Gene Page:SLC6A1

Summary?
GeneID 6529
Symbol SLC6A1
Synonyms GABATHG|GABATR|GAT1|MAE
Description solute carrier family 6 member 1
Reference MIM:137165|HGNC:HGNC:11042|Ensembl:ENSG00000157103|HPRD:00664|Vega:OTTHUMG00000044208
Gene type protein-coding
Map location 3p25.3
Pascal p-value 0.427
Fetal beta -2.042
DMG 1 (# studies)
eGene Cerebellar Hemisphere
Myers' cis & trans
Support NEUROTRANSMITTER METABOLISM
CompositeSet
Darnell FMRP targets

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
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 系统的搜索在酒吧Med for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
GSMA_I Genome scan meta-analysis Psr: 0.006
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: 5

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

Probe Chromosome Position Nearest gene P (dis) Beta (dis) FDR (dis) Study
cg00162231 3 11035357 SLC6A1 6.019E-4 -0.779 0.05 DMG:Wockner_2014

@eQTL annotation

SNP ID Chromosome Position eGene Gene Entrez ID pvalue qvalue TSS distance eQTL type
rs1707266 chr1 211554194 SLC6A1 6529 0.07 trans
rs7124090 chr11 3744078 SLC6A1 6529 0.12 trans

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
Gene Pearson's Correlation Spearman's Correlation
PPAP2B 0.87 0.87
PON2 0.86 0.87
PLSCR4 0.86 0.83
PSAT1 0.85 0.82
AQP4 0.84 0.87
S1PR1 0.83 0.86
GLUD1 0.83 0.83
SLC1A3 0.82 0.89
RAB31 0.82 0.82
GJA1 0.81 0.82
Top 10 negatively co-expressed genes
Gene Pearson'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 function 去的术语 Evidence Neuro keywords PubMed ID
GO:0005332 gamma-aminobutyric acid:sodium symporter activity IEA GABA, Neurotransmitter (GO term level: 11) -
GO:0005328 neurotransmitter:sodium symporter activity IEA Neurotransmitter (GO term level: 9) -
GO:0015293 symporter activity IEA -
Biological process 去的术语 Evidence Neuro keywords PubMed ID
GO:0007268 synaptic transmission TAS neuron, Synap, Neurotransmitter (GO term level: 6) 8530094
GO:0006836 neurotransmitter transport IEA neuron, Neurotransmitter (GO term level: 5) -
Cellular component 去的术语 Evidence Neuro keywords PubMed ID
GO:0030424 axon IEA neuron, axon, Neurotransmitter (GO term level: 6) -
GO:0005624 membrane fraction TAS 2387399
GO:0005886 plasma membrane IEA -
GO:0005887 integral to plasma membrane IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
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神经递质释放周期 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 GLUCOSE AND OTHER SUGARS BILE SALTS AND ORGANIC ACIDS METAL IONS AND AMINE COMPOUNDS 89 54 All SZGR 2.0 genes in this pathway
REACTOME NA CL DEPENDENT NEUROTRANSMITTER TRANSPORTERS 17 12 All SZGR 2.0 genes in this pathway
REACTOME AMINE COMPOUND SLC TRANSPORTERS 27 16 All SZGR 2.0 genes in this pathway
REACTOME GABA SYNTHESIS RELEASE REUPTAKE AND DEGRADATION 17 16 All SZGR 2.0 genes in this pathway
DELYS THYROID CANCER UP 443 294 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
CHESLER BRAIN D6MIT150 QTL CIS 7 6 All SZGR 2.0 genes in this pathway
