SZGR2

Summary ?

GeneID	1284
Symbol	COL4A2
Synonyms	ICH\|POREN2
Description	collagen type IV alpha 2
Reference	MIM:120090\|HGNC:HGNC:2203\|Ensembl:ENSG00000134871\|HPRD:00355\|Vega:OTTHUMG00000017344
Gene type	protein-coding
Map location	13q34
Pascal p-value	0.963
Sherlock p-value	0.843
Fetal beta	0.652
eGene	Putamen basal ganglia Myers' cis & trans Meta

Gene in Data Sources

Gene set name	Method of gene set	Description
CV:GWAScat	Genome-wide Association Studies	This data set includes 560 SNPs associated with schizophrenia. A total of 486 genes were mapped to these SNPs within 50kb.
CV:GWASdb	Genome-wide Association Studies	GWASdb records for schizophrenia
CV:PGCnp	Genome-wide Association Study	GWAS

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs16846456	chr3	172757337	COL4A2	1284		0.02		trans
rs17007781	chr4	124977313	COL4A2	1284		9.519E-4		trans
rs1028198	chr4	124977733	COL4A2	1284		0.05		trans
rs1492754	chr4	125421168	COL4A2	1284		0.15		trans
rs1492753	chr4	125421324	COL4A2	1284		0.15		trans
rs4425392	chr4	133569611	COL4A2	1284		0.05		trans
rs7906863	chr10	71176334	COL4A2	1284		0.04		trans
rs7078328	chr10	124029258	COL4A2	1284		0.04		trans
rs10510107	chr10	124029470	COL4A2	1284		0.03		trans
rs4317918	chr10	124065869	COL4A2	1284		0.04		trans
rs10887122	chr10	124071344	COL4A2	1284		0.04		trans
rs2175465	chr13	31797640	COL4A2	1284		0.1		trans
rs5806894	13	111942142	COL4A2	ENSG00000134871.13	1.685E-6	0.05	983983	gtex_brain_putamen_basal

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
IGF2	0.92	0.86
COL1A1	0.91	0.77
ITIH2	0.89	0.80
NID2	0.88	0.39
COL3A1	0.88	0.57
ALX4	0.88	0.49
OSR1	0.88	0.66
SLC6A4	0.84	0.47
COL1A2	0.84	0.72
NID1	0.84	0.41

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
LHPP	-0.29	0.18
MRPL41	-0.27	-0.01
ACOT13	-0.27	0.08
C5orf53	-0.27	0.05
PIR	-0.26	0.02
AF347015.33	-0.26	-0.01
HEPN1	-0.26	0.13
HLA-C	-0.26	0.14
MT-CO2	-0.26	-0.03
AF347015.31	-0.26	-0.00

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005488	binding	IEA		-
GO:0005201	extracellular matrix structural constituent	TAS		8317999
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016525	negative regulation of angiogenesis	IDA		10625665
GO:0030198	extracellular matrix organization	NAS		8317999
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005576	extracellular region	IEA		-
GO:0005581	collagen	IEA		-
GO:0005587	collagen type IV	TAS		2846280 \|3345760

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
APP	AAA \| ABETA \| ABPP \| AD1 \| APPI \| CTFgamma \| CVAP \| PN2	amyloid beta (A4) precursor protein	-	HPRD	9136074
BGN	DSPG1 \| PG-S1 \| PGI \| SLRR1A	biglycan	-	HPRD	11259413
CD93	C1QR1 \| C1qR(P) \| C1qRP \| CDw93 \| MXRA4 \| dJ737E23.1	CD93 molecule	-	HPRD	1377218
COL4A1	arresten	collagen, type IV, alpha 1	-	HPRD,BioGRID	12011424
COL4A2	DKFZp686I14213 \| FLJ22259	collagen, type IV, alpha 2	-	HPRD,BioGRID	12011424
DCN	CSCD \| DSPG2 \| PG40 \| PGII \| PGS2 \| SLRR1B	decorin	-	HPRD	10382266
FBLN2	-	fibulin 2	-	HPRD,BioGRID	7500359
FN1	CIG \| DKFZp686F10164 \| DKFZp686H0342 \| DKFZp686I1370 \| DKFZp686O13149 \| ED-B \| FINC \| FN \| FNZ \| GFND \| GFND2 \| LETS \| MSF	fibronectin 1	-	HPRD	3997552
HABP2	FSAP \| HABP \| HGFAL \| PHBP	hyaluronan binding protein 2	in vivo	BioGRID	1724753
MATN2	-	matrilin 2	-	HPRD	12180907
MMP9	CLG4B \| GELB \| MMP-9	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	-	HPRD,BioGRID	9878537
OSM	MGC20461	oncostatin M	-	HPRD,BioGRID	11711546
SAA1	MGC111216 \| PIG4 \| SAA \| TP53I4	serum amyloid A1	-	HPRD	8995276
SERPINE2	GDN \| PI7 \| PN1 \| PNI	serpin peptidase inhibitor, clade E (nexin, plasminogen activator inhibitor type 1), member 2	-	HPRD,BioGRID	8006028
TGFBI	BIGH3 \| CDB1 \| CDG2 \| CDGG1 \| CSD \| CSD1 \| CSD2 \| CSD3 \| EBMD \| LCD1	transforming growth factor, beta-induced, 68kDa	-	HPRD	11867580

