Gene Page: SLC1A4

Summary ?
GeneID6509
SymbolSLC1A4
SynonymsASCT1|SATT|SPATCCM
Descriptionsolute carrier family 1 member 4
ReferenceMIM:600229|HGNC:HGNC:10942|Ensembl:ENSG00000115902|HPRD:02576|Vega:OTTHUMG00000129537
Gene typeprotein-coding
Map location2p14
Pascal p-value0.686
Sherlock p-value0.548
Fetal beta-0.039
DMG1 (# studies)
eGeneCerebellum
Myers' cis & trans
Meta
SupportMETABOTROPIC GLUTAMATE RECEPTOR
NEUROTRANSMITTER METABOLISM

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Jaffe_2016Genome-wide DNA methylation analysisThis dataset includes 2,104 probes/CpGs associated with SZ patients (n=108) compared to 136 controls at Bonferroni-adjusted P < 0.05. 1
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: 1 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg00877964265215638SLC1A45.39E-11-0.0144.23E-7DMG:Jaffe_2016

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs4763076chr1263677933SLC1A465090.06trans

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
SLC22A170.880.90
LENG40.870.88
PLD30.860.88
AP001107.10.850.90
TMEM1300.840.90
TMEM59L0.840.91
RHBDD20.830.87
RP11-401M16.20.830.86
PINK10.830.88
BSCL20.820.87
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
RBMX2-0.44-0.46
EIF5B-0.43-0.47
GTF3C6-0.39-0.37
FAM36A-0.38-0.32
AC005921.3-0.38-0.55
C21orf57-0.37-0.35
ANP32B-0.37-0.44
BAZ1A-0.37-0.52
ANP32C-0.36-0.41
CWF19L2-0.36-0.38

