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TNF-like superfamily

SCOP classification
Root:   SCOP hierarchy in SUPERFAMILY [ 0] (11)
Class:   All beta proteins [ 48724] (174)
Fold:   TNF-like [ 49841]
Superfamily:   TNF-like [ 49842]
Families:   TNF-like [ 49843] (14)


Superfamily statistics
Genomes (259) Uniprot 2014_06 PDB chains (SCOP 1.75)
Domains 4,658 6,296 40
Proteins 4,472 6,104 40


Functional annotation
General category Processes_EC
Detailed category Immune response

Document:
Function annotation of SCOP domain superfamilies

Gene Ontology (high-coverage)

(show details)
GO term FDR (all) SDFO level Annotation (direct or inherited)
Biological Process (BP) response to stimulus 0 Least Informative Direct
Biological Process (BP) biological regulation 0 Least Informative Direct
Biological Process (BP) single-organism cellular process 0.0000006941 Least Informative Direct
Biological Process (BP) single-organism metabolic process 1 Least Informative Inherited
Biological Process (BP) primary metabolic process 1 Least Informative Inherited
Biological Process (BP) cellular component organization or biogenesis 1 Least Informative Inherited
Biological Process (BP) macromolecule metabolic process 0.7875 Least Informative Inherited
Biological Process (BP) cell communication 0 Moderately Informative Direct
Biological Process (BP) signaling 0 Moderately Informative Direct
Biological Process (BP) immune system process 0 Moderately Informative Direct
Biological Process (BP) regulation of protein metabolic process 0.000000000002861 Moderately Informative Direct
Biological Process (BP) regulation of response to stimulus 0.00000000001134 Moderately Informative Direct
Biological Process (BP) response to organic substance 0.0000000001257 Moderately Informative Direct
Biological Process (BP) regulation of cell communication 0.0000000002225 Moderately Informative Direct
Biological Process (BP) regulation of signaling 0.00000000209 Moderately Informative Direct
Biological Process (BP) regulation of molecular function 0.000000006657 Moderately Informative Direct
Biological Process (BP) macromolecular complex subunit organization 0.00002176 Moderately Informative Direct
Biological Process (BP) oxidation-reduction process 0.00009172 Moderately Informative Direct
Biological Process (BP) positive regulation of metabolic process 0.0001418 Moderately Informative Direct
Biological Process (BP) single-organism catabolic process 0.0001709 Moderately Informative Direct
Biological Process (BP) macromolecule localization 0.0001711 Moderately Informative Direct
Biological Process (BP) carbohydrate metabolic process 0.0001965 Moderately Informative Direct
Biological Process (BP) positive regulation of cellular process 0.000199 Moderately Informative Direct
Biological Process (BP) cellular component assembly 0.0002478 Moderately Informative Direct
Biological Process (BP) system development 0.0003564 Moderately Informative Direct
Biological Process (BP) monocarboxylic acid metabolic process 0.000386 Moderately Informative Direct
Biological Process (BP) regulation of multicellular organismal process 0.1513 Moderately Informative Inherited
Biological Process (BP) regulation of biosynthetic process 1 Moderately Informative Inherited
Biological Process (BP) cellular localization 0.02992 Moderately Informative Inherited
Biological Process (BP) cellular response to chemical stimulus 0.7199 Moderately Informative Inherited
Biological Process (BP) cellular catabolic process 0.1042 Moderately Informative Inherited
Biological Process (BP) response to oxygen-containing compound 0.002239 Moderately Informative Inherited
Biological Process (BP) response to stress 1 Moderately Informative Inherited
Biological Process (BP) cellular protein modification process 0.69 Moderately Informative Inherited
Biological Process (BP) regulation of nitrogen compound metabolic process 1 Moderately Informative Inherited
Biological Process (BP) regulation of gene expression 1 Moderately Informative Inherited
Biological Process (BP) negative regulation of metabolic process 0.8733 Moderately Informative Inherited
Biological Process (BP) regulation of cellular metabolic process 0.4749 Moderately Informative Inherited
Biological Process (BP) regulation of cellular component organization 0.006003 Moderately Informative Inherited
