SZGR2

Summary ?

GeneID	1282
Symbol	COL4A1
Synonyms	BSVD\|RATOR
Description	collagen type IV alpha 1
Reference	MIM:120130\|HGNC:HGNC:2202\|Ensembl:ENSG00000187498\|HPRD:00359\|Vega:OTTHUMG00000017342
Gene type	protein-coding
Map location	13q34
Pascal p-value	0.757
Sherlock p-value	0.758
eGene	Myers' cis & trans

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
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	qvalue	eQTL type
rs16846456	chr3	172757337	COL4A1	1282	0.01	trans
rs4484667	chr8	77440301	COL4A1	1282	0.06	trans
rs12254965	chr10	127297037	COL4A1	1282	0.07	trans
rs11856277	chr15	29722087	COL4A1	1282	0.18	trans
rs4780219	chr15	29726087	COL4A1	1282	0.16	trans

Section II. Transcriptome annotation

General gene expression (GTEx)

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
CDAN1	0.84	0.83
GLIS2	0.83	0.89
SEMA4B	0.82	0.84
NCAN	0.81	0.85
RELA	0.81	0.83
SEPN1	0.81	0.86
PLXNB2	0.80	0.89
ARSD	0.80	0.79
HDAC6	0.80	0.81
ARHGEF10L	0.80	0.82

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
C5orf53	-0.63	-0.68
ACOT13	-0.60	-0.66
FAM162A	-0.57	-0.64
AF347015.27	-0.56	-0.65
AF347015.31	-0.55	-0.65
CA4	-0.54	-0.57
CA11	-0.54	-0.63
S100B	-0.54	-0.61
B2M	-0.54	-0.64
MYL3	-0.53	-0.62

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005488	binding	IEA		-
GO:0005201	extracellular matrix structural constituent	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005576	extracellular region	NAS		14718574
GO:0005581	collagen	IEA		-
GO:0005604	basement membrane	IEA		-

Section IV. Protein-protein interaction annotation

Interactors	Aliases B	Official full name B	Experimental	Source	PubMed ID
ACHE	ARACHE \| N-ACHE \| YT	acetylcholinesterase (Yt blood group)	-	HPRD	12524166
APP	AAA \| ABETA \| ABPP \| AD1 \| APPI \| CTFgamma \| CVAP \| PN2	amyloid beta (A4) precursor protein	-	HPRD	9136074
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
COL7A1	EBD1 \| EBDCT \| EBR1	collagen, type VII, alpha 1	-	HPRD,BioGRID	9169408
DCN	CSCD \| DSPG2 \| PG40 \| PGII \| PGS2 \| SLRR1B	decorin	-	HPRD	10382266
DISC1	C1orf136 \| FLJ13381 \| FLJ21640 \| FLJ25311 \| FLJ41105 \| KIAA0457 \| SCZD9	disrupted in schizophrenia 1	Two-hybrid	BioGRID	12812986
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	-	HPRD,BioGRID	1724753
MAG	GMA \| S-MAG \| SIGLEC-4A \| SIGLEC4A	myelin associated glycoprotein	Reconstituted Complex	BioGRID	2446864
MATN2	-	matrilin 2	-	HPRD	12180907
MMP9	CLG4B \| GELB \| MMP-9	matrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)	-	HPRD,BioGRID	9878537
NID1	NID	nidogen 1	Reconstituted Complex	BioGRID	9733643
NID2	-	nidogen 2 (osteonidogen)	Reconstituted Complex	BioGRID	9733643
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
THBS1	THBS \| TSP \| TSP1	thrombospondin 1	Reconstituted Complex	BioGRID	3571333