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 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
BIOCARTA AMI PATHWAY	20	13	All SZGR 2.0 genes in this pathway
BIOCARTA ACE2 PATHWAY	13	7	All SZGR 2.0 genes in this pathway
BIOCARTA INTRINSIC PATHWAY	23	15	All SZGR 2.0 genes in this pathway
BIOCARTA PLATELETAPP PATHWAY	14	10	All SZGR 2.0 genes in this pathway
BIOCARTA VITCB PATHWAY	11	6	All SZGR 2.0 genes in this pathway
REACTOME DEVELOPMENTAL BIOLOGY	396	292	All SZGR 2.0 genes in this pathway
REACTOME EXTRACELLULAR MATRIX ORGANIZATION	87	42	All SZGR 2.0 genes in this pathway
REACTOME COLLAGEN FORMATION	58	31	All SZGR 2.0 genes in this pathway
REACTOME INTEGRIN CELL SURFACE INTERACTIONS	79	48	All SZGR 2.0 genes in this pathway
REACTOME SIGNALING BY PDGF	122	93	All SZGR 2.0 genes in this pathway
REACTOME AXON GUIDANCE	251	188	All SZGR 2.0 genes in this pathway
REACTOME NCAM1 INTERACTIONS	39	27	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
PICCALUGA ANGIOIMMUNOBLASTIC LYMPHOMA UP	205	140	All SZGR 2.0 genes in this pathway
LIU PROSTATE CANCER DN	481	290	All SZGR 2.0 genes in this pathway
SCHUETZ BREAST CANCER DUCTAL INVASIVE UP	351	230	All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA UP	294	178	All SZGR 2.0 genes in this pathway
TURASHVILI BREAST LOBULAR CARCINOMA VS LOBULAR NORMAL DN	74	42	All SZGR 2.0 genes in this pathway
LIU TARGETS OF VMYB VS CMYB DN	43	30	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
CHARAFE BREAST CANCER LUMINAL VS MESENCHYMAL DN	460	312	All SZGR 2.0 genes in this pathway
DITTMER PTHLH TARGETS UP	112	68	All SZGR 2.0 genes in this pathway
DODD NASOPHARYNGEAL CARCINOMA DN	1375	806	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN	805	505	All SZGR 2.0 genes in this pathway
PROVENZANI METASTASIS DN	136	94	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION KRAS DN	142	95	All SZGR 2.0 genes in this pathway
CHIARADONNA NEOPLASTIC TRANSFORMATION CDC25 DN	153	100	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
LINDGREN BLADDER CANCER CLUSTER 1 DN	378	231	All SZGR 2.0 genes in this pathway
VANHARANTA UTERINE FIBROID UP	45	26	All SZGR 2.0 genes in this pathway
WANG BARRETTS ESOPHAGUS AND ESOPHAGUS CANCER UP	26	12	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER HIGH RECURRENCE	49	31	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER	747	453	All SZGR 2.0 genes in this pathway
LI WILMS TUMOR VS FETAL KIDNEY 2 DN	51	42	All SZGR 2.0 genes in this pathway
WATTEL AUTONOMOUS THYROID ADENOMA UP	73	47	All SZGR 2.0 genes in this pathway
TSAI RESPONSE TO IONIZING RADIATION	149	101	All SZGR 2.0 genes in this pathway
KHETCHOUMIAN TRIM24 TARGETS UP	47	38	All SZGR 2.0 genes in this pathway
GROSS HYPOXIA VIA ELK3 UP	209	139	All SZGR 2.0 genes in this pathway
GROSS HYPOXIA VIA ELK3 AND HIF1A DN	103	71	All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS UP	769	437	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
WEI MIR34A TARGETS	148	97	All SZGR 2.0 genes in this pathway
WU CELL MIGRATION	184	114	All SZGR 2.0 genes in this pathway
GOTZMANN EPITHELIAL TO MESENCHYMAL TRANSITION UP	69	55	All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 480 HELA	164	118	All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS SUBSET	33	20	All SZGR 2.0 genes in this pathway
ROZANOV MMP14 TARGETS UP	266	171	All SZGR 2.0 genes in this pathway
LEE LIVER CANCER ACOX1 UP	64	40	All SZGR 2.0 genes in this pathway