Biological Process (BP) negative regulation of cellular process 0.4377 Moderately Informative Inherited
Biological Process (BP) cellular developmental process 1 Moderately Informative Inherited
Biological Process (BP) anatomical structure morphogenesis 1 Moderately Informative Inherited
Biological Process (BP) regulation of localization 0.04678 Moderately Informative Inherited
Biological Process (BP) organic substance catabolic process 0.1782 Moderately Informative Inherited
Biological Process (BP) regulation of developmental process 0.8968 Moderately Informative Inherited
Biological Process (BP) multi-organism process 0.3106 Moderately Informative Inherited
Biological Process (BP) organic substance transport 0.9749 Moderately Informative Inherited
Biological Process (BP) single-organism transport 1 Moderately Informative Inherited
Biological Process (BP) regulation of biological quality 0.6555 Moderately Informative Inherited
Biological Process (BP) lipid metabolic process 0.01621 Moderately Informative Inherited
Biological Process (BP) response to external stimulus 1 Moderately Informative Inherited
Biological Process (BP) regulation of apoptotic process 0 Informative Direct
Biological Process (BP) positive regulation of cell death 0 Informative Direct
Biological Process (BP) positive regulation of cellular protein metabolic process 0 Informative Direct
Biological Process (BP) negative regulation of cellular component organization 0 Informative Direct
Biological Process (BP) cell death 0 Informative Direct
Biological Process (BP) response to cytokine 0 Informative Direct
Biological Process (BP) regulation of cytokine production 0 Informative Direct
Biological Process (BP) regulation of phosphorylation 0 Informative Direct
Biological Process (BP) regulation of transferase activity 0.000000000000001902 Informative Direct
Biological Process (BP) positive regulation of immune system process 0.00000000000007564 Informative Direct
Biological Process (BP) response to bacterium 0.00000000001056 Informative Direct
Biological Process (BP) monosaccharide metabolic process 0.00000000001148 Informative Direct
Biological Process (BP) positive regulation of catalytic activity 0.00000000006005 Informative Direct
Biological Process (BP) positive regulation of signal transduction 0.000000000101 Informative Direct
Biological Process (BP) positive regulation of phosphate metabolic process 0.0000000001191 Informative Direct
Biological Process (BP) lipid catabolic process 0.000000000619 Informative Direct
Biological Process (BP) regulation of protein modification process 0.00000001993 Informative Direct
Biological Process (BP) protein oligomerization 0.00000003445 Informative Direct
Biological Process (BP) carboxylic acid catabolic process 0.0000001208 Informative Direct
Biological Process (BP) regulation of cell proliferation 0.0000001766 Informative Direct
Biological Process (BP) fatty acid metabolic process 0.0000001902 Informative Direct
Biological Process (BP) immune response 0.0000002024 Informative Direct
Biological Process (BP) regulation of intracellular signal transduction 0.0000003414 Informative Direct
Biological Process (BP) negative regulation of transport 0.0000005304 Informative Direct
Biological Process (BP) regulation of lipid metabolic process 0.000002509 Informative Direct
Biological Process (BP) response to nitrogen compound 0.000003963 Informative Direct
Biological Process (BP) positive regulation of multicellular organismal process 0.000005204 Informative Direct
Biological Process (BP) cell adhesion 0.000007459 Informative Direct
Biological Process (BP) positive regulation of transport 0.00003368 Informative Direct
Biological Process (BP) single-organism membrane organization 0.0000448 Informative Direct
Biological Process (BP) regulation of protein localization 0.0001227 Informative Direct
Biological Process (BP) positive regulation of cellular component organization 0.0002797 Informative Direct
Biological Process (BP) regulation of system process 0.0003454 Informative Direct
Biological Process (BP) regulation of cellular component movement 0.0007161 Informative Direct
Biological Process (BP) positive regulation of developmental process 0.04615 Informative Inherited
Biological Process (BP) negative regulation of multicellular organismal process 0.01246 Informative Inherited
Biological Process (BP) regulation of cell differentiation 0.08185 Informative Inherited
