Gene Page: LAT

Summary ?
GeneID27040
SymbolLAT
SynonymsLAT1|pp36
Descriptionlinker for activation of T-cells
ReferenceMIM:602354|HGNC:HGNC:18874|Ensembl:ENSG00000213658|HPRD:03832|Vega:OTTHUMG00000131761
Gene typeprotein-coding
Map location16p11.2
Pascal p-value0.274
Fetal beta0.013
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.
GSMA_IIEGenome scan meta-analysis (European-ancestry samples)Psr: 0.01775 
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophrenic,schizophrenics,schizophrenias,schizotypalClick 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
rs6687849chr1175904808LAT270400.15trans
rs2502827chr1176044216LAT270400.01trans
rs16829545chr2151977407LAT270400trans
rs3845734chr2171125572LAT270400trans
rs7584986chr2184111432LAT270402.313E-4trans
rs2090117chr454300590LAT270400.08trans
rs504836chr456285304LAT270400.13trans
rs534654chr456290219LAT270400.16trans
rs10491487chr580323367LAT270400.07trans
rs1368303chr5147672388LAT270400.01trans
rs17263352chr9124811572LAT270400.04trans
rs17104720chr1477127308LAT270400.01trans
rs16955618chr1529937543LAT270402.165E-9trans
rs749043chr2046995700LAT270400.18trans

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
CCDC80.820.49
EFNA40.800.62
NECAP20.800.62
PDPN0.780.52
RASSF100.770.52
CD990.770.66
ABHD40.770.64
RFX20.760.51
SIX50.760.62
SULT1C40.750.62
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
NDRG1-0.37-0.50
FBXW7-0.37-0.50
AC016910.1-0.36-0.53
AC079953.2-0.34-0.50
MEF2C-0.34-0.51
ARHGAP20-0.33-0.48
DOCK9-0.32-0.44
C1orf115-0.32-0.40
LMO7-0.32-0.50
DYNC1I1-0.32-0.48

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005070SH3/SH2 adaptor activityIDA9489702 
GO:0005515protein bindingIPI16938345 
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0043303mast cell degranulationIEAserotonin (GO term level: 9)-
GO:0007265Ras protein signal transductionIMP12646565 
GO:0007242intracellular signaling cascadeIDA12646565 
GO:0007229integrin-mediated signaling pathwayIDA15100278 
GO:0006955immune responseIDA15100278 
GO:0019722calcium-mediated signalingIMP12646565 
GO:0050863regulation of T cell activationIMP12646565 
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0001772immunological synapseIDASynap (GO term level: 7)12646565 
GO:0016021integral to membraneIDA12646565 
GO:0005886plasma membraneEXP11048639 |11607830 |17652306 
GO:0005886plasma membraneIEA-
GO:0045121membrane raftTAS14722116 

Section IV. Protein-protein interaction annotation

InteractorsAliases BOfficial full name BExperimentalSourcePubMed ID
CD2442B4 | NAIL | NKR2B4 | Nmrk | SLAMF4CD244 molecule, natural killer cell receptor 2B4-HPRD12077228 
CD4CD4mutCD4 molecule-HPRD10562325 
CD8ACD8 | Leu2 | MAL | p32CD8a molecule-HPRD10562325 
CLYBLCLB | bA134O15.1citrate lyase beta likeAffinity Capture-WesternBioGRID11368773 
FCGR1ACD64 | CD64A | FCRI | FLJ18345 | IGFR1Fc fragment of IgG, high affinity Ia, receptor (CD64)-HPRD,BioGRID10781611 
FCGR2ACD32 | CD32A | CDw32 | FCG2 | FCGR2 | FCGR2A1 | FcGR | IGFR2 | MGC23887 | MGC30032Fc fragment of IgG, low affinity IIa, receptor (CD32)-HPRD,BioGRID10781611 
GAB2KIAA0571GRB2-associated binding protein 2-HPRD,BioGRID11572860 
GRAPMGC64880GRB2-related adaptor proteinAffinity Capture-Western
Reconstituted Complex		BioGRID9489702 |12186560 
GRAP2GADS | GRAP-2 | GRB2L | GRBLG | GRID | GRPL | GrbX | Grf40 | Mona | P38GRB2-related adaptor protein 2-HPRD,BioGRID10021361 
GRB2ASH | EGFRBP-GRB2 | Grb3-3 | MST084 | MSTP084growth factor receptor-bound protein 2-HPRD9489702 |12359715 
GRB2ASH | EGFRBP-GRB2 | Grb3-3 | MST084 | MSTP084growth factor receptor-bound protein 2Affinity Capture-Western
Reconstituted Complex		BioGRID9489702 |11368773 
|12186560 
ITKEMT | LYK | MGC126257 | MGC126258 | PSCTK2IL2-inducible T-cell kinase-HPRD10506192|12186560 
ITKEMT | LYK | MGC126257 | MGC126258 | PSCTK2IL2-inducible T-cell kinaseAffinity Capture-Western
Biochemical Activity		BioGRID10506192 |12186560 
LCP2SLP-76 | SLP76lymphocyte cytosolic protein 2 (SH2 domain containing leukocyte protein of 76kDa)-HPRD9489702 
PIK3R1GRB1 | p85 | p85-ALPHAphosphoinositide-3-kinase, regulatory subunit 1 (alpha)Affinity Capture-Western
Reconstituted Complex		BioGRID11368773 
PLCG1PLC-II | PLC1 | PLC148 | PLCgamma1phospholipase C, gamma 1-HPRD,BioGRID9729044 |11368773 
PLCG1PLC-II | PLC1 | PLC148 | PLCgamma1phospholipase C, gamma 1LAT interacts with an unspecified isoform of PLC-gamma-1.BIND15696170 
PLCG2-phospholipase C, gamma 2 (phosphatidylinositol-specific)-HPRD,BioGRID10469124 
PTPRJCD148 | DEP1 | HPTPeta | R-PTP-ETA | SCC1protein tyrosine phosphatase, receptor type, J-HPRD,BioGRID11259588 
SH3BP23BP2 | CRBM | CRPM | FLJ42079 | RES4-23SH3-domain binding protein 2-HPRD,BioGRID11390470 
SHBRP11-3J10.8 | bA3J10.2Src homology 2 domain containing adaptor protein B-HPRD,BioGRID12084069 
SLASLA1 | SLAPSrc-like-adaptor-HPRD,BioGRID10449770 
SYKDKFZp313N1010 | FLJ25043 | FLJ37489spleen tyrosine kinaseBiochemical ActivityBioGRID11368773 
SYKDKFZp313N1010 | FLJ25043 | FLJ37489spleen tyrosine kinase-HPRD9891970 
VAV1VAVvav 1 guanine nucleotide exchange factor-HPRD,BioGRID11368773 
ZAP70FLJ17670 | FLJ17679 | SRK | STD | TZK | ZAP-70zeta-chain (TCR) associated protein kinase 70kDaBiochemical ActivityBioGRID11368773 |12186560 


Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG NATURAL KILLER CELL MEDIATED CYTOTOXICITY 13792All SZGR 2.0 genes in this pathway
KEGG T CELL RECEPTOR SIGNALING PATHWAY 10889All SZGR 2.0 genes in this pathway
KEGG FC EPSILON RI SIGNALING PATHWAY 7958All SZGR 2.0 genes in this pathway
KEGG FC GAMMA R MEDIATED PHAGOCYTOSIS 9771All SZGR 2.0 genes in this pathway
BIOCARTA NKCELLS PATHWAY 2013All SZGR 2.0 genes in this pathway
BIOCARTA TCR PATHWAY 4937All SZGR 2.0 genes in this pathway
ST T CELL SIGNAL TRANSDUCTION 4533All SZGR 2.0 genes in this pathway
PID FCER1 PATHWAY 6243All SZGR 2.0 genes in this pathway
PID TCR PATHWAY 6651All SZGR 2.0 genes in this pathway
PID PTP1B PATHWAY 5240All SZGR 2.0 genes in this pathway
PID CD8 TCR PATHWAY 5342All SZGR 2.0 genes in this pathway
PID PI3KCI PATHWAY 4940All SZGR 2.0 genes in this pathway
PID TCR JNK PATHWAY 1411All SZGR 2.0 genes in this pathway
REACTOME TCR SIGNALING 5446All SZGR 2.0 genes in this pathway
REACTOME GENERATION OF SECOND MESSENGER MOLECULES 2725All SZGR 2.0 genes in this pathway
REACTOME GPVI MEDIATED ACTIVATION CASCADE 3125All SZGR 2.0 genes in this pathway
REACTOME HEMOSTASIS 466331All SZGR 2.0 genes in this pathway
REACTOME IMMUNE SYSTEM 933616All SZGR 2.0 genes in this pathway
REACTOME ADAPTIVE IMMUNE SYSTEM 539350All SZGR 2.0 genes in this pathway
REACTOME PLATELET ACTIVATION SIGNALING AND AGGREGATION 208138All SZGR 2.0 genes in this pathway
KIM MYC AMPLIFICATION TARGETS UP 201127All SZGR 2.0 genes in this pathway
NUYTTEN EZH2 TARGETS DN 1024594All SZGR 2.0 genes in this pathway
MOREIRA RESPONSE TO TSA DN 1816All SZGR 2.0 genes in this pathway
QI PLASMACYTOMA UP 259185All SZGR 2.0 genes in this pathway
VILIMAS NOTCH1 TARGETS UP 5241All SZGR 2.0 genes in this pathway
MIKKELSEN ES ICP WITH H3K4ME3 718401All SZGR 2.0 genes in this pathway
HUANG GATA2 TARGETS DN 7252All SZGR 2.0 genes in this pathway
KRIEG HYPOXIA NOT VIA KDM3A 770480All SZGR 2.0 genes in this pathway
BOSCO INTERFERON INDUCED ANTIVIRAL MODULE 7848All SZGR 2.0 genes in this pathway