SZGR2

Summary ?

GeneID	6505
Symbol	SLC1A1
Synonyms	DCBXA\|EAAC1\|EAAT3\|SCZD18
Description	solute carrier family 1 member 1
Reference	MIM:133550\|HGNC:HGNC:10939\|Ensembl:ENSG00000106688\|HPRD:00597\|Vega:OTTHUMG00000019468
Gene type	protein-coding
Map location	9p24
Pascal p-value	0.412
Sherlock p-value	0.125
eGene	Cerebellar Hemisphere Myers' cis & trans
Support	METABOTROPIC GLUTAMATE RECEPTOR NEUROTRANSMITTER METABOLISM Potential synaptic genes

Gene in Data Sources

Gene set name	Method of gene set	Description	Info
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,schizophrenic,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	pvalue	qvalue	TSS distance	eQTL type
rs7084863	chr10	6753797	SLC1A1	6505		0.15		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
ATRN	0.91	0.93
LARP4B	0.89	0.90
ABHD2	0.89	0.90
MGAT5	0.89	0.90
CEP68	0.88	0.89
ATP9A	0.88	0.90
KIAA1432	0.88	0.90
MTOR	0.88	0.90
HDAC4	0.87	0.89
SRGAP3	0.87	0.89

Top 10 negatively co-expressed genes
Gene	Pearson's Correlation	Spearman's Correlation
C1orf54	-0.63	-0.71
AF347015.21	-0.62	-0.68
FXYD1	-0.62	-0.61
MT-CO2	-0.60	-0.64
AF347015.31	-0.60	-0.63
HIGD1B	-0.59	-0.62
SAT1	-0.59	-0.63
S100A13	-0.59	-0.63
AC021016.1	-0.57	-0.58
VAMP5	-0.57	-0.55

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:0005887	integral to plasma membrane	TAS		7521911

Section V. Pathway annotation

Pathway name	Pathway size	# SZGR 2.0 genes in pathway	Info
REACTOME GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE	15	13	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 NEUROTRANSMITTER RELEASE CYCLE	34	30	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
NAKAMURA TUMOR ZONE PERIPHERAL VS CENTRAL DN	634	384	All SZGR 2.0 genes in this pathway
ONKEN UVEAL MELANOMA UP	783	507	All SZGR 2.0 genes in this pathway
DEURIG T CELL PROLYMPHOCYTIC LEUKEMIA UP	368	234	All SZGR 2.0 genes in this pathway
NEWMAN ERCC6 TARGETS DN	39	24	All SZGR 2.0 genes in this pathway
BASAKI YBX1 TARGETS DN	384	230	All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR UP	557	331	All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA POORLY DIFFERENTIATED DN	805	505	All SZGR 2.0 genes in this pathway
GOZGIT ESR1 TARGETS DN	781	465	All SZGR 2.0 genes in this pathway
COLDREN GEFITINIB RESISTANCE DN	230	115	All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER DN	232	154	All SZGR 2.0 genes in this pathway
CONCANNON APOPTOSIS BY EPOXOMICIN DN	172	112	All SZGR 2.0 genes in this pathway
MAHADEVAN IMATINIB RESISTANCE UP	23	15	All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN DN	584	395	All SZGR 2.0 genes in this pathway
NUYTTEN NIPP1 TARGETS DN	848	527	All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN	428	306	All SZGR 2.0 genes in this pathway
BENPORATH NANOG TARGETS	988	594	All SZGR 2.0 genes in this pathway
CERVERA SDHB TARGETS 1 UP	118	66	All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN	546	351	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
PETROVA ENDOTHELIUM LYMPHATIC VS BLOOD DN	162	102	All SZGR 2.0 genes in this pathway
LU AGING BRAIN DN	153	120	All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN	1237	837	All SZGR 2.0 genes in this pathway
KAYO AGING MUSCLE UP	244	165	All SZGR 2.0 genes in this pathway
EHRLICH ICF SYNDROM DN	15	13	All SZGR 2.0 genes in this pathway
IVANOVA HEMATOPOIESIS STEM CELL AND PROGENITOR	681	420	All SZGR 2.0 genes in this pathway
KAYO CALORIE RESTRICTION MUSCLE UP	95	64	All SZGR 2.0 genes in this pathway
RIGGINS TAMOXIFEN RESISTANCE DN	220	147	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN BONE UP	97	61	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER RELAPSE IN LUNG DN	37	22	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B UP	172	109	All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN	701	446	All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL CULTURED VS FRESH UP	425	298	All SZGR 2.0 genes in this pathway
MOOTHA HUMAN MITODB 6 2002	429	260	All SZGR 2.0 genes in this pathway
MOOTHA MITOCHONDRIA	447	277	All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP	1305	895	All SZGR 2.0 genes in this pathway
HAN SATB1 TARGETS DN	442	275	All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A12	317	177	All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3 UNMETHYLATED	536	296	All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA DN	267	160	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 9	76	45	All SZGR 2.0 genes in this pathway
VERHAAK GLIOBLASTOMA PRONEURAL	177	132	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
FEVR CTNNB1 TARGETS UP	682	433	All SZGR 2.0 genes in this pathway
GOBERT OLIGODENDROCYTE DIFFERENTIATION DN	1080	713	All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A	770	480	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-101	606	613	1A,m8	hsa-miR-101	UACAGUACUGUGAUAACUGAAG
miR-141/200a	638	644	m8	hsa-miR-141	UAACACUGUCUGGUAAAGAUGG
miR-141/200a	638	644	m8	hsa-miR-200a	UAACACUGUCUGGUAACGAUGU
miR-144	607	613	1A	hsa-miR-144	UACAGUAUAGAUGAUGUACUAG
miR-182	1525	1531	1A	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-182	1525	1531	1A	hsa-miR-182	UUUGGCAAUGGUAGAACUCACA
miR-23	729	736	1A,m8	hsa-miR-23a^brain	AUCACAUUGCCAGGGAUUUCC
miR-23	729	736	1A,m8	hsa-miR-23b^brain	AUCACAUUGCCAGGGAUUACC
miR-26	754	761	1A,m8	hsa-miR-26a^brain	UUCAAGUAAUCCAGGAUAGGC
miR-26	754	761	1A,m8	hsa-miR-26b^SZ	UUCAAGUAAUUCAGGAUAGGUU
miR-323	729	735	1A	hsa-miR-323^brain	GCACAUUACACGGUCGACCUCU
miR-374	441	447	1A	hsa-miR-374	UUAUAAUACAACCUGAUAAGUG
miR-539	322	328	1A	hsa-miR-539	GGAGAAAUUAUCCUUGGUGUGU
miR-9	1527	1533	1A	hsa-miR-9^SZ	UCUUUGGUUAUCUAGCUGUAUGA
miR-96	1524	1531	1A,m8	hsa-miR-96^brain	UUUGGCACUAGCACAUUUUUGC
miR-96	1524	1531	1A,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: SLC1A1