Gene Page: LTA

Summary ?
GeneID4049
SymbolLTA
SynonymsLT|TNFB|TNFSF1|TNLG1E
Descriptionlymphotoxin alpha
ReferenceMIM:153440|HGNC:HGNC:6709|Ensembl:ENSG00000226979|HPRD:01084|Vega:OTTHUMG00000031135
Gene typeprotein-coding
Map location6p21.3
Pascal p-value9.851E-8
Fetal beta0.006

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.
AssociationA combined odds ratio method (Sun et al. 2008), association studies2Link to SZGene
GSMA_IGenome scan meta-analysisPsr: 0.033 
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophreniasClick to show details

Section I. Genetics and epigenetics annotation


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
WDR42A0.890.84
APLP20.880.86
APP0.860.85
SRPR0.850.86
AARS0.850.84
TK20.850.83
HDHD20.850.81
PROSC0.850.83
RAB5B0.840.81
SYT110.840.81
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
AF347015.21-0.53-0.27
IL32-0.50-0.33
AF347015.18-0.49-0.25
AC098691.2-0.48-0.39
FAM159B-0.47-0.46
GNG11-0.44-0.29
MT-CO2-0.44-0.26
C1orf54-0.43-0.30
AF347015.2-0.42-0.22
C1orf61-0.42-0.37

Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005125cytokine activityIEA-
GO:0005164tumor necrosis factor receptor bindingIEA-
GO:0004197cysteine-type endopeptidase activityIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0006508proteolysisIEA-
GO:0007267cell-cell signalingTAS6334807 
GO:0006917induction of apoptosisTAS6334807 
GO:0007165signal transductionTAS6334807 
GO:0006959humoral immune responseIEA-
GO:0006955immune responseIEA-
GO:0048535lymph node developmentIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005576extracellular regionIEA-
GO:0005615extracellular spaceIEA-
GO:0016020membraneIEA-

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION 267161All SZGR 2.0 genes in this pathway
KEGG ANTIGEN PROCESSING AND PRESENTATION 8965All SZGR 2.0 genes in this pathway
KEGG TYPE I DIABETES MELLITUS 4438All SZGR 2.0 genes in this pathway
BIOCARTA CYTOKINE PATHWAY 2216All SZGR 2.0 genes in this pathway
BIOCARTA INFLAM PATHWAY 2924All SZGR 2.0 genes in this pathway
BIOCARTA STRESS PATHWAY 2518All SZGR 2.0 genes in this pathway
BIOCARTA TNFR2 PATHWAY 1815All SZGR 2.0 genes in this pathway
PID IL4 2PATHWAY 6543All SZGR 2.0 genes in this pathway
PID IL2 STAT5 PATHWAY 3023All SZGR 2.0 genes in this pathway
WANG BARRETTS ESOPHAGUS AND ESOPHAGUS CANCER UP 2612All SZGR 2.0 genes in this pathway
DIRMEIER LMP1 RESPONSE EARLY 6648All SZGR 2.0 genes in this pathway
FUNG IL2 SIGNALING 1 117All SZGR 2.0 genes in this pathway
FUNG IL2 TARGETS WITH STAT5 BINDING SITES 75All SZGR 2.0 genes in this pathway
YAN ESCAPE FROM ANOIKIS 2419All SZGR 2.0 genes in this pathway
JAZAG TGFB1 SIGNALING VIA SMAD4 DN 6638All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP 479299All 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
SHEN SMARCA2 TARGETS DN 357212All SZGR 2.0 genes in this pathway
SHIPP DLBCL CURED VS FATAL UP 3922All SZGR 2.0 genes in this pathway
MAGRANGEAS MULTIPLE MYELOMA IGLL VS IGLK DN 2418All SZGR 2.0 genes in this pathway
PENG RAPAMYCIN RESPONSE UP 203130All SZGR 2.0 genes in this pathway
XU CREBBP TARGETS DN 4431All SZGR 2.0 genes in this pathway
BASSO CD40 SIGNALING UP 10176All SZGR 2.0 genes in this pathway
LEE CALORIE RESTRICTION MUSCLE UP 4333All SZGR 2.0 genes in this pathway
ACEVEDO METHYLATED IN LIVER CANCER DN 940425All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305895All SZGR 2.0 genes in this pathway
VANASSE BCL2 TARGETS DN 7450All SZGR 2.0 genes in this pathway
MIKKELSEN MEF ICP WITH H3K27ME3 206108All SZGR 2.0 genes in this pathway
MIKKELSEN IPS ICP WITH H3K4ME3 AND H327ME3 12683All SZGR 2.0 genes in this pathway
KUROZUMI RESPONSE TO ONCOCYTIC VIRUS 4430All SZGR 2.0 genes in this pathway
KUROZUMI RESPONSE TO ONCOCYTIC VIRUS AND CYCLIC RGD 2115All SZGR 2.0 genes in this pathway
MIKKELSEN ES ICP WITH H3K4ME3 AND H3K27ME3 13785All SZGR 2.0 genes in this pathway
LI INDUCED T TO NATURAL KILLER UP 307182All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR DN 8859All SZGR 2.0 genes in this pathway
KASLER HDAC7 TARGETS 1 UP 194133All SZGR 2.0 genes in this pathway
SMIRNOV RESPONSE TO IR 6HR DN 11469All SZGR 2.0 genes in this pathway
ZWANG CLASS 1 TRANSIENTLY INDUCED BY EGF 516308All SZGR 2.0 genes in this pathway
NABA SECRETED FACTORS 344197All SZGR 2.0 genes in this pathway
NABA MATRISOME ASSOCIATED 753411All SZGR 2.0 genes in this pathway
NABA MATRISOME 1028559All SZGR 2.0 genes in this pathway