Gene Page: SLC1A6

Summary ?
GeneID6511
SymbolSLC1A6
SynonymsEAAT4
Descriptionsolute carrier family 1 member 6
ReferenceMIM:600637|HGNC:HGNC:10944|Ensembl:ENSG00000105143|HPRD:09005|Vega:OTTHUMG00000183351
Gene typeprotein-coding
Map location19p13.12
Pascal p-value0.445
Sherlock p-value0.892
Fetal beta-0.533
DMG1 (# studies)
eGeneCaudate basal ganglia
Nucleus accumbens basal ganglia
Myers' cis & trans
SupportMETABOTROPIC GLUTAMATE RECEPTOR
NEUROTRANSMITTER METABOLISM
Potential synaptic genes

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 1
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
AssociationA combined odds ratio method (Sun et al. 2008), association studies1Link to SZGene
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 4 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg103852901915083818SLC1A61.662E-40.7030.033DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs6424090chr13628676SLC1A665110.03trans
rs4950337chr1147193821SLC1A665110.01trans
snp_a-42901430SLC1A665110.02trans
rs17572651chr1218943612SLC1A665110.15trans
rs16829545chr2151977407SLC1A665114.003E-9trans
rs16858054chr2171105787SLC1A665110.08trans
rs3845734chr2171125572SLC1A665117.721E-6trans
rs7584986chr2184111432SLC1A665111.137E-11trans
snp_a-18157710SLC1A665110.09trans
rs7655318chr4153620763SLC1A665110.16trans
rs2183142chr4159232695SLC1A665110trans
rs17762315chr576807576SLC1A665110.12trans
rs10491487chr580323367SLC1A665110.07trans
rs9461864chr633481468SLC1A665110.01trans
rs1929780chr640757438SLC1A665110.05trans
rs1929769chr640765977SLC1A665110.01trans
rs2251379chr873623854SLC1A665110.05trans
rs16924081chr96169134SLC1A665110.1trans
rs9406868chr925223372SLC1A665110.09trans
rs2225105chr925480908SLC1A665110.03trans
rs11139334chr984209393SLC1A665110.01trans
rs7036187chr988602015SLC1A665110.06trans
snp_a-42676730SLC1A665110.01trans
rs3765543chr9134458323SLC1A665110.17trans
rs754765chr10132013664SLC1A665110.04trans
rs4076396chr117490235SLC1A665110.18trans
rs17070045chr1358400458SLC1A665110.18trans
rs17746210chr1527882820SLC1A665110.03trans
rs16955618chr1529937543SLC1A665112.173E-16trans
rs2077735chr1558479024SLC1A665110.09trans
snp_a-42512820SLC1A665110.08trans
rs4782029chr1617248015SLC1A665110.17trans
rs16952513chr1680165482SLC1A665110.16trans
rs16945437chr1711797650SLC1A665118.747E-5trans
rs16978352chr1842944875SLC1A665110.03trans
rs17761686chr1856647634SLC1A665110.14trans
rs11882889chr1919887684SLC1A665118.43E-4trans
rs7274477chr201676942SLC1A665110.11trans
rs1041786chr2122617710SLC1A665110.02trans
rs16986332chrX10958354SLC1A665110.07trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

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
GenePearson's Correlation Spearman's Correlation
KIAA03170.890.92
TTC90.870.90
KIF3C0.870.90
HGSNAT0.870.90
NRXN10.860.89
PCDHAC10.860.90
MAPT0.860.91
PCYOX10.860.88
KLHL180.850.91
AC092324.10.850.91
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.31-0.71-0.75
FXYD1-0.70-0.73
MT-CO2-0.69-0.74
AC021016.1-0.69-0.76
AF347015.33-0.68-0.70
AF347015.27-0.67-0.72
COPZ2-0.67-0.71
AF347015.8-0.67-0.73
HIGD1B-0.66-0.74
MT-CYB-0.66-0.70

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0015183L-aspartate transmembrane transporter activityTASglutamate (GO term level: 9)7791878 
GO:0015293symporter activityIEA-
GO:0017153sodium:dicarboxylate symporter activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007268synaptic transmissionTASneuron, Synap, Neurotransmitter (GO term level: 6)7791878 
GO:0015813L-glutamate transportTASglutamate (GO term level: 9)7791878 
GO:0015810aspartate transportTASglutamate (GO term level: 9)7791878 
GO:0006835dicarboxylic acid transportIEA-
GO:0006810transportIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005624membrane fractionTAS7791878 
GO:0016020membraneIEA-
GO:0005887integral to plasma membraneTAS7791878 

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
REACTOME GLUTAMATE NEUROTRANSMITTER RELEASE CYCLE 1513All SZGR 2.0 genes in this pathway
REACTOME TRANSMISSION ACROSS CHEMICAL SYNAPSES 186155All SZGR 2.0 genes in this pathway
REACTOME NEURONAL SYSTEM 279221All SZGR 2.0 genes in this pathway
REACTOME NEUROTRANSMITTER RELEASE CYCLE 3430All SZGR 2.0 genes in this pathway
REACTOME TRANSMEMBRANE TRANSPORT OF SMALL MOLECULES 413270All SZGR 2.0 genes in this pathway
REACTOME SLC MEDIATED TRANSMEMBRANE TRANSPORT 241157All SZGR 2.0 genes in this pathway
REACTOME TRANSPORT OF INORGANIC CATIONS ANIONS AND AMINO ACIDS OLIGOPEPTIDES 9465All SZGR 2.0 genes in this pathway
REACTOME AMINO ACID AND OLIGOPEPTIDE SLC TRANSPORTERS 4936All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 6HR DN 4129All SZGR 2.0 genes in this pathway
ENK UV RESPONSE EPIDERMIS DN 508354All SZGR 2.0 genes in this pathway
ENK UV RESPONSE KERATINOCYTE UP 530342All SZGR 2.0 genes in this pathway
MARKEY RB1 CHRONIC LOF DN 11878All SZGR 2.0 genes in this pathway
GAUSSMANN MLL AF4 FUSION TARGETS E UP 9760All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN 428306All SZGR 2.0 genes in this pathway
LEE TARGETS OF PTCH1 AND SUFU DN 8369All SZGR 2.0 genes in this pathway
AFFAR YY1 TARGETS UP 214133All SZGR 2.0 genes in this pathway
WANG SMARCE1 TARGETS DN 371218All SZGR 2.0 genes in this pathway
LABBE TARGETS OF TGFB1 AND WNT3A DN 10868All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305895All SZGR 2.0 genes in this pathway
MEISSNER NPC HCP WITH H3K4ME2 491319All SZGR 2.0 genes in this pathway