Gene Page: LTB

Summary ?
GeneID4050
SymbolLTB
SynonymsTNFC|TNFSF3|TNLG1C|p33
Descriptionlymphotoxin beta
ReferenceMIM:600978|HGNC:HGNC:6711|Ensembl:ENSG00000227507|HPRD:02987|Vega:OTTHUMG00000031136
Gene typeprotein-coding
Map location6p21.3
Pascal p-value1.256E-10
Fetal beta-1.342
DMG1 (# studies)

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DMG:Wockner_2014Genome-wide DNA methylation analysisThis dataset includes 4641 differentially methylated probes corresponding to 2929 unique genes between schizophrenia patients (n=24) and controls (n=24). 1
GSMA_IGenome scan meta-analysisPsr: 0.033 

Section I. Genetics and epigenetics annotation

@Differentially methylated gene

ProbeChromosomePositionNearest geneP (dis)Beta (dis)FDR (dis)Study
cg14868222631548340LTB4.35E-40.2740.045DMG:Wockner_2014


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.

No co-expressed genes in brain regions


Section III. Gene Ontology annotation

Molecular functionGO termEvidenceNeuro keywordsPubMed ID
GO:0005125cytokine activityIEA-
GO:0005164tumor necrosis factor receptor bindingIEA-
Biological processGO termEvidenceNeuro keywordsPubMed ID
GO:0007267cell-cell signalingTAS7916655 
GO:0007165signal transductionTAS7916655 
GO:0006955immune responseIEA-
GO:0045084positive regulation of interleukin-12 biosynthetic processISS-
GO:0048535lymph node developmentIEA-
Cellular componentGO termEvidenceNeuro keywordsPubMed ID
GO:0005575cellular_componentND9299492 
GO:0005615extracellular spaceIEA-
GO:0016020membraneIEA-
GO:0016021integral to membraneIEA-

