Gene Page: SLC6A1

Summary ?
GeneID6529
SymbolSLC6A1
SynonymsGABATHG|GABATR|GAT1|MAE
Descriptionsolute carrier family 6 member 1
ReferenceMIM:137165|HGNC:HGNC:11042|Ensembl:ENSG00000157103|HPRD:00664|Vega:OTTHUMG00000044208
Gene typeprotein-coding
Map location3p25.3
Pascal p-value0.427
Fetal beta-2.042
DMG1 (# studies)
eGeneCerebellar Hemisphere
Myers' cis & trans
SupportNEUROTRANSMITTER METABOLISM
CompositeSet
Darnell FMRP targets

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:GWASdbGenome-wide Association StudiesGWASdb records for schizophrenia
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.
GSMA_IGenome scan meta-analysisPsr: 0.006 
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenics,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 5 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg00162231311035357SLC6A16.019E-4-0.7790.05DMG:Wockner_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs1707266chr1211554194SLC6A165290.07trans
rs7124090chr113744078SLC6A165290.12trans

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
PPAP2B0.870.87
PON20.860.87
PLSCR40.860.83
PSAT10.850.82
AQP40.840.87
S1PR10.830.86
GLUD10.830.83
SLC1A30.820.89
RAB310.820.82
GJA10.810.82
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
DPF1-0.40-0.50
MYT1L-0.40-0.48
FAM131B-0.40-0.48
NELL2-0.40-0.51
CAMKV-0.40-0.45
FAM49A-0.39-0.49
RAB33A-0.39-0.53
ADD2-0.39-0.49
MARCH4-0.39-0.48
MPPED1-0.39-0.50

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005332gamma-aminobutyric acid:sodium symporter activityIEAGABA, Neurotransmitter (GO term level: 11)-
GO:0005328neurotransmitter:sodium symporter activityIEANeurotransmitter (GO term level: 9)-
GO:0015293symporter activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007268synaptic transmissionTASneuron, Synap, Neurotransmitter (GO term level: 6)8530094 
GO:0006836neurotransmitter transportIEAneuron, Neurotransmitter (GO term level: 5)-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0030424axonIEAneuron, axon, Neurotransmitter (GO term level: 6)-
GO:0005624membrane fractionTAS2387399 
GO:0005886plasma membraneIEA-
GO:0005887integral to plasma membraneIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
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 GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 8954All SZGR 2.0 genes in this pathway
REACTOME NA CL DEPENDENT NEUROTRANSMITTER TRANSPORTERS 1712All SZGR 2.0 genes in this pathway
REACTOME AMINE COMPOUND SLC TRANSPORTERS 2716All SZGR 2.0 genes in this pathway
REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION 1716All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP 443294All SZGR 2.0 genes in this pathway
BENPORATH SUZ12 TARGETS 1038678All SZGR 2.0 genes in this pathway
BENPORATH EED TARGETS 1062725All SZGR 2.0 genes in this pathway
BENPORATH ES WITH H3K27ME3 1118744All SZGR 2.0 genes in this pathway
BENPORATH PRC2 TARGETS 652441All SZGR 2.0 genes in this pathway
STARK PREFRONTAL CORTEX 22Q11 DELETION UP 195138All SZGR 2.0 genes in this pathway
CHESLER BRAIN D6MIT150 QTL CIS 76All SZGR 2.0 genes in this pathway
CHESLER BRAIN D6MIT150 QTL TRANS 97All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237837All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE BY GAMMA AND UV RADIATION 8865All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE UP 226164All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP 863514All SZGR 2.0 genes in this pathway
HUNSBERGER EXERCISE REGULATED GENES 3126All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 1069729All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3 435318All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SUBCLASS S3 266180All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES DN 210141All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC UP 7253All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3 590403All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 1HR UP 6144All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM B 517302All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
let-7/989399m8hsa-let-7abrainUGAGGUAGUAGGUUGUAUAGUU
hsa-let-7bbrainUGAGGUAGUAGGUUGUGUGGUU
hsa-let-7cbrainUGAGGUAGUAGGUUGUAUGGUU
hsa-let-7dbrainAGAGGUAGUAGGUUGCAUAGU
hsa-let-7ebrainUGAGGUAGGAGGUUGUAUAGU
hsa-let-7fbrainUGAGGUAGUAGAUUGUAUAGUU
hsa-miR-98brainUGAGGUAGUAAGUUGUAUUGUU
hsa-let-7gSZUGAGGUAGUAGUUUGUACAGU
hsa-let-7ibrainUGAGGUAGUAGUUUGUGCUGU
miR-12816881694m8hsa-miR-128aUCACAGUGAACCGGUCUCUUUU
hsa-miR-128bUCACAGUGAACCGGUCUCUUUC
hsa-miR-128aUCACAGUGAACCGGUCUCUUUU
hsa-miR-128bUCACAGUGAACCGGUCUCUUUC
miR-132/212353359m8hsa-miR-212SZUAACAGUCUCCAGUCACGGCC
hsa-miR-132brainUAACAGUCUACAGCCAUGGUCG
miR-133214921551Ahsa-miR-133aUUGGUCCCCUUCAACCAGCUGU
hsa-miR-133bUUGGUCCCCUUCAACCAGCUA
miR-138140114071Ahsa-miR-138brainAGCUGGUGUUGUGAAUC
miR-200bc/429211821251A,m8hsa-miR-200bUAAUACUGCCUGGUAAUGAUGAC
hsa-miR-200cUAAUACUGCCGGGUAAUGAUGG
hsa-miR-429UAAUACUGUCUGGUAAAACCGU
miR-21814461452m8hsa-miR-218brainUUGUGCUUGAUCUAACCAUGU
hsa-miR-218brainUUGUGCUUGAUCUAACCAUGU
hsa-miR-218brainUUGUGCUUGAUCUAACCAUGU
miR-22544550m8hsa-miR-22brainAAGCUGCCAGUUGAAGAACUGU
miR-25/32/92/363/367201120171Ahsa-miR-25brainCAUUGCACUUGUCUCGGUCUGA
hsa-miR-32UAUUGCACAUUACUAAGUUGC
hsa-miR-92UAUUGCACUUGUCCCGGCCUG
hsa-miR-367AAUUGCACUUUAGCAAUGGUGA
hsa-miR-92bSZUAUUGCACUCGUCCCGGCCUC
hsa-miR-25brainCAUUGCACUUGUCUCGGUCUGA
hsa-miR-32UAUUGCACAUUACUAAGUUGC
hsa-miR-92UAUUGCACUUGUCCCGGCCUG
hsa-miR-367AAUUGCACUUUAGCAAUGGUGA
hsa-miR-92bSZUAUUGCACUCGUCCCGGCCUC
miR-27193619431A,m8hsa-miR-27abrainUUCACAGUGGCUAAGUUCCGC
hsa-miR-27bbrainUUCACAGUGGCUAAGUUCUGC
miR-369-3p21202126m8hsa-miR-369-3pAAUAAUACAUGGUUGAUCUUU
hsa-miR-369-3pAAUAAUACAUGGUUGAUCUUU
miR-37622682274m8hsa-miR-376aAUCAUAGAGGAAAAUCCACGU
hsa-miR-376bAUCAUAGAGGAAAAUCCAUGUU
miR-496215621621Ahsa-miR-496AUUACAUGGCCAAUCUC