Pharos : Target Details

Tbio

Protein Classes

Protein Summary

Description

Cytokine that in its homotrimeric form binds to TNFRSF1A/TNFR1, TNFRSF1B/TNFBR and TNFRSF14/HVEM. In its heterotrimeric form with LTB binds to TNFRSF3/LTBR. Lymphotoxin is produced by lymphocytes and cytotoxic for a wide range of tumor cells in vitro and in vivo. The encoded protein, a member of the tumor necrosis factor family, is a cytokine produced by lymphocytes. The protein is highly inducible, secreted, and forms heterotrimers with lymphotoxin-beta which anchor lymphotoxin-alpha to the cell surface. This protein also mediates a large variety of inflammatory, immunostimulatory, and antiviral responses, is involved in the formation of secondary lymphoid organs during development and plays a role in apoptosis. Genetic variations in this gene are associated with susceptibility to leprosy type 4, myocardial infarction, non-Hodgkin's lymphoma, and psoriatic arthritis. Alternatively spliced transcript variants have been observed for this gene. [provided by RefSeq, Jul 2012]

Uniprot Accession IDs

Gene Name

Ensembl ID

ENST00000412851
ENSP00000412555
ENSG00000230279
ENST00000418386
ENSP00000413450
ENSG00000226979
ENST00000426845
ENSP00000402413
ENST00000436519
ENSP00000395976
ENSG00000231408
ENST00000454550
ENSP00000416509
ENST00000454783
ENSP00000403495

Symbol

TNFB
TNFSF1
LT
TNFB
TNFSF1
TNLG1E

Illumination Graph

Knowledge Table

Most Knowledge About	Knowledge Value (0 to 1 scale)
biological term	0.94

disease	0.94

phenotype	0.9

biological process	0.87

cell type or tissue	0.83

Related Tools

Target Illumination GWAS Analytics (TIGA)

TIGA scores and ranks GWAS discovered associations according to the quantity and quality of the evidence supporting the association.

View Data

GENEVA

GENEVA (GENe Expression Variance Analysis) allows you to identify RNA-sequencing datasets from the Gene Expression Omnibus (GEO) that contain conditions modulating a gene or a gene signature.

GlyGen

GlyGen is a data integration and dissemination project for carbohydrate and glycoconjugate related data.

IDG Development Level Summary

Tdark

These are targets about which virtually nothing is known. They do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 802.12 (req: < 5)

View Publications

Gene RIFs: 221 (req: <= 3)

View Gene RIFs

Antibodies: 701 (req: <= 50)

View Antibodies

Tbio

These targets do not have known drug or small molecule activities
- AND - satisfy two or more of the following criteria:

Pubmed score: 802.12 (req: >= 5)

Gene RIFs: 221 (req: > 3)

Antibodies: 701 (req: > 50)

- OR - satisfy the following criterion:

Gene Ontology Terms: 21

View GO Terms

Tchem

Target has at least one ChEMBL compound with an activity cutoff of < 30 nM - AND - satisfies the preceding conditions

Active Ligand: 0

Tclin

Target has at least one approved drug - AND - satisfies the preceding conditions

Active Drug: 0

GWAS Traits (339)

Items per page:

1 – 5 of 339

GWAS Trait	EFO ID	ENSG ID	Study Count	SNP Count	Beta Count	Odds Ratio	Evidence (Mean Rank Score)
lymphocyte count	EFO_0004587	ENSG00000230279	3	5	7		98.6

lymphocyte count	EFO_0004587	ENSG00000231408	3	5	7		98.6

lymphocyte count	EFO_0004587	ENSG00000226979	3	5	7		98.6

myositis	EFO_0000783	ENSG00000226979	1	9	0	2.3	98.1

myositis	EFO_0000783	ENSG00000230279	1	9	0	2.3	98.1

Items per page:

1 – 5 of 339

GWAS Trait	EFO ID	Beta Count	Odds Ratio	Evidence (Mean Rank Score)
lymphocyte count	EFO_0004587	7		98.6

lymphocyte count	EFO_0004587	7		98.6

lymphocyte count	EFO_0004587	7		98.6

myositis	EFO_0000783	0	2.3	98.1

myositis	EFO_0000783	0	2.3	98.1

Beta Count

Odds Ratio

Orthologs (11)

1 – 5 of 11

Species	Name	Source ID	Gene ID
Chimp	lymphotoxin alpha	VGNC:11106	494185

Macaque	lymphotoxin alpha		715425

Mouse	lymphotoxin A	MGI:104797	16992

Rat	lymphotoxin alpha	RGD:3020	25008

Dog	lymphotoxin alpha	VGNC:42852	607183

Species	Name	OMA	EggNOG	Inparanoid
Chimp	lymphotoxin alpha

Macaque	lymphotoxin alpha

Mouse	lymphotoxin A

Rat	lymphotoxin alpha

Dog	lymphotoxin alpha

Protein Structure (3 Structures, 1 AlphaFold Model)

1 – 3 of 3

PDB Structure Id	Ligand	Method	Resolution (Å)	Residues	Fraction of Total Protein	Pub Year	Title

PDB Structure Id	Fraction of Total Protein	Resolution	Pub Year

Pathways (53)

Reactome (5)

KEGG (7)

PathwayCommons (10)

WikiPathways (31)

Cytokine Signaling in Immune system (R-HSA-1280215)

Click on a row in the table to change the structure displayed.

Items per page:

1 – 5 of 5

Data Source	Name	Explore in Pharos	Explore in Source
Reactome	Cytokine Signaling in Immune system	922 targets	R-HSA-1280215

Reactome	Immune System	2246 targets	R-HSA-168256

Reactome	TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway	17 targets	R-HSA-5676594

Reactome	TNFR2 non-canonical NF-kB pathway	101 targets	R-HSA-5668541

Reactome	TNFs bind their physiological receptors	28 targets	R-HSA-5669034

Name	Explore in Pharos	Explore in Source
Cytokine Signaling in Immune system	922 targets	R-HSA-1280215

Immune System	2246 targets	R-HSA-168256

TNF receptor superfamily (TNFSF) members mediating non-canonical NF-kB pathway	17 targets	R-HSA-5676594

TNFR2 non-canonical NF-kB pathway	101 targets	R-HSA-5668541

TNFs bind their physiological receptors	28 targets	R-HSA-5669034

Gene Ontology Terms (23)

Functions (3)

Components (2)

Processes (18)

Items per page:

1 – 3 of 3

GO Term	Evidence	Assigned by
signaling receptor binding	Traceable Author Statement (TAS)	ProtInc

cytokine activity	Inferred from Electronic Annotation (IEA)	UniProtKB-KW

tumor necrosis factor receptor binding	Inferred from Electronic Annotation (IEA)	InterPro

Protein-Protein Interactions (207)

1 – 10 of 207

See Interactions on String-DB

ANKRD40

Tdark

Novelty: 1.06633958

p_int: 0.956792251

p_ni: 0.043207749

Score: 0.282

Data Source: BioPlex,STRINGDB

TNFRSF1A

Tchem

Novelty: 0.00037847

Score: 0.997