Gene Page:LTA

Summary?
GeneID 4049
Symbol LTA
Synonyms LT|TNFB|TNFSF1|TNLG1E
Description lymphotoxin alpha
Reference MIM:153440|HGNC:HGNC:6709|Ensembl:ENSG00000226979|HPRD:01084|Vega:OTTHUMG00000031135
Gene type protein-coding
Map location 6p21.3
Pascal p-value 9.851E-8
Fetal beta 0.006

Gene in Data Sources
Gene set name Method of gene set Description Info
CV:PGCnp Genome-wide Association Study GWAS
PMID:cooccur High-throughput literature-search Systematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
Association A combined odds ratio method (Sun et al. 2008), association studies 2 Link to SZGene
GSMA_I Genome scan meta-analysis Psr: 0.033
Literature High-throughput literature-search Co-occurance with Schizophrenia keywords: schizophrenia,schizophrenias Click 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
Gene Pearson's Correlation Spearman's Correlation
WDR42A 0.89 0.84
APLP2 0.88 0.86
应用程序 0.86 0.85
SRPR 0.85 0.86
AARS 0.85 0.84
TK2 0.85 0.83
HDHD2 0.85 0.81
PROSC 0.85 0.83
RAB5B 0.84 0.81
SYT11 0.84 0.81
Top 10 negatively co-expressed genes
Gene Pearson'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 function 去的术语 Evidence Neuro keywords PubMed ID
GO:0005125 cytokine activity IEA -
GO:0005164 tumor necrosis factor receptor binding IEA -
GO:0004197 cysteine-type endopeptidase activity IEA -
Biological process 去的术语 Evidence Neuro keywords PubMed ID
GO:0006508 proteolysis IEA -
GO:0007267 cell-cell signaling TAS 6334807
GO:0006917 induction of apoptosis TAS 6334807
GO:0007165 signal transduction TAS 6334807
GO:0006959 humoral immune response IEA -
GO:0006955 immune response IEA -
GO:0048535 lymph node development IEA -
Cellular component 去的术语 Evidence Neuro keywords PubMed ID
GO:0005576 extracellular region IEA -
GO:0005615 extracellular space IEA -
GO:0016020 membrane IEA -

Section V. Pathway annotation

Pathway name Pathway size # SZGR 2.0 genes in pathway Info
KEGG CYTOKINE CYTOKINE RECEPTOR INTERACTION 267 161 All SZGR 2.0 genes in this pathway
KEGG ANTIGEN PROCESSING AND PRESENTATION 89 65 All SZGR 2.0 genes in this pathway
KEGG TYPE I DIABETES MELLITUS 44 38 All SZGR 2.0 genes in this pathway
BIOCARTACYTOKINE PATHWAY 22 16 All SZGR 2.0 genes in this pathway
BIOCARTAINFLAM PATHWAY 29 24 All SZGR 2.0 genes in this pathway
BIOCARTA应力路径 25 18 All SZGR 2.0 genes in this pathway
BIOCARTATNFR2 PATHWAY 18 15 All SZGR 2.0 genes in this pathway
PID IL4 2PATHWAY 65 43 All SZGR 2.0 genes in this pathway
PID IL2 STAT5 PATHWAY 30 23 All SZGR 2.0 genes in this pathway
WANG BARRETTS ESOPHAGUS AND ESOPHAGUS CANCER UP 26 12 All SZGR 2.0 genes in this pathway
DIRMEIER LMP1 RESPONSE EARLY 66 48 All SZGR 2.0 genes in this pathway
FUNG IL2 SIGNALING 1 11 7 All SZGR 2.0 genes in this pathway
FUNG IL2 TARGETS WITH STAT5 BINDING SITES 7 5 All SZGR 2.0 genes in this pathway
YAN ESCAPE FROM ANOIKIS 24 19 All SZGR 2.0 genes in this pathway
JAZAG TGFB1 SIGNALING VIA SMAD4 DN 66 38 All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP 479 299 All SZGR 2.0 genes in this pathway
PUJANA BRCA1 PCC NETWORK 1652 1023 All SZGR 2.0 genes in this pathway
PUJANA ATM PCC NETWORK 1442 892 All SZGR 2.0 genes in this pathway
SHEN SMARCA2 TARGETS DN 357 212 All SZGR 2.0 genes in this pathway
SHIPP DLBCL CURED VS FATAL UP 39 22 All SZGR 2.0 genes in this pathway
MAGRANGEAS MULTIPLE MYELOMA IGLL VS IGLK DN 24 18 All SZGR 2.0 genes in this pathway
PENG RAPAMYCIN RESPONSE UP 203 130 All SZGR 2.0 genes in this pathway
XU CREBBP TARGETS DN 44 31 All SZGR 2.0 genes in this pathway
BASSO CD40 SIGNALING UP 101 76 All SZGR 2.0 genes in this pathway
LEE CALORIE RESTRICTION MUSCLE UP 43 33 All SZGR 2.0 genes in this pathway
ACEVEDO METHYLATED IN LIVER CANCER DN 940 425 All SZGR 2.0 genes in this pathway
YOSHIMURA MAPK8 TARGETS UP 1305 895 All SZGR 2.0 genes in this pathway
VANASSE BCL2 TARGETS DN 74 50 All SZGR 2.0 genes in this pathway
MIKKELSEN MEF ICP WITH H3K27ME3 206 108 All SZGR 2.0 genes in this pathway
MIKKELSEN IPS ICP WITH H3K4ME3 AND H327ME3 126 83 All SZGR 2.0 genes in this pathway
KUROZUMI RESPONSE TO ONCOCYTIC VIRUS 44 30 All SZGR 2.0 genes in this pathway
KUROZUMI RESPONSE TO ONCOCYTIC VIRUS AND CYCLIC RGD 21 15 All SZGR 2.0 genes in this pathway
MIKKELSEN ES ICP WITH H3K4ME3 AND H3K27ME3 137 85 All SZGR 2.0 genes in this pathway
LI INDUCED T TO NATURAL KILLER UP 307 182 All SZGR 2.0 genes in this pathway
KIM BIPOLAR DISORDER OLIGODENDROCYTE DENSITY CORR DN 88 59 All SZGR 2.0 genes in this pathway
KASLER HDAC7 TARGETS 1 UP 194 133 All SZGR 2.0 genes in this pathway
SMIRNOV RESPONSE TO IR 6HR DN 114 69 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
NABA SECRETED FACTORS 344 197 All SZGR 2.0 genes in this pathway
NABA MATRISOME ASSOCIATED 753 411 All SZGR 2.0 genes in this pathway
NABA MATRISOME 1028 559 All SZGR 2.0 genes in this pathway