 \|3546305
ITGB5	FLJ26658	integrin, beta 5	-	HPRD	7592829\|11462216
L1CAM	CAML1 \| CD171 \| HSAS \| HSAS1 \| MASA \| MIC5 \| N-CAML1 \| S10 \| SPG1	L1 cell adhesion molecule	-	HPRD,BioGRID	10871287
NISCH	FLJ14425 \| FLJ40413 \| FLJ90519 \| I-1 \| IRAS \| KIAA0975	nischarin	-	HPRD	12868002 \|15028619
PECAM1	CD31 \| PECAM-1	platelet/endothelial cell adhesion molecule	-	HPRD	10982404
SPP1	BNSP \| BSPI \| ETA-1 \| MGC110940 \| OPN	secreted phosphoprotein 1	-	HPRD,BioGRID	7592829
TNC	HXB \| MGC167029 \| TN	tenascin C	-	HPRD	9314546

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 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 ANGIOPOIETIN RECEPTOR PATHWAY	50	41	All SZGR 2.0 genes in this pathway
PID CXCR4 PATHWAY	102	78	All SZGR 2.0 genes in this pathway
PID SYNDECAN 4 PATHWAY	32	25	All SZGR 2.0 genes in this pathway
PID UPA UPAR PATHWAY	42	30	All SZGR 2.0 genes in this pathway
PID SYNDECAN 2 PATHWAY	33	27	All SZGR 2.0 genes in this pathway
PID LYMPH ANGIOGENESIS PATHWAY	25	16	All SZGR 2.0 genes in this pathway
PID FAK PATHWAY	59	45	All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY	396	292	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 INTEGRIN CELL SURFACE INTERACTIONS	79	48	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 SIGNAL TRANSDUCTION BY L1	34	25	All SZGR 2.0 genes in this pathway
REACTOME HEMOSTASIS	466	331	All SZGR 2.0 genes in this pathway
MULLIGHAN NPM1 SIGNATURE 3 DN	162	116	All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY DOXORUBICIN DN	1781	1082	All SZGR 2.0 genes in this pathway
GRAESSMANN RESPONSE TO MC AND DOXORUBICIN DN	770	415	All SZGR 2.0 genes in this pathway
HUMMERICH SKIN CANCER PROGRESSION UP	88	58	All SZGR 2.0 genes in this pathway
LA MEN1 TARGETS	24	15	All SZGR 2.0 genes in this pathway
LOPEZ MBD TARGETS	957	597	All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 480 HELA	164	118	All SZGR 2.0 genes in this pathway
AMIT SERUM RESPONSE 240 MCF10A	57	36	All SZGR 2.0 genes in this pathway
NING CHRONIC OBSTRUCTIVE PULMONARY DISEASE UP	157	105	All SZGR 2.0 genes in this pathway
GALINDO IMMUNE RESPONSE TO ENTEROTOXIN	85	67	All SZGR 2.0 genes in this pathway
ALCALAY AML BY NPM1 LOCALIZATION UP	140	83	All SZGR 2.0 genes in this pathway
PETROVA ENDOTHELIUM LYMPHATIC VS BLOOD DN	162	102	All SZGR 2.0 genes in this pathway
CHIARETTI ACUTE LYMPHOBLASTIC LEUKEMIA ZAP70	67	33	All SZGR 2.0 genes in this pathway
PETROVA PROX1 TARGETS DN	64	38	All SZGR 2.0 genes in this pathway
REN ALVEOLAR RHABDOMYOSARCOMA DN	408	274	All SZGR 2.0 genes in this pathway
WEIGEL OXIDATIVE STRESS RESPONSE	35	28	All SZGR 2.0 genes in this pathway
HENDRICKS SMARCA4 TARGETS UP	56	35	All SZGR 2.0 genes in this pathway
ZHANG PROLIFERATING VS QUIESCENT	51	41	All SZGR 2.0 genes in this pathway
VERRECCHIA RESPONSE TO TGFB1 C5	21	11	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 2	72	52	All SZGR 2.0 genes in this pathway
VERRECCHIA DELAYED RESPONSE TO TGFB1	39	26	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS PEAK AT 8HR	39	31	All SZGR 2.0 genes in this pathway
GHO ATF5 TARGETS DN	16	10	All SZGR 2.0 genes in this pathway
ITO PTTG1 TARGETS DN	9	7	All SZGR 2.0 genes in this pathway
ZHENG GLIOBLASTOMA PLASTICITY DN	58	39	All SZGR 2.0 genes in this pathway
HUANG DASATINIB RESISTANCE UP	81	53	All SZGR 2.0 genes in this pathway
WINTER HYPOXIA METAGENE	242	168	All SZGR 2.0 genes in this pathway
GU PDEF TARGETS UP	71	49	All SZGR 2.0 genes in this pathway
LINDSTEDT DENDRITIC CELL MATURATION D	68	44	All SZGR 2.0 genes in this pathway
ZHANG TLX TARGETS 36HR UP	221	150	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
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
BOYAULT LIVER CANCER SUBCLASS G2	27	17	All SZGR 2.0 genes in this pathway
YAMANAKA GLIOBLASTOMA SURVIVAL UP	11	7	All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA MESENCHYMAL	216	130	All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT	567	365	All SZGR 2.0 genes in this pathway
WANG RESPONSE TO GSK3 INHIBITOR SB216763 DN	374	217	All SZGR 2.0 genes in this pathway
QI HYPOXIA TARGETS OF HIF1A AND FOXA2	37	27	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP A	898	516	All SZGR 2.0 genes in this pathway
PEDERSEN METASTASIS BY ERBB2 ISOFORM 7	403	240	All SZGR 2.0 genes in this pathway
PEDERSEN TARGETS OF 611CTF ISOFORM OF ERBB2	76	45	All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG BOUND 8D	658	397	All SZGR 2.0 genes in this pathway
PLASARI TGFB1 TARGETS 10HR UP	199	143	All SZGR 2.0 genes in this pathway
DELACROIX RAR BOUND ES	462	273	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE VIA P38 COMPLETE	227	151	All SZGR 2.0 genes in this pathway
LIM MAMMARY LUMINAL PROGENITOR DN	14	9	All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY	1725	838	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-128	189	196	1A,m8	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
miR-128	189	196	1A,m8	hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-148/152	902	909	1A,m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-25/32/92/363/367	989	996	1A,m8	hsa-miR-25^brain	CAUUGCACUUGUCUCGGUCUGA
				hsa-miR-32	UAUUGCACAUUACUAAGUUGC
				hsa-miR-92	UAUUGCACUUGUCCCGGCCUG
				hsa-miR-367	AAUUGCACUUUAGCAAUGGUGA
				hsa-miR-92b^SZ	UAUUGCACUCGUCCCGGCCUC
miR-26	134	141	1A,m8	hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
miR-26	134	141	1A,m8	hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
miR-27	190	197	1A,m8	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	190	197	1A,m8	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-30-5p	205	212	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-31	405	411	1A	hsa-miR-31	AGGCAAGAUGCUGGCAUAGCUG
miR-326	409	415	1A	hsa-miR-326	CCUCUGGGCCCUUCCUCCAG
miR-328	141	147	m8	hsa-miR-328^brain	CUGGCCCUCUCUGCCCUUCCGU

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: ITGA5