SZGR2

Summary ?

GeneID	6506
Symbol	SLC1A2
Synonyms	EAAT2\|GLT-1\|HBGT
Description	solute carrier family 1 member 2
Reference	MIM:600300\|HGNC:HGNC:10940\|Ensembl:ENSG00000110436\|HPRD:02625\|Vega:OTTHUMG00000044391
Gene type	protein-coding
Map location	11p13
Pascal p-value	0.729
Sherlock p-value	0.502
Fetal beta	-1.608
eGene	Cerebellar Hemisphere Myers' cis & trans
Support	NEUROTRANSMITTER METABOLISM G2Cdb.human_BAYES-COLLINS-HUMAN-PSD-FULL G2Cdb.human_BAYES-COLLINS-MOUSE-PSD-CONSENSUS G2Cdb.human_clathrin G2Cdb.human_Synaptosome G2Cdb.human_TAP-PSD-95-CORE G2Cdb.humanNRC G2Cdb.humanPSD G2Cdb.humanPSP CompositeSet Darnell FMRP targets Potential synaptic genes

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
PMID:cooccur	High-throughput literature-search	Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Association	A combined odds ratio method (Sun et al. 2008), association studies	2	Link to SZGene
Expression	Meta-analysis of gene expression	P value: 1.818
Literature	High-throughput literature-search	Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenics,schizophrenias	Click to show details
GO_Annotation	Mapping neuro-related keywords to Gene Ontology annotations	Hits with neuro-related keywords: 3

Section I. Genetics and epigenetics annotation

eQTL annotation

SNP ID	Chromosome	Position	eGene	Gene Entrez ID	qvalue	eQTL type
rs17014160	chr1	206855799	SLC1A2	6506	0.07	trans
rs12997903	chr2	1952083	SLC1A2	6506	0.04	trans
rs6733654	chr2	1963270	SLC1A2	6506	9.781E-4	trans
rs6737451	chr2	189039508	SLC1A2	6506	0.02	trans
rs1395163	chr3	31028951	SLC1A2	6506	0.01	trans
rs17029291	chr3	32402138	SLC1A2	6506	0.04	trans
rs6446109	chr3	60076988	SLC1A2	6506	0.12	trans
rs624496	chr3	120506736	SLC1A2	6506	0.06	trans
rs7630338	chr3	173953886	SLC1A2	6506	0.05	trans
rs16858348	chr3	173958675	SLC1A2	6506	0.02	trans
rs2193745	chr3	173964139	SLC1A2	6506	0.07	trans
rs17049650	chr4	119097017	SLC1A2	6506	0.17	trans
rs17049690	chr4	119154023	SLC1A2	6506	0.04	trans
snp_a-4197792		0	SLC1A2	6506	0.17	trans
rs17030258	chr4	154546102	SLC1A2	6506	0.18	trans
rs16895745	chr5	26523381	SLC1A2	6506	0.07	trans
rs3733925	chr5	150090343	SLC1A2	6506	0.17	trans
rs4576244	chr6	9525542	SLC1A2	6506	0.17	trans
rs10968711	chr9	28676294	SLC1A2	6506	0.17	trans
rs11259374	chr10	14917473	SLC1A2	6506	0.12	trans
rs3912874	chr10	66571456	SLC1A2	6506	0.19	trans
rs909288	chr10	124257417	SLC1A2	6506	0.01	trans
rs7111397	chr11	20133985	SLC1A2	6506	0.19	trans
rs7294586	chr12	100890454	SLC1A2	6506	0.12	trans
rs10492317	chr12	100899426	SLC1A2	6506	0.02	trans
rs1954396	chr14	43601835	SLC1A2	6506	0.01	trans
rs2327968	chr20	15813490	SLC1A2	6506	0.13	trans
rs6098023	chr20	53113740	SLC1A2	6506	0.18	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
TGFBR3	0.81	0.85
FGL2	0.67	0.70
TLR4	0.67	0.79
PRRX1	0.66	0.76
SLC7A11	0.64	0.82
SIX1	0.63	0.54
CFH	0.63	0.63
GJA1	0.63	0.75
ITGBL1	0.63	0.56
ABCA9	0.62	0.69

