SZGR2

Summary ?

GeneID	10082
Symbol	GPC6
Synonyms	OMIMD1
Description	glypican 6
Reference	MIM:604404\|HGNC:HGNC:4454\|Ensembl:ENSG00000183098\|HPRD:05099\|Vega:OTTHUMG00000017205
Gene type	protein-coding
Map location	13q32
Pascal p-value	0.004
DMG	1 (# studies)

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
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
DMG:Nishioka_2013	Genome-wide DNA methylation analysis	The authors investigated the methylation profiles of DNA in peripheral blood cells from 18 patients with first-episode schizophrenia (FESZ) and from 15 normal controls.	1
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

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg23246978	13	93879042	GPC6		-0.027	0.41	DMG:Nishioka_2013

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
THUMPD1	0.94	0.95
NFX1	0.94	0.94
TERF2	0.93	0.94
JAKMIP2	0.93	0.94
TP53BP1	0.93	0.94
ZNF134	0.93	0.94
ZNF623	0.93	0.95
ARIH1	0.93	0.94
HMG20A	0.93	0.94
SRGAP2P2	0.93	0.94

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
AF347015.31	-0.78	-0.86
MT-CO2	-0.77	-0.86
FXYD1	-0.77	-0.86
AF347015.27	-0.76	-0.84
AF347015.33	-0.75	-0.82
AF347015.8	-0.74	-0.85
MT-CYB	-0.74	-0.82
HIGD1B	-0.74	-0.84
HSD17B14	-0.74	-0.79
IFI27	-0.74	-0.83

Section III. Gene Ontology annotation

Cellular component	GO term	Evidence	PubMed ID
GO:0005576	extracellular region	IEA	-
GO:0005578	proteinaceous extracellular matrix	IEA	-
GO:0005886	plasma membrane	IEA	-
GO:0005887	integral to plasma membrane	TAS	10329016
GO:0031225	anchored to membrane	IEA	-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
REACTOME HS GAG DEGRADATION	20	15	All SZGR 2.0 genes in this pathway
REACTOME CHONDROITIN SULFATE DERMATAN SULFATE METABOLISM	49	33	All SZGR 2.0 genes in this pathway
REACTOME HS GAG BIOSYNTHESIS	31	17	All SZGR 2.0 genes in this pathway
REACTOME HEPARAN SULFATE HEPARIN HS GAG METABOLISM	52	33	All SZGR 2.0 genes in this pathway
REACTOME GLYCOSAMINOGLYCAN METABOLISM	111	69	All SZGR 2.0 genes in this pathway
REACTOME A TETRASACCHARIDE LINKER SEQUENCE IS REQUIRED FOR GAG SYNTHESIS	25	17	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF CARBOHYDRATES	247	154	All SZGR 2.0 genes in this pathway
LIU PROSTATE CANCER DN	481	290	All SZGR 2.0 genes in this pathway
CHEMNITZ RESPONSE TO PROSTAGLANDIN E2 DN	391	222	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
SABATES COLORECTAL ADENOMA DN	291	176	All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS D DN	9	6	All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 2B	392	251	All SZGR 2.0 genes in this pathway
MOHANKUMAR TLX1 TARGETS DN	193	112	All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM1	229	137	All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS	988	594	All SZGR 2.0 genes in this pathway
BENPORATH SOX2 TARGETS	734	436	All SZGR 2.0 genes in this pathway
MEDINA SMARCA4 TARGETS	44	29	All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 UP	428	266	All SZGR 2.0 genes in this pathway
KONDO EZH2 TARGETS	245	148	All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR DN	191	123	All SZGR 2.0 genes in this pathway
MOLENAAR TARGETS OF CCND1 AND CDK4 DN	58	25	All SZGR 2.0 genes in this pathway
ACEVEDO LIVER CANCER WITH H3K27ME3 DN	228	114	All SZGR 2.0 genes in this pathway
SHARMA PILOCYTIC ASTROCYTOMA LOCATION UP	25	12	All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS GROWING	243	155	All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT	567	365	All SZGR 2.0 genes in this pathway
PILON KLF1 TARGETS UP	504	321	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION UP	570	339	All SZGR 2.0 genes in this pathway
IKEDA MIR133 TARGETS UP	43	27	All SZGR 2.0 genes in this pathway
PLASARI TGFB1 SIGNALING VIA NFIC 1HR DN	106	77	All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM B	517	302	All SZGR 2.0 genes in this pathway
NABA ECM AFFILIATED	171	89	All SZGR 2.0 genes in this pathway
NABA MATRISOME ASSOCIATED	753	411	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
miR-103/107	289	296	1A,m8	hsa-miR-103^brain	AGCAGCAUUGUACAGGGCUAUGA
miR-103/107	289	296	1A,m8	hsa-miR-107^brain	AGCAGCAUUGUACAGGGCUAUCA
miR-376	109	115	m8	hsa-miR-376a	AUCAUAGAGGAAAAUCCACGU
miR-376	109	115	m8	hsa-miR-376b	AUCAUAGAGGAAAAUCCAUGUU
miR-431	396	402	1A	hsa-miR-431	UGUCUUGCAGGCCGUCAUGCA
miR-9	156	162	1A	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: GPC6