VANTVEER BREAST CANCER METASTASIS DN	121	65	All SZGR 2.0 genes in this pathway
FERNANDEZ BOUND BY MYC	182	116	All SZGR 2.0 genes in this pathway
SWEET KRAS TARGETS UP	84	51	All SZGR 2.0 genes in this pathway
LEE LIVER CANCER CIPROFIBRATE UP	60	42	All SZGR 2.0 genes in this pathway
MANALO HYPOXIA UP	207	145	All SZGR 2.0 genes in this pathway
LEE LIVER CANCER DENA UP	60	40	All SZGR 2.0 genes in this pathway
YAMAZAKI TCEB3 TARGETS UP	175	116	All SZGR 2.0 genes in this pathway
MARIADASON REGULATED BY HISTONE ACETYLATION DN	54	30	All SZGR 2.0 genes in this pathway
TSENG IRS1 TARGETS DN	135	88	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 4	48	32	All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION DN	287	208	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL AND PROGENITOR	681	420	All SZGR 2.0 genes in this pathway
TSENG ADIPOGENIC POTENTIAL DN	46	28	All SZGR 2.0 genes in this pathway
URS ADIPOCYTE DIFFERENTIATION DN	30	20	All SZGR 2.0 genes in this pathway
MARCHINI TRABECTEDIN RESISTANCE DN	49	34	All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP	566	371	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR DN	911	527	All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR DN	1011	592	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP	973	570	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE DN	315	197	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B DN	564	326	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL UP	648	398	All SZGR 2.0 genes in this pathway
WEST ADRENOCORTICAL TUMOR UP	294	199	All SZGR 2.0 genes in this pathway
BRUECKNER TARGETS OF MIRLET7A3 DN	78	49	All SZGR 2.0 genes in this pathway
QI PLASMACYTOMA DN	100	63	All SZGR 2.0 genes in this pathway
CROMER TUMORIGENESIS UP	63	36	All SZGR 2.0 genes in this pathway
VART KSHV INFECTION ANGIOGENIC MARKERS UP	165	118	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
PARK APL PATHOGENESIS DN	50	35	All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS DN	668	419	All SZGR 2.0 genes in this pathway
FOURNIER ACINAR DEVELOPMENT LATE 2	277	172	All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SUBCLASS S1	237	159	All SZGR 2.0 genes in this pathway
VANTVEER BREAST CANCER POOR PROGNOSIS	55	30	All SZGR 2.0 genes in this pathway
BYSTRYKH HEMATOPOIESIS STEM CELL SCP2 QTL TRANS	25	13	All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC	1103	714	All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE	721	492	All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 16	79	47	All SZGR 2.0 genes in this pathway
KANG AR TARGETS UP	17	10	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE VIA TP53 GROUP B	549	316	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE LATE	1137	655	All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4	227	149	All SZGR 2.0 genes in this pathway
LIM MAMMARY STEM CELL UP	489	314	All SZGR 2.0 genes in this pathway
LIM MAMMARY LUMINAL MATURE DN	99	74	All SZGR 2.0 genes in this pathway
NABA COLLAGENS	44	26	All SZGR 2.0 genes in this pathway
NABA CORE MATRISOME	275	148	All SZGR 2.0 genes in this pathway
NABA BASEMENT MEMBRANES	40	22	All SZGR 2.0 genes in this pathway
NABA MATRISOME	1028	559	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	49	55	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-29	28	34	m8	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
miR-9	107	113	m8	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA

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: COL4A2