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005254chloride channel activityIDA8910405 
GO:0015293symporter activityIEA-
GO:0015195L-threonine transmembrane transporter activityIDA8340364 
GO:0015194L-serine transmembrane transporter activityIDA8101838 |8340364 |8910405 
GO:0015193L-proline transmembrane transporter activityIDA14502423 
GO:0015184L-cystine transmembrane transporter activityIDA8101838 |8910405 
GO:0015184L-cystine transmembrane transporter activityIDA8340364 
GO:0015180L-alanine transmembrane transporter activityIDA8101838 |8340364 |8910405 
GO:0034590L-hydroxyproline transmembrane transporter activityIDA14502423 
GO:0017153sodium:dicarboxylate symporter activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0035249synaptic transmission, glutamatergicNASneuron, glutamate, Synap, Neurotransmitter (GO term level: 8)16897601 
GO:0015811L-cystine transportIDA8101838 |8910405 
GO:0015811L-cystine transportIDA8340364 
GO:0015824proline transportIDA14502423 
GO:0015826threonine transportIDA8340364 
GO:0015825L-serine transportIDA8101838 |8340364 |8910405 
GO:0015808L-alanine transportIDA8101838 |8340364 |8910405 
GO:0006835dicarboxylic acid transportIEA-
GO:0006810transportIEA-
GO:0034589hydroxyproline transportIDA14502423 
GO:0050890cognitionIMP16897601 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005882intermediate filamentISS-
GO:0016020membraneIEA-
GO:0005887integral to plasma membraneIC8910405 
GO:0042470melanosomeIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
REACTOME AMINO ACID TRANSPORT ACROSS THE PLASMA MEMBRANE 3121All 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
ONKEN UVEAL MELANOMA UP 783507All SZGR 2.0 genes in this pathway
SCHUETZ BREAST CANCER DUCTAL INVASIVE DN 8453All SZGR 2.0 genes in this pathway
IGARASHI ATF4 TARGETS DN 9065All SZGR 2.0 genes in this pathway
GARY CD5 TARGETS UP 473314All SZGR 2.0 genes in this pathway
SAMOLS TARGETS OF KHSV MIRNAS DN 6235All SZGR 2.0 genes in this pathway
LIU CMYB TARGETS UP 165106All SZGR 2.0 genes in this pathway
LIU VMYB TARGETS UP 12778All SZGR 2.0 genes in this pathway
CHARAFE BREAST CANCER LUMINAL VS BASAL UP 380215All SZGR 2.0 genes in this pathway
JAEGER METASTASIS DN 258141All SZGR 2.0 genes in this pathway
OSMAN BLADDER CANCER UP 404246All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 1 UP 380236All SZGR 2.0 genes in this pathway
MULLIGHAN MLL SIGNATURE 2 UP 418263All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION HSC DN 187115All SZGR 2.0 genes in this pathway
LEE NEURAL CREST STEM CELL DN 11879All SZGR 2.0 genes in this pathway
TIEN INTESTINE PROBIOTICS 24HR DN 214133All SZGR 2.0 genes in this pathway
KINSEY TARGETS OF EWSR1 FLII FUSION UP 1278748All SZGR 2.0 genes in this pathway
MAYBURD RESPONSE TO L663536 UP 2918All SZGR 2.0 genes in this pathway
RODRIGUES THYROID CARCINOMA ANAPLASTIC UP 722443All SZGR 2.0 genes in this pathway
PACHER TARGETS OF IGF1 AND IGF2 UP 3527All SZGR 2.0 genes in this pathway
GRAESSMANN APOPTOSIS BY SERUM DEPRIVATION DN 234147All SZGR 2.0 genes in this pathway
PATIL LIVER CANCER 747453All SZGR 2.0 genes in this pathway
AMUNDSON RESPONSE TO ARSENITE 217143All SZGR 2.0 genes in this pathway
GRUETZMANN PANCREATIC CANCER DN 203134All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM2 153102All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 16521023All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442892All SZGR 2.0 genes in this pathway
PUJANA CHEK2 PCC NETWORK 779480All SZGR 2.0 genes in this pathway
GROSS HYPOXIA VIA HIF1A UP 7749All SZGR 2.0 genes in this pathway
BUYTAERT PHOTODYNAMIC THERAPY STRESS UP 811508All SZGR 2.0 genes in this pathway
SCHAEFFER PROSTATE DEVELOPMENT 48HR DN 428306All 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
BENPORATH MYC MAX TARGETS 775494All SZGR 2.0 genes in this pathway
GEORGES TARGETS OF MIR192 AND MIR215 893528All SZGR 2.0 genes in this pathway
ROSS AML WITH PML RARA FUSION 7762All SZGR 2.0 genes in this pathway
PENG LEUCINE DEPRIVATION UP 14293All SZGR 2.0 genes in this pathway
LEE LIVER CANCER MYC UP 5430All SZGR 2.0 genes in this pathway
LEE LIVER CANCER MYC TGFA UP 6140All SZGR 2.0 genes in this pathway
LEE LIVER CANCER MYC E2F1 UP 5634All SZGR 2.0 genes in this pathway
CHEOK RESPONSE TO HD MTX UP 2313All SZGR 2.0 genes in this pathway
ZHANG TARGETS OF EWSR1 FLI1 FUSION 8868All SZGR 2.0 genes in this pathway
ALCALAY AML BY NPM1 LOCALIZATION DN 184132All SZGR 2.0 genes in this pathway
BLALOCK ALZHEIMERS DISEASE DN 1237837All SZGR 2.0 genes in this pathway
HU GENOTOXIC DAMAGE 24HR 3522All SZGR 2.0 genes in this pathway
BURTON ADIPOGENESIS 8 8657All SZGR 2.0 genes in this pathway
BROWNE HCMV INFECTION 18HR UP 178111All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES DN 245144All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES UP 253147All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 6HR UP 953554All SZGR 2.0 genes in this pathway
KRIGE RESPONSE TO TOSEDOSTAT 24HR UP 783442All SZGR 2.0 genes in this pathway
CREIGHTON ENDOCRINE THERAPY RESISTANCE 4 307185All SZGR 2.0 genes in this pathway
HELLER SILENCED BY METHYLATION DN 10567All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS DN 292189All SZGR 2.0 genes in this pathway
HELLER HDAC TARGETS SILENCED BY METHYLATION DN 281179All SZGR 2.0 genes in this pathway
LEE METASTASIS AND ALTERNATIVE SPLICING UP 7451All SZGR 2.0 genes in this pathway
MASSARWEH TAMOXIFEN RESISTANCE DN 258160All SZGR 2.0 genes in this pathway
MASSARWEH RESPONSE TO ESTRADIOL 6147All SZGR 2.0 genes in this pathway
SMID BREAST CANCER BASAL DN 701446All SZGR 2.0 genes in this pathway
BUCKANOVICH T LYMPHOCYTE HOMING ON TUMOR DN 2416All SZGR 2.0 genes in this pathway
CHUNG BLISTER CYTOTOXICITY UP 13484All SZGR 2.0 genes in this pathway
BOQUEST STEM CELL CULTURED VS FRESH UP 425298All SZGR 2.0 genes in this pathway
CHAUHAN RESPONSE TO METHOXYESTRADIOL DN 10265All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO CSF2RB AND IL4 UP 338225All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF UP 418282All SZGR 2.0 genes in this pathway
RUTELLA RESPONSE TO HGF VS CSF2RB AND IL4 UP 408276All SZGR 2.0 genes in this pathway
LEE EARLY T LYMPHOCYTE UP 10759All SZGR 2.0 genes in this pathway
SHEDDEN LUNG CANCER GOOD SURVIVAL A12 317177All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA CHEMOTAXIS DN 457302All SZGR 2.0 genes in this pathway
YAGI AML WITH T 8 21 TRANSLOCATION 368247All SZGR 2.0 genes in this pathway
YAGI AML WITH 11Q23 REARRANGED 351238All SZGR 2.0 genes in this pathway
CAIRO HEPATOBLASTOMA UP 207143All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
YAO TEMPORAL RESPONSE TO PROGESTERONE CLUSTER 10 6938All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR UP 682440All SZGR 2.0 genes in this pathway
HIRSCH CELLULAR TRANSFORMATION SIGNATURE UP 242159All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS GROWING 243155All SZGR 2.0 genes in this pathway
CHICAS RB1 TARGETS CONFLUENT 567365All SZGR 2.0 genes in this pathway
WANG RESPONSE TO GSK3 INHIBITOR SB216763 DN 374217All SZGR 2.0 genes in this pathway
DUTERTRE ESTRADIOL RESPONSE 6HR UP 229149All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS NOT VIA AKT1 UP 211131All SZGR 2.0 genes in this pathway
BHAT ESR1 TARGETS VIA AKT1 UP 281183All SZGR 2.0 genes in this pathway
MIYAGAWA TARGETS OF EWSR1 ETS FUSIONS UP 259159All SZGR 2.0 genes in this pathway
DELPUECH FOXO3 TARGETS DN 4127All SZGR 2.0 genes in this pathway
PEDERSEN METASTASIS BY ERBB2 ISOFORM 7 403240All SZGR 2.0 genes in this pathway
HUANG GATA2 TARGETS DN 7252All SZGR 2.0 genes in this pathway

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-124.1266726741A,m8hsa-miR-124aUUAAGGCACGCGGUGAAUGCCA
miR-124/506266726731Ahsa-miR-506UAAGGCACCCUUCUGAGUAGA
hsa-miR-124brainUAAGGCACGCGGUGAAUGCC