SZGR2

Summary ?

GeneID	9945
Symbol	GFPT2
Synonyms	GFAT\|GFAT 2\|GFAT2
Description	glutamine-fructose-6-phosphate transaminase 2
Reference	MIM:603865\|HGNC:HGNC:4242\|Ensembl:ENSG00000131459\|HPRD:04842\|Vega:OTTHUMG00000163442
Gene type	protein-coding
Map location	5q34-q35
Pascal p-value	0.65
Sherlock p-value	0.731
DMG	1 (# studies)
eGene	Putamen basal ganglia Meta

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
CV:PGCnp	Genome-wide Association Study	GWAS
DMG:Wockner_2014	Genome-wide DNA methylation analysis	This dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24).	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.
GSMA_IIA	Genome scan meta-analysis (All samples)	Psr: 0.0276
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 1

Section I. Genetics and epigenetics annotation

Differentially methylated gene

Probe	Chromosome	Position	Nearest gene	P (dis)	Beta (dis)	FDR (dis)	Study
cg23260877	5	179742954	GFPT2	2.207E-4	-0.527	0.036	DMG:Wockner_2014

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	pvalue	qvalue	TSS distance	eQTL type
rs76025377	5	179722398	GFPT2	ENSG00000131459.8	5.549E-7	0.01	57989	gtex_brain_putamen_basal
rs6866031	5	179724471	GFPT2	ENSG00000131459.8	2.932E-7	0.01	55916	gtex_brain_putamen_basal
rs7711688	5	179725224	GFPT2	ENSG00000131459.8	1.893E-7	0.01	55163	gtex_brain_putamen_basal
rs7728939	5	179725264	GFPT2	ENSG00000131459.8	1.893E-7	0.01	55123	gtex_brain_putamen_basal
rs11748698	5	179727677	GFPT2	ENSG00000131459.8	6.505E-7	0.01	52710	gtex_brain_putamen_basal
rs7725	5	179727957	GFPT2	ENSG00000131459.8	6.754E-7	0.01	52430	gtex_brain_putamen_basal
rs11740631	5	179731113	GFPT2	ENSG00000131459.8	4.935E-7	0.01	49274	gtex_brain_putamen_basal
rs77017168	5	179731297	GFPT2	ENSG00000131459.8	4.935E-7	0.01	49090	gtex_brain_putamen_basal
rs57931856	5	179731328	GFPT2	ENSG00000131459.8	4.935E-7	0.01	49059	gtex_brain_putamen_basal
rs3763131	5	179734312	GFPT2	ENSG00000131459.8	4.934E-7	0.01	46075	gtex_brain_putamen_basal
rs888924	5	179738213	GFPT2	ENSG00000131459.8	6.894E-7	0.01	42174	gtex_brain_putamen_basal
rs116634077	5	179739034	GFPT2	ENSG00000131459.8	1.342E-7	0.01	41353	gtex_brain_putamen_basal
rs75664354	5	179740108	GFPT2	ENSG00000131459.8	1.141E-6	0.01	40279	gtex_brain_putamen_basal
rs11744073	5	179740239	GFPT2	ENSG00000131459.8	1.262E-6	0.01	40148	gtex_brain_putamen_basal
rs190440456	5	179740527	GFPT2	ENSG00000131459.8	5.69E-7	0.01	39860	gtex_brain_putamen_basal
rs2303007	5	179740827	GFPT2	ENSG00000131459.8	1.321E-6	0.01	39560	gtex_brain_putamen_basal
rs77381392	5	179745413	GFPT2	ENSG00000131459.8	6.343E-7	0.01	34974	gtex_brain_putamen_basal

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
ARHGAP20	0.77	0.80
JAZF1	0.76	0.78
TM6SF1	0.75	0.79
HIVEP2	0.74	0.77
DLG2	0.74	0.80
PRPS2	0.74	0.79
PTCHD1	0.74	0.77
PCDHA5	0.74	0.75
CDH10	0.74	0.79
PVRL3	0.74	0.73

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
C11orf67	-0.49	-0.51
AC098691.2	-0.47	-0.54
RAB34	-0.46	-0.51
FXYD1	-0.46	-0.38
AP002478.3	-0.45	-0.47
ACSF2	-0.45	-0.46
SLC2A4RG	-0.45	-0.45
AC021016.1	-0.44	-0.41
HSD17B14	-0.44	-0.43
AL138743.2	-0.44	-0.48

