Gene Page: SLC6A13

Summary ?
GeneID6540
SymbolSLC6A13
SynonymsGAT-2|GAT2|GAT3
Descriptionsolute carrier family 6 member 13
ReferenceMIM:615097|HGNC:HGNC:11046|Ensembl:ENSG00000010379|HPRD:10239|Vega:OTTHUMG00000168053
Gene typeprotein-coding
Map location12p13.3
Pascal p-value0.811
Sherlock p-value0.936
Fetal beta-0.22
eGeneMyers' cis & trans

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophreniasClick to show details
GO_AnnotationMapping neuro-related keywords to Gene Ontology annotationsHits with neuro-related keywords: 2 

Section I. Genetics and epigenetics annotation

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs4654497chr14224557SLC6A1365400.12trans
rs2976809chr3125451738SLC6A1365400.13trans
rs3110902chr765375101SLC6A1365400.14trans
rs4725560chr7139640566SLC6A1365400.15trans
rs680372chr836999626SLC6A1365400.16trans
rs7041951chr920275353SLC6A1365400.07trans
rs10733768chr1052667246SLC6A1365400.17trans
rs11016704chr10128989145SLC6A1365400.03trans
rs481843chr11116525866SLC6A1365400.06trans
rs6589566chr11116652422SLC6A1365400.01trans
rs9529974chr1372821935SLC6A1365400.1trans
rs17540750chr1775205144SLC6A1365400.05trans
rs6095741chr2048666589SLC6A1365400.03trans
rs17255719chrX12144766SLC6A1365400.13trans
rs5991662chrX43335796SLC6A1365400.1trans
rs12556892chrX93417735SLC6A1365400.17trans
rs808754chrX93438033SLC6A1365400.17trans
rs6529399chrX128763582SLC6A1365400.03trans
rs3761581chrX128789720SLC6A1365400.01trans

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
PTOV10.930.86
TSEN340.930.89
WDR340.930.89
PPP4C0.920.85
RALY0.920.85
PYCR10.920.87
WRAP530.920.82
NT5DC20.920.88
DDAH20.910.88
MARCKSL10.910.89
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
C5orf53-0.69-0.71
AF347015.27-0.66-0.74
AF347015.31-0.64-0.73
CA4-0.64-0.68
MT-CO2-0.63-0.73
HLA-F-0.63-0.61
AF347015.33-0.63-0.72
MT-CYB-0.62-0.72
CCNI2-0.62-0.63
PLA2G4A-0.61-0.68

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005328neurotransmitter:sodium symporter activityIEANeurotransmitter (GO term level: 9)-
GO:0015293symporter activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0006836neurotransmitter transportIEAneuron, Neurotransmitter (GO term level: 5)-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0016020membraneIEA-
GO:0005887integral to plasma membraneIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
ST WNT CA2 CYCLIC GMP PATHWAY 2014All SZGR 2.0 genes in this pathway
SENGUPTA NASOPHARYNGEAL CARCINOMA WITH LMP1 DN 17582All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 8D UP 15791All SZGR 2.0 genes in this pathway
TAKEDA TARGETS OF NUP98 HOXA9 FUSION 10D UP 194122All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC DN 537339All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747453All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS DN 357212All SZGR 2.0 genes in this pathway
SHEPARD BMYB MORPHOLINO DN 200112All SZGR 2.0 genes in this pathway
MOREAUX MULTIPLE MYELOMA BY TACI UP 412249All SZGR 2.0 genes in this pathway
SU KIDNEY 158All SZGR 2.0 genes in this pathway
ZAMORA NOS2 TARGETS DN 9671All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305895All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A12 317177All SZGR 2.0 genes in this pathway
MIKKELSEN MCV6 LCP WITH H3K27ME3 2911All SZGR 2.0 genes in this pathway
TORCHIA TARGETS OF EWSR1 FLI1 FUSION TOP20 DN 1812All SZGR 2.0 genes in this pathway
TORCHIA TARGETS OF EWSR1 FLI1 FUSION DN 321200All SZGR 2.0 genes in this pathway
FOSTER KDM1A TARGETS UP 266142All SZGR 2.0 genes in this pathway