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
PID INTEGRIN1 PATHWAY	66	44	All SZGR 2.0 genes in this pathway
PID INTEGRIN3 PATHWAY	43	25	All SZGR 2.0 genes in this pathway
PID AVB3 INTEGRIN PATHWAY	75	53	All SZGR 2.0 genes in this pathway
PID SYNDECAN 1 PATHWAY	46	29	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
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL UP	285	181	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
ONKEN UVEAL MELANOMA UP	783	507	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 DUCTAL CARCINOMA VS DUCTAL NORMAL UP	44	25	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
ZHOU INFLAMMATORY RESPONSE LIVE UP	485	293	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
ROY WOUND BLOOD VESSEL UP	50	30	All SZGR 2.0 genes in this pathway
HORIUCHI WTAP TARGETS UP	306	188	All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER ADVANCED VS EARLY UP	175	120	All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP	1278	748	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
LANDIS BREAST CANCER PROGRESSION DN	70	43	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
VANHARANTA UTERINE FIBROID UP	45	26	All SZGR 2.0 genes in this pathway
LANDIS ERBB2 BREAST TUMORS 324 DN	149	93	All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER	747	453	All SZGR 2.0 genes in this pathway
BORLAK LIVER CANCER EGF UP	57	41	All SZGR 2.0 genes in this pathway
OXFORD RALA AND RALB TARGETS DN	9	5	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
KHETCHOUMIAN TRIM24 TARGETS UP	47	38	All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS DN	637	377	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
TARTE PLASMA CELL VS PLASMABLAST UP	398	262	All SZGR 2.0 genes in this pathway
UEDA PERIFERAL CLOCK	169	111	All SZGR 2.0 genes in this pathway
CHESLER BRAIN HIGHEST GENETIC VARIANCE	37	21	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
BYSTRYKH HEMATOPOIESIS STEM CELL QTL TRANS	882	572	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
FLECHNER BIOPSY KIDNEY TRANSPLANT OK VS DONOR UP	555	346	All SZGR 2.0 genes in this pathway
CROMER METASTASIS UP	79	46	All SZGR 2.0 genes in this pathway
IGLESIAS E2F TARGETS UP	151	103	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
MODY HIPPOCAMPUS NEONATAL	35	25	All SZGR 2.0 genes in this pathway
YAMAZAKI TCEB3 TARGETS UP	175	116	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL	254	164	All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 2	72	52	All SZGR 2.0 genes in this pathway
TSENG IRS1 TARGETS DN	135	88	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE INCIPIENT DN	165	106	All SZGR 2.0 genes in this pathway
LEE CALORIE RESTRICTION NEOCORTEX DN	88	58	All SZGR 2.0 genes in this pathway
DEBIASI APOPTOSIS BY REOVIRUS INFECTION DN	287	208	All SZGR 2.0 genes in this pathway
BACOLOD RESISTANCE TO ALKYLATING AGENTS DN	60	45	All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS UP	566	371	All SZGR 2.0 genes in this pathway
IWANAGA CARCINOGENESIS BY KRAS PTEN DN	353	226	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER UP	973	570	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP	863	514	All SZGR 2.0 genes in this pathway
ZHENG GLIOBLASTOMA PLASTICITY DN	58	39	All SZGR 2.0 genes in this pathway
GRADE COLON AND RECTAL CANCER UP	285	167	All SZGR 2.0 genes in this pathway
CROMER TUMORIGENESIS UP	63	36	All SZGR 2.0 genes in this pathway
TSAI RESPONSE TO RADIATION THERAPY	32	20	All SZGR 2.0 genes in this pathway
GU PDEF TARGETS UP	71	49	All SZGR 2.0 genes in this pathway
ICHIBA GRAFT VERSUS HOST DISEASE D7 UP	107	67	All SZGR 2.0 genes in this pathway
CHEN METABOLIC SYNDROM NETWORK	1210	725	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
CROONQUIST NRAS VS STROMAL STIMULATION DN	99	65	All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SURVIVAL UP	73	49	All SZGR 2.0 genes in this pathway
NAKAYAMA FGF2 TARGETS	29	17	All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SUBCLASS S1	237	159	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
LU EZH2 TARGETS DN	414	237	All SZGR 2.0 genes in this pathway
KANG AR TARGETS UP	17	10	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS UP	504	321	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
KIM GLIS2 TARGETS UP	84	61	All SZGR 2.0 genes in this pathway
WAKABAYASHI ADIPOGENESIS PPARG RXRA BOUND 8D	882	506	All SZGR 2.0 genes in this pathway
DELACROIX RAR BOUND ES	462	273	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
ZWANG CLASS 1 TRANSIENTLY INDUCED BY EGF	516	308	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	88	94	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-124.1	119	125	m8	hsa-miR-124a	UUAAGGCACGCGGUGAAUGCCA
miR-124/506	118	125	1A,m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	118	125	1A,m8	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-205	174	180	1A	hsa-miR-205	UCCUUCAUUCCACCGGAGUCUG
miR-29	308	314	1A	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
				hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
miR-381	1292	1298	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-410	655	661	1A	hsa-miR-410	AAUAUAACACAGAUGGCCUGU

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: COL4A1