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0004360	glutamine-fructose-6-phosphate transaminase (isomerizing) activity	TAS	glutamate (GO term level: 6)	10198162
GO:0005529	sugar binding	IEA		-
GO:0016740	transferase activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0016051	carbohydrate biosynthetic process	IEA		-
GO:0006112	energy reserve metabolic process	TAS		10198162
GO:0006002	fructose 6-phosphate metabolic process	TAS		10198162
GO:0008152	metabolic process	IEA		-
GO:0006541	glutamine metabolic process	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005737	cytoplasm	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG ALANINE ASPARTATE AND GLUTAMATE METABOLISM	32	26	All SZGR 2.0 genes in this pathway
KEGG AMINO SUGAR AND NUCLEOTIDE SUGAR METABOLISM	44	30	All SZGR 2.0 genes in this pathway
REACTOME METABOLISM OF PROTEINS	518	242	All SZGR 2.0 genes in this pathway
REACTOME POST TRANSLATIONAL PROTEIN MODIFICATION	188	116	All SZGR 2.0 genes in this pathway
REACTOME SYNTHESIS OF SUBSTRATES IN N GLYCAN BIOSYTHESIS	14	8	All SZGR 2.0 genes in this pathway
REACTOME ASPARAGINE N LINKED GLYCOSYLATION	81	54	All SZGR 2.0 genes in this pathway
REACTOME BIOSYNTHESIS OF THE N GLYCAN PRECURSOR DOLICHOL LIPID LINKED OLIGOSACCHARIDE LLO AND TRANSFER TO A NASCENT PROTEIN	29	17	All SZGR 2.0 genes in this pathway
SCHUETZ BREAST CANCER DUCTAL INVASIVE UP	351	230	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
CHARAFE BREAST CANCER BASAL VS MESENCHYMAL DN	50	36	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
SENESE HDAC1 AND HDAC2 TARGETS UP	238	144	All SZGR 2.0 genes in this pathway
SENESE HDAC2 TARGETS UP	114	66	All SZGR 2.0 genes in this pathway
SENESE HDAC3 TARGETS UP	501	327	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS UP	214	155	All SZGR 2.0 genes in this pathway
KIM WT1 TARGETS 8HR UP	164	122	All SZGR 2.0 genes in this pathway
KAN RESPONSE TO ARSENIC TRIOXIDE	123	80	All SZGR 2.0 genes in this pathway
PEREZ TP63 TARGETS	355	243	All SZGR 2.0 genes in this pathway
DAUER STAT3 TARGETS UP	49	35	All SZGR 2.0 genes in this pathway
HATADA METHYLATED IN LUNG CANCER UP	390	236	All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS UP	1037	673	All SZGR 2.0 genes in this pathway
AMIT EGF RESPONSE 240 HELA	60	43	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE UP	1691	1088	All SZGR 2.0 genes in this pathway
STEIN ESRRA TARGETS UP	388	234	All SZGR 2.0 genes in this pathway
OUILLETTE CLL 13Q14 DELETION DN	60	38	All SZGR 2.0 genes in this pathway
RIGGI EWING SARCOMA PROGENITOR DN	191	123	All SZGR 2.0 genes in this pathway
ZHANG BREAST CANCER PROGENITORS DN	145	93	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL UP	260	174	All SZGR 2.0 genes in this pathway
FONTAINE FOLLICULAR THYROID ADENOMA DN	68	45	All SZGR 2.0 genes in this pathway
FONTAINE PAPILLARY THYROID CARCINOMA DN	80	53	All SZGR 2.0 genes in this pathway
STEIN ESRRA TARGETS	535	325	All SZGR 2.0 genes in this pathway
TIAN TNF SIGNALING VIA NFKB	28	21	All SZGR 2.0 genes in this pathway
MARTENS TRETINOIN RESPONSE UP	857	456	All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS SENESCENT	572	352	All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 3 UP	430	288	All SZGR 2.0 genes in this pathway
MIYAGAWA TARGETS OF EWSR1 ETS FUSIONS DN	229	135	All SZGR 2.0 genes in this pathway
IKEDA MIR30 TARGETS UP	116	87	All SZGR 2.0 genes in this pathway
PLASARI TGFB1 TARGETS 10HR UP	199	143	All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE NOT VIA P38	337	236	All SZGR 2.0 genes in this pathway
FOSTER KDM1A TARGETS DN	211	119	All SZGR 2.0 genes in this pathway
ZWANG CLASS 2 TRANSIENTLY INDUCED BY EGF	51	29	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-124/506	136	142	m8	hsa-miR-506	UAAGGCACCCUUCUGAGUAGA
miR-124/506	136	142	m8	hsa-miR-124^brain	UAAGGCACGCGGUGAAUGCC
miR-128	287	293	1A	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
miR-128	287	293	1A	hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-143	469	476	1A,m8	hsa-miR-143^brain	UGAGAUGAAGCACUGUAGCUCA
miR-153	830	837	1A,m8	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-219	817	823	1A	hsa-miR-219^brain	UGAUUGUCCAAACGCAAUUCU
miR-25/32/92/363/367	256	263	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-27	287	294	1A,m8	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
miR-27	287	294	1A,m8	hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-30-5p	217	224	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-448	831	837	1A	hsa-miR-448	UUGCAUAUGUAGGAUGUCCCAU

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: GFPT2