Biological Process (BP) negative regulation of molecular function 0.9331 Informative Inherited
Biological Process (BP) cellular response to oxygen-containing compound 0.1041 Informative Inherited
Biological Process (BP) cellular response to hormone stimulus 0.01014 Informative Inherited
Biological Process (BP) response to oxidative stress 0.001898 Informative Inherited
Biological Process (BP) phosphorylation 0.007616 Informative Inherited
Biological Process (BP) negative regulation of nitrogen compound metabolic process 0.009464 Informative Inherited
Biological Process (BP) regulation of transcription, DNA-templated 0.1213 Informative Inherited
Biological Process (BP) regulation of defense response 1 Informative Inherited
Biological Process (BP) negative regulation of biosynthetic process 0.001655 Informative Inherited
Biological Process (BP) animal organ morphogenesis 0.6881 Informative Inherited
Biological Process (BP) regulation of locomotion 0.003485 Informative Inherited
Biological Process (BP) regulation of anatomical structure morphogenesis 0.006198 Informative Inherited
Biological Process (BP) cell surface receptor signaling pathway 1 Informative Inherited
Biological Process (BP) regulation of cellular localization 0.007111 Informative Inherited
Biological Process (BP) regulation of response to external stimulus 0.09773 Informative Inherited
Biological Process (BP) negative regulation of cellular protein metabolic process 0.5973 Informative Inherited
Biological Process (BP) regulation of hydrolase activity 1 Informative Inherited
Biological Process (BP) regulation of proteolysis 1 Informative Inherited
Biological Process (BP) negative regulation of response to stimulus 0.4338 Informative Inherited
Biological Process (BP) secretion 0.0521 Informative Inherited
Biological Process (BP) system process 0.1248 Informative Inherited
Biological Process (BP) intracellular signal transduction 1 Informative Inherited
Biological Process (BP) regulation of immune response 0.189 Informative Inherited
Biological Process (BP) negative regulation of signaling 0.1273 Informative Inherited
Biological Process (BP) negative regulation of cell communication 0.2145 Informative Inherited
Biological Process (BP) cytokine-mediated signaling pathway 0 Highly Informative Direct
Biological Process (BP) regulation of carbohydrate biosynthetic process 0 Highly Informative Direct
Biological Process (BP) glucose metabolic process 0 Highly Informative Direct
Biological Process (BP) positive regulation of apoptotic process 0 Highly Informative Direct
Biological Process (BP) regulation of leukocyte differentiation 0 Highly Informative Direct
Biological Process (BP) regulation of protein complex disassembly 0 Highly Informative Direct
Biological Process (BP) regulation of protein serine/threonine kinase activity 0 Highly Informative Direct
Biological Process (BP) positive regulation of cytokine production 0 Highly Informative Direct
Biological Process (BP) negative regulation of carbohydrate metabolic process 0 Highly Informative Direct
Biological Process (BP) regulation of inflammatory response 0.000000000000003692 Highly Informative Direct
Biological Process (BP) fatty acid catabolic process 0.000000000000007239 Highly Informative Direct
Biological Process (BP) negative regulation of cellular protein localization 0.00000000000007089 Highly Informative Direct
Biological Process (BP) inflammatory response 0.0000000000003682 Highly Informative Direct
Biological Process (BP) regulation of cellular response to stress 0.0000000000004825 Highly Informative Direct
Biological Process (BP) lipid modification 0.0000000000007749 Highly Informative Direct
Biological Process (BP) cell proliferation 0.00000000001738 Highly Informative Direct
Biological Process (BP) endomembrane system organization 0.00000000002782 Highly Informative Direct
Biological Process (BP) negative regulation of establishment of protein localization 0.0000000003401 Highly Informative Direct
Biological Process (BP) positive regulation of leukocyte proliferation 0.0000000006366 Highly Informative Direct
Biological Process (BP) coagulation 0.000000002078 Highly Informative Direct
Biological Process (BP) regulation of cellular carbohydrate metabolic process 0.000000002131 Highly Informative Direct
Biological Process (BP) regulation