Gene Page: SLC6A5
Summary ?
| GeneID | 9152 |
| Symbol | SLC6A5 |
| Synonyms | GLYT-2|GLYT2|HKPX3|NET1 |
| Description | solute carrier family 6 member 5 |
| Reference | MIM:604159|HGNC:HGNC:11051|HPRD:08378| |
| Gene type | protein-coding |
| Map location | 11p15.1 |
| Pascal p-value | 0.882 |
| Sherlock p-value | 0.407 |
| Fetal beta | 0.145 |
| DMG | 1 (# studies) |
| eGene | Myers' cis & trans |
| Support | NEUROTRANSMITTER METABOLISM |
Gene in Data Sources
| Gene set name | Method of gene set | Description | Info |
|---|---|---|---|
| CV:PGCnp | Genome-wide Association Study | GWAS | |
| DMG:Jaffe_2016 | Genome-wide DNA methylation analysis | This dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. | 1 |
| 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
Differentially methylated gene
| Probe | Chromosome | Position | Nearest gene | P (dis) | Beta (dis) | FDR (dis) | Study |
|---|---|---|---|---|---|---|---|
| cg20632573 | 11 | 20621341 | SLC6A5 | 1.6E-8 | -0.025 | 5.94E-6 | DMG:Jaffe_2016 |
eQTL annotation
| SNP ID | Chromosome | Position | eGene | Gene Entrez ID | pvalue | qvalue | TSS distance | eQTL type |
|---|---|---|---|---|---|---|---|---|
| rs2385509 | chr1 | 237006972 | SLC6A5 | 9152 | 0.14 | trans |
Section II. Transcriptome annotation
General gene expression (GTEx)
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 |
| ACSBG1 | 0.95 | 0.96 |
| SFXN5 | 0.93 | 0.92 |
| SLC13A5 | 0.92 | 0.88 |
| GRIN2C | 0.92 | 0.91 |
| ATP1A2 | 0.91 | 0.84 |
| ACOT11 | 0.91 | 0.90 |
| SCARA3 | 0.90 | 0.82 |
| ACSS1 | 0.90 | 0.80 |
| ATP1B2 | 0.90 | 0.75 |
| SLC25A18 | 0.90 | 0.93 |
| Top 10 negatively co-expressed genes | ||
| Gene | Pearson's Correlation | Spearman's Correlation |
| MED19 | -0.68 | -0.80 |
| MLLT11 | -0.68 | -0.80 |
| DUSP12 | -0.67 | -0.82 |
| ASNSD1 | -0.66 | -0.80 |
| SPATS2 | -0.66 | -0.81 |
| PPP3CC | -0.65 | -0.79 |
| UBE2E3 | -0.65 | -0.76 |
| GSTA4 | -0.65 | -0.81 |
| SUPV3L1 | -0.65 | -0.81 |
| RAE1 | -0.65 | -0.77 |
Section III. Gene Ontology annotation
| Molecular function | GO term | Evidence | Neuro keywords | PubMed ID |
|---|---|---|---|---|
| GO:0005328 | neurotransmitter:sodium symporter activity | IEA | Neurotransmitter (GO term level: 9) | - |
| GO:0016855 | racemase and epimerase activity, acting on amino acids and derivatives | IEA | - | |
| GO:0015375 | glycine:sodium symporter activity | TAS | 9845349 | |
| GO:0015293 | symporter activity | IEA | - | |
| Biological process | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0007268 | synaptic transmission | TAS | neuron, Synap, Neurotransmitter (GO term level: 6) | 9845349 |
| GO:0006836 | neurotransmitter transport | IEA | neuron, Neurotransmitter (GO term level: 5) | - |
| GO:0008152 | metabolic process | IEA | - | |
| Cellular component | GO term | Evidence | Neuro keywords | PubMed ID |
| GO:0016020 | 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 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 |
| ROVERSI GLIOMA LOH REGIONS | 44 | 30 | 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 |
| LEIN PONS MARKERS | 89 | 59 | All SZGR 2.0 genes in this pathway |
| LEIN MEDULLA MARKERS | 81 | 48 | 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 S2 | 115 | 74 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN NPC HCP WITH H3K27ME3 | 341 | 243 | All SZGR 2.0 genes in this pathway |
| MIKKELSEN MEF HCP WITH H3K27ME3 | 590 | 403 | All SZGR 2.0 genes in this pathway |
| ZWANG CLASS 1 TRANSIENTLY INDUCED BY EGF | 516 | 308 | All SZGR 2.0 genes in this pathway |