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
GARY CD5 TARGETS DN 431263All SZGR 2.0 genes in this pathway
OSMAN BLADDER CANCER DN 406230All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION HSC DN 187115All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION MONOCYTE DN 5438All SZGR 2.0 genes in this pathway
TONKS TARGETS OF RUNX1 RUNX1T1 FUSION SUSTAINED IN MONOCYTE DN 87All SZGR 2.0 genes in this pathway
SENESE HDAC1 TARGETS UP 457269All SZGR 2.0 genes in this pathway
SENESE HDAC1 AND HDAC2 TARGETS UP 238144All SZGR 2.0 genes in this pathway
GRAHAM CML DIVIDING VS NORMAL DIVIDING DN 106All SZGR 2.0 genes in this pathway
SCHLOSSER SERUM RESPONSE UP 13493All SZGR 2.0 genes in this pathway
XU HGF SIGNALING NOT VIA AKT1 48HR UP 3520All SZGR 2.0 genes in this pathway
BORLAK LIVER CANCER EGF UP 5741All SZGR 2.0 genes in this pathway
SHETH LIVER CANCER VS TXNIP LOSS PAM3 7037All SZGR 2.0 genes in this pathway
SPIELMAN LYMPHOBLAST EUROPEAN VS ASIAN UP 479299All SZGR 2.0 genes in this pathway
RICKMAN TUMOR DIFFERENTIATED WELL VS POORLY UP 236139All SZGR 2.0 genes in this pathway
SHIN B CELL LYMPHOMA CLUSTER 3 2823All SZGR 2.0 genes in this pathway
MORI LARGE PRE BII LYMPHOCYTE DN 5839All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 2 DN 464276All SZGR 2.0 genes in this pathway
ONDER CDH1 TARGETS 1 UP 14085All SZGR 2.0 genes in this pathway
TARTE PLASMA CELL VS B LYMPHOCYTE DN 3825All SZGR 2.0 genes in this pathway
FERNANDEZ BOUND BY MYC 182116All SZGR 2.0 genes in this pathway
FLECHNER PBL KIDNEY TRANSPLANT REJECTED VS OK DN 5135All SZGR 2.0 genes in this pathway
ALCALAY AML BY NPM1 LOCALIZATION UP 14083All SZGR 2.0 genes in this pathway
ZHAN MULTIPLE MYELOMA SPIKED 2213All SZGR 2.0 genes in this pathway
NEMETH INFLAMMATORY RESPONSE LPS UP 8864All SZGR 2.0 genes in this pathway
YU MYC TARGETS DN 5538All SZGR 2.0 genes in this pathway
BASSO CD40 SIGNALING DN 6844All SZGR 2.0 genes in this pathway
THEILGAARD NEUTROPHIL AT SKIN WOUND DN 225163All SZGR 2.0 genes in this pathway
HADDAD T LYMPHOCYTE AND NK PROGENITOR DN 6341All SZGR 2.0 genes in this pathway
KUMAR TARGETS OF MLL AF9 FUSION 405264All SZGR 2.0 genes in this pathway
LEE AGING NEOCORTEX DN 8049All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES DN 245144All SZGR 2.0 genes in this pathway
RODWELL AGING KIDNEY UP 487303All SZGR 2.0 genes in this pathway
SATO SILENCED BY METHYLATION IN PANCREATIC CANCER 1 419273All SZGR 2.0 genes in this pathway
MCLACHLAN DENTAL CARIES UP 253147All SZGR 2.0 genes in this pathway
MARSON BOUND BY FOXP3 STIMULATED 1022619All SZGR 2.0 genes in this pathway
MARSON FOXP3 TARGETS STIMULATED DN 119All SZGR 2.0 genes in this pathway
OSADA ASCL1 TARGETS UP 4630All SZGR 2.0 genes in this pathway
ACEVEDO METHYLATED IN LIVER CANCER DN 940425All SZGR 2.0 genes in this pathway
SMID BREAST CANCER LUMINAL B DN 564326All SZGR 2.0 genes in this pathway
SMID BREAST CANCER NORMAL LIKE UP 476285All SZGR 2.0 genes in this pathway
LABBE WNT3A TARGETS UP 11271All SZGR 2.0 genes in this pathway
BREDEMEYER RAG SIGNALING VIA ATM NOT VIA NFKB UP 4932All SZGR 2.0 genes in this pathway
QI PLASMACYTOMA UP 259185All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA C D DN 252155All SZGR 2.0 genes in this pathway
BOHN PRIMARY IMMUNODEFICIENCY SYNDROM DN 4031All SZGR 2.0 genes in this pathway
SWEET LUNG CANCER KRAS DN 435289All SZGR 2.0 genes in this pathway
HOFFMANN PRE BI TO LARGE PRE BII LYMPHOCYTE DN 7561All SZGR 2.0 genes in this pathway
HOFFMANN SMALL PRE BII TO IMMATURE B LYMPHOCYTE UP 7049All SZGR 2.0 genes in this pathway
LEE DIFFERENTIATING T LYMPHOCYTE 200115All SZGR 2.0 genes in this pathway
ZHAN EARLY DIFFERENTIATION GENES DN 4229All SZGR 2.0 genes in this pathway
IRITANI MAD1 TARGETS UP 138All SZGR 2.0 genes in this pathway
POOLA INVASIVE BREAST CANCER UP 288168All SZGR 2.0 genes in this pathway
WINNEPENNINCKX MELANOMA METASTASIS DN 4626All SZGR 2.0 genes in this pathway
KUROZUMI RESPONSE TO ONCOCYTIC VIRUS 4430All SZGR 2.0 genes in this pathway
BOYLAN MULTIPLE MYELOMA PCA1 UP 10166All SZGR 2.0 genes in this pathway
DANG BOUND BY MYC 1103714All SZGR 2.0 genes in this pathway
WONG ADULT TISSUE STEM MODULE 721492All SZGR 2.0 genes in this pathway
BAUS TFF2 TARGETS UP 3222All SZGR 2.0 genes in this pathway
WIERENGA STAT5A TARGETS UP 217131All SZGR 2.0 genes in this pathway
WIERENGA STAT5A TARGETS GROUP1 13676All SZGR 2.0 genes in this pathway
KIM GLIS2 TARGETS UP 8461All SZGR 2.0 genes in this pathway
PASINI SUZ12 TARGETS DN 315215All SZGR 2.0 genes in this pathway
PEDRIOLI MIR31 TARGETS DN 418245All SZGR 2.0 genes in this pathway
PHONG TNF RESPONSE NOT VIA P38 337236All SZGR 2.0 genes in this pathway
RATTENBACHER BOUND BY CELF1 467251All SZGR 2.0 genes in this pathway
GENTLES LEUKEMIC STEM CELL UP 2915All SZGR 2.0 genes in this pathway
ZWANG TRANSIENTLY UP BY 2ND EGF PULSE ONLY 1725838All 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

Section VI. microRNA annotation

miRNA familyTarget positionmiRNA IDmiRNA seq
UTR startUTR endMatch method
miR-15/16/195/424/497251257m8hsa-miR-15abrainUAGCAGCACAUAAUGGUUUGUG
hsa-miR-16brainUAGCAGCACGUAAAUAUUGGCG
hsa-miR-15bbrainUAGCAGCACAUCAUGGUUUACA
hsa-miR-195SZUAGCAGCACAGAAAUAUUGGC
hsa-miR-424CAGCAGCAAUUCAUGUUUUGAA
hsa-miR-497CAGCAGCACACUGUGGUUUGU