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
STRA13	-0.36	-0.53
SNHG12	-0.35	-0.47
RP9	-0.34	-0.46
RP9P	-0.33	-0.51
TCTEX1D2	-0.33	-0.45
FAM128A	-0.33	-0.38
COMTD1	-0.32	-0.38
AC006273.1	-0.32	-0.31
LSM7	-0.32	-0.46
NR2C2AP	-0.32	-0.43

Section III. Gene Ontology annotation

Molecular function	GO term	Evidence	Neuro keywords	PubMed ID
GO:0015501	glutamate:sodium symporter activity	IEA	glutamate (GO term level: 11)	-
GO:0015293	symporter activity	IEA		-
GO:0017153	sodium:dicarboxylate symporter activity	IEA		-
Biological process	GO term	Evidence	Neuro keywords	PubMed ID
GO:0007268	synaptic transmission	TAS	neuron, Synap, Neurotransmitter (GO term level: 6)	7521911
GO:0015813	L-glutamate transport	TAS	glutamate (GO term level: 9)	7521911
GO:0006835	dicarboxylic acid transport	IEA		-
GO:0006810	transport	IEA		-
Cellular component	GO term	Evidence	Neuro keywords	PubMed ID
GO:0005624	membrane fraction	TAS		7521911
GO:0016020	membrane	IEA		-
GO:0016021	integral to membrane	IEA		-