CHESLER BRAIN D6MIT150 QTL TRANS 9 7 All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237 837 All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE BY GAMMA AND UV RADIATION 88 65 All SZGR 2.0 genes in this pathway
KYNG DNA DAMAGE UP 226 164 All SZGR 2.0 genes in this pathway
ACEVEDO LIVER TUMOR VS NORMAL ADJACENT TISSUE UP 863 514 All SZGR 2.0 genes in this pathway
HUNSBERGER EXERCISE REGULATED GENES 31 26 All SZGR 2.0 genes in this pathway
MEISSNER BRAIN HCP WITH H3K4ME3 AND H3K27ME3 1069 729 All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 HCP WITH H3K27ME3 435 318 All SZGR 2.0 genes in this pathway
HOSHIDA LIVER CANCER SUBCLASS S3 266 180 All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA CLASSES DN 210 141 All SZGR 2.0 genes in this pathway
DANG REGULATED BY MYC UP 72 53 All SZGR 2.0 genes in this pathway
MIKKELSEN MEF HCP WITH H3K27ME3 590 403 All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 1HR UP 61 44 All SZGR 2.0 genes in this pathway
RAO BOUND BY SALL4 ISOFORM B 517 302 All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA family Target position miRNA ID miRNA seq
UTR start UTR end Match method
let-7/98 93 99 m8 hsa-let-7abrain UGAGGUAGUAGGUUGUAUAGUU
hsa-let-7bbrain UGAGGUAGUAGGUUGUGUGGUU
hsa-let-7cbrain UGAGGUAGUAGGUUGUAUGGUU
hsa-let-7dbrain AGAGGUAGUAGGUUGCAUAGU
hsa-let-7ebrain UGAGGUAGGAGGUUGUAUAGU
hsa-let-7fbrain UGAGGUAGUAGAUUGUAUAGUU
hsa-miR-98brain UGAGGUAGUAAGUUGUAUUGUU
hsa-let-7gSZ UGAGGUAGUAGUUUGUACAGU
hsa-let-7ibrain UGAGGUAGUAGUUUGUGCUGU
miR-128 1688 1694 m8 hsa-miR-128a UCACAGUGAACCGGUCUCUUUU
hsa-miR-128b UCACAGUGAACCGGUCUCUUUC
hsa-miR-128a UCACAGUGAACCGGUCUCUUUU
hsa-miR-128b UCACAGUGAACCGGUCUCUUUC
miR-132/212 353 359 m8 hsa-miR-212SZ UAACAGUCUCCAGUCACGGCC
hsa-miR-132brain UAACAGUCUACAGCCAUGGUCG
miR-133 2149 2155 1A hsa-miR-133a UUGGUCCCCUUCAACCAGCUGU
hsa-miR-133b UUGGUCCCCUUCAACCAGCUA
miR-138 1401 1407 1A hsa-miR-138brain AGCUGGUGUUGUGAAUC
miR-200bc/429 2118 2125 1A,m8 hsa-miR-200b UAAUACUGCCUGGUAAUGAUGAC
hsa-miR-200c UAAUACUGCCGGGUAAUGAUGG
hsa-miR-429 UAAUACUGUCUGGUAAAACCGU
miR-218 1446 1452 m8 hsa-miR-218brain UUGUGCUUGAUCUAACCAUGU
hsa-miR-218brain UUGUGCUUGAUCUAACCAUGU
hsa-miR-218brain UUGUGCUUGAUCUAACCAUGU
miR-22 544 550 m8 hsa-miR-22brain AAGCUGCCAGUUGAAGAACUGU
miR-25/32/92/363/367 2011 2017 1A hsa-miR-25brain CAUUGCACUUGUCUCGGUCUGA
hsa-miR-32 UAUUGCACAUUACUAAGUUGC
hsa-miR-92 UAUUGCACUUGUCCCGGCCUG
hsa-miR-367 AAUUGCACUUUAGCAAUGGUGA
hsa-miR-92bSZ UAUUGCACUCGUCCCGGCCUC
hsa-miR-25brain CAUUGCACUUGUCUCGGUCUGA
hsa-miR-32 UAUUGCACAUUACUAAGUUGC
hsa-miR-92 UAUUGCACUUGUCCCGGCCUG
hsa-miR-367 AAUUGCACUUUAGCAAUGGUGA
hsa-miR-92bSZ UAUUGCACUCGUCCCGGCCUC
miR-27 1936 1943 1A,m8 hsa-miR-27abrain UUCACAGUGGCUAAGUUCCGC
hsa-miR-27bbrain UUCACAGUGGCUAAGUUCUGC
miR-369-3p 2120 2126 m8 hsa-miR-369-3p AAUAAUACAUGGUUGAUCUUU
hsa-miR-369-3p AAUAAUACAUGGUUGAUCUUU
miR-376 2268 2274 m8 hsa-miR-376a AUCAUAGAGGAAAAUCCACGU
hsa-miR-376b AUCAUAGAGGAAAAUCCAUGUU
miR-496 2156 2162 1A hsa-miR-496 AUUACAUGGCCAAUCUC