SZGR2

Summary ?

GeneID	2823
Symbol	GPM6A
Synonyms	GPM6\|M6A
Description	glycoprotein M6A
Reference	MIM:601275\|HGNC:HGNC:4460\|Ensembl:ENSG00000150625\|HPRD:03174\|Vega:OTTHUMG00000160760
Gene type	protein-coding
Map location	4q34
Pascal p-value	7.289E-6
Sherlock p-value	0.618
Fetal beta	0.245
eGene	Myers' cis & trans
Support	CELL ADHESION AND TRANSSYNAPTIC SIGNALING G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS CompositeSet Darnell FMRP targets

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:PGC128	Genome-wide Association Study	A multi-stage schizophrenia GWAS of up to 36,989 cases and 113,075 controls. Reported by the Schizophrenia Working Group of PGC. 128 independent associations spanning 108 loci
CV:PGCnp	Genome-wide Association Study	GWAS
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

CV:PGC128

SNP ID	Chromosome	Position	Allele	P	Function	Gene	Up/Down Distance
rs1106568	chr4	176861301	AG	1.145E-8	intronic	GPM6A

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs7372527		0	GPM6A	2823		0.2		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
LIMS2	0.81	0.77
RHBDF1	0.81	0.82
CHAD	0.75	0.83
SLC7A10	0.73	0.75
OLIG1	0.72	0.85
MMD2	0.71	0.79
CSPG4	0.71	0.65
RIN3	0.71	0.84
DOCK6	0.70	0.66
NEU4	0.70	0.76

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
KLHDC2	-0.61	-0.65
COQ3	-0.60	-0.74
SETD4	-0.58	-0.67
FARSB	-0.57	-0.68
UBE2D2	-0.57	-0.63
FRG1	-0.56	-0.76
ASNSD1	-0.56	-0.73
TSG101	-0.56	-0.73
POLB	-0.56	-0.78
SUPV3L1	-0.56	-0.72

Section III. Gene Ontology annotation

Cellular component	GO term	Evidence	PubMed ID
GO:0016020	membrane	IEA	-
GO:0016021	integral to membrane	IEA	-
GO:0009986	cell surface	IDA	12493773

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
ZHOU INFLAMMATORY RESPONSE LIVE UP	485	293	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC DN	537	339	All SZGR 2.0 genes in this pathway
BEGUM TARGETS OF PAX3 FOXO1 FUSION UP	60	45	All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE DN	712	443	All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM4	261	153	All SZGR 2.0 genes in this pathway
PASQUALUCCI LYMPHOMA BY GC STAGE UP	283	177	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 14HR UP	156	101	All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES DN	245	144	All SZGR 2.0 genes in this pathway
DOUGLAS BMI1 TARGETS DN	314	188	All SZGR 2.0 genes in this pathway
YEGNASUBRAMANIAN PROSTATE CANCER	128	60	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS UP	317	208	All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION UP	461	298	All SZGR 2.0 genes in this pathway
WALLACE PROSTATE CANCER RACE UP	299	167	All SZGR 2.0 genes in this pathway
ZHENG GLIOBLASTOMA PLASTICITY UP	250	168	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA C D DN	252	155	All SZGR 2.0 genes in this pathway
YAGI AML WITH 11Q23 REARRANGED	351	238	All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA PCA1 UP	101	66	All SZGR 2.0 genes in this pathway
MIKKELSEN NPC ICP WITH H3K4ME3	445	257	All SZGR 2.0 genes in this pathway
KARLSSON TGFB1 TARGETS DN	207	139	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS CALB1 CORR UP	548	370	All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA PRONEURAL	177	132	All SZGR 2.0 genes in this pathway
KIM PTEN TARGETS UP	18	9	All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4	227	149	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-133	1246	1252	1A	hsa-miR-133a	UUGGUCCCCUUCAACCAGCUGU
miR-133	1246	1252	1A	hsa-miR-133b	UUGGUCCCCUUCAACCAGCUA
miR-148/152	1386	1393	1A,m8	hsa-miR-148a	UCAGUGCACUACAGAACUUUGU
				hsa-miR-152^brain	UCAGUGCAUGACAGAACUUGGG
				hsa-miR-148b	UCAGUGCAUCACAGAACUUUGU
miR-181	1108	1114	1A	hsa-miR-181a^brain	AACAUUCAACGCUGUCGGUGAGU
				hsa-miR-181b^SZ	AACAUUCAUUGCUGUCGGUGGG
				hsa-miR-181c^brain	AACAUUCAACCUGUCGGUGAGU
				hsa-miR-181d^brain	AACAUUCAUUGUUGUCGGUGGGUU
miR-200bc/429	1675	1681	1A	hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
				hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
				hsa-miR-200b	UAAUACUGCCUGGUAAUGAUGAC
				hsa-miR-200c	UAAUACUGCCGGGUAAUGAUGG
				hsa-miR-429	UAAUACUGUCUGGUAAAACCGU
miR-204/211	433	439	m8	hsa-miR-204^brain	UUCCCUUUGUCAUCCUAUGCCU
miR-204/211	433	439	m8	hsa-miR-211	UUCCCUUUGUCAUCCUUCGCCU
miR-205	892	898	m8	hsa-miR-205	UCCUUCAUUCCACCGGAGUCUG
miR-217	1649	1656	1A,m8	hsa-miR-217	UACUGCAUCAGGAACUGAUUGGAU
miR-218	914	920	m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-221/222	1835	1841	1A	hsa-miR-221^brain	AGCUACAUUGUCUGCUGGGUUUC
miR-221/222	1835	1841	1A	hsa-miR-222^brain	AGCUACAUCUGGCUACUGGGUCUC
miR-28	208	215	1A,m8	hsa-miR-28^brain	AAGGAGCUCACAGUCUAUUGAG
miR-323	868	874	m8	hsa-miR-323^brain	GCACAUUACACGGUCGACCUCU
miR-328	50	56	m8	hsa-miR-328^brain	CUGGCCCUCUCUGCCCUUCCGU
miR-330	1830	1836	m8	hsa-miR-330^brain	GCAAAGCACACGGCCUGCAGAGA
miR-365	1842	1848	1A	hsa-miR-365	UAAUGCCCCUAAAAAUCCUUAU
miR-369-3p	1702	1708	1A	hsa-miR-369-3p	AAUAAUACAUGGUUGAUCUUU
miR-374	1702	1708	m8	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-376c	1055	1061	m8	hsa-miR-376c	AACAUAGAGGAAAUUCCACG
miR-409-5p	423	429	m8	hsa-miR-409-5p	AGGUUACCCGAGCAACUUUGCA
miR-448	1647	1653	m8	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU
miR-485-3p	996	1002	m8	hsa-miR-485-3p	GUCAUACACGGCUCUCCUCUCU
miR-493-5p	1465	1471	1A	hsa-miR-493-5p	UUGUACAUGGUAGGCUUUCAUU
miR-495	617	623	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-495	617	623	1A	hsa-miR-495^brain	AAACAAACAUGGUGCACUUCUUU
miR-500	562	569	1A,m8	hsa-miR-500	AUGCACCUGGGCAAGGAUUCUG
miR-96	1874	1880	m8	hsa-miR-96^brain	UUUGGCACUAGCACAUUUUUGC

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: GPM6A