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
KEGG AMYOTROPHIC LATERAL SCLEROSIS ALS	53	43	All SZGR 2.0 genes in this pathway
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES	186	155	All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM	279	221	All SZGR 2.0 genes in this pathway
REACTOME TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES	413	270	All SZGR 2.0 genes in this pathway
REACTOME SLC MEDIATED TRANSMEMBRANE TRANSPORT	241	157	All SZGR 2.0 genes in this pathway
REACTOME TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES	94	65	All SZGR 2.0 genes in this pathway
REACTOME AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS	49	36	All SZGR 2.0 genes in this pathway
TURASHVILI BREAST CARCINOMA DUCTAL VS LOBULAR UP	21	14	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LIVE UP	485	293	All SZGR 2.0 genes in this pathway
GAL LEUKEMIC STEM CELL UP	133	78	All SZGR 2.0 genes in this pathway
VECCHI GASTRIC CANCER EARLY DN	367	220	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE FIMA UP	544	308	All SZGR 2.0 genes in this pathway
ZHOU INFLAMMATORY RESPONSE LPS UP	431	237	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
KIM MYCN AMPLIFICATION TARGETS UP	92	64	All SZGR 2.0 genes in this pathway
WEI MYCN TARGETS WITH E BOX	795	478	All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS	1038	678	All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS	1062	725	All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3	1118	744	All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS	652	441	All SZGR 2.0 genes in this pathway
STARK PREFRONTAL CORTEX 22Q11 DELETION UP	195	138	All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS DN	357	212	All SZGR 2.0 genes in this pathway
LEE LIVER CANCER CIPROFIBRATE DN	66	43	All SZGR 2.0 genes in this pathway
LEE LIVER CANCER MYC UP	54	30	All SZGR 2.0 genes in this pathway
POMEROY MEDULLOBLASTOMA DESMOPLASIC VS CLASSIC UP	62	38	All SZGR 2.0 genes in this pathway
LEE LIVER CANCER DENA DN	74	45	All SZGR 2.0 genes in this pathway
HU GENOTOXIN ACTION DIRECT VS INDIRECT 4HR	37	22	All SZGR 2.0 genes in this pathway
SANSOM APC TARGETS	212	121	All SZGR 2.0 genes in this pathway
KONDO PROSTATE CANCER HCP WITH H3K27ME3	97	72	All SZGR 2.0 genes in this pathway
HUANG DASATINIB RESISTANCE DN	69	44	All SZGR 2.0 genes in this pathway
MOOTHA MITOCHONDRIA	447	277	All SZGR 2.0 genes in this pathway
ICHIBA GRAFT VERSUS HOST DISEASE 35D DN	49	34	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO CSF2RB AND IL4 UP	338	225	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF UP	418	282	All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF VS CSF2RB AND IL4 DN	245	150	All SZGR 2.0 genes in this pathway
CHIANG LIVER CANCER SUBCLASS CTNNB1 UP	176	110	All SZGR 2.0 genes in this pathway
KIM ALL DISORDERS OLIGODENDROCYTE NUMBER CORR DN	36	19	All SZGR 2.0 genes in this pathway
BRUINS UVC RESPONSE EARLY LATE	317	190	All SZGR 2.0 genes in this pathway
PEDERSEN METASTASIS BY ERBB2 ISOFORM 4	110	66	All SZGR 2.0 genes in this pathway
RATTENBACHER BOUND BY CELF1	467	251	All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY	1725	838	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-128	6738	6744	1A	hsa-miR-128a	UCACAGUGAACCGGUCUCUUUU
miR-128	6738	6744	1A	hsa-miR-128b	UCACAGUGAACCGGUCUCUUUC
miR-140	7101	7107	1A	hsa-miR-140^brain	AGUGGUUUUACCCUAUGGUAG
miR-145	9582	9588	m8	hsa-miR-145	GUCCAGUUUUCCCAGGAAUCCCUU
miR-153	8054	8060	m8	hsa-miR-153	UUGCAUAGUCACAAAAGUGA
miR-17-5p/20/93.mr/106/519.d	8058	8064	m8	hsa-miR-17-5p	CAAAGUGCUUACAGUGCAGGUAGU
				hsa-miR-20a^brain	UAAAGUGCUUAUAGUGCAGGUAG
				hsa-miR-106a	AAAAGUGCUUACAGUGCAGGUAGC
				hsa-miR-106b^SZ	UAAAGUGCUGACAGUGCAGAU
				hsa-miR-20b^SZ	CAAAGUGCUCAUAGUGCAGGUAG
				hsa-miR-519d	CAAAGUGCCUCCCUUUAGAGUGU
miR-182	182	189	1A,m8	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-182	182	189	1A,m8	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-19	6614	6620	1A	hsa-miR-19a	UGUGCAAAUCUAUGCAAAACUGA
miR-19	6614	6620	1A	hsa-miR-19b	UGUGCAAAUCCAUGCAAAACUGA
miR-200bc/429	1806	1813	1A,m8	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-203.1	9564	9571	1A,m8	hsa-miR-203	UGAAAUGUUUAGGACCACUAG
miR-218	8735	8741	m8	hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
				hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
				hsa-miR-218^brain	UUGUGCUUGAUCUAACCAUGU
miR-24*	2362	2368	1A	hsa-miR-189	GUGCCUACUGAGCUGAUAUCAGU
miR-27	9613	9619	1A	hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
				hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
				hsa-miR-27a^brain	UUCACAGUGGCUAAGUUCCGC
				hsa-miR-27b^brain	UUCACAGUGGCUAAGUUCUGC
miR-29	7323	7329	m8	hsa-miR-29a^SZ	UAGCACCAUCUGAAAUCGGUU
				hsa-miR-29b^SZ	UAGCACCAUUUGAAAUCAGUGUU
				hsa-miR-29c^SZ	UAGCACCAUUUGAAAUCGGU
miR-30-5p	108	114	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-31	277	284	1A,m8	hsa-miR-31	AGGCAAGAUGCUGGCAUAGCUG
miR-31	277	284	1A,m8	hsa-miR-31	AGGCAAGAUGCUGGCAUAGCUG
miR-338	244	250	1A	hsa-miR-338^brain	UCCAGCAUCAGUGAUUUUGUUGA
miR-381	6654	6660	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-381	6654	6660	1A	hsa-miR-381	UAUACAAGGGCAAGCUCUCUGU
miR-96	4388	4394	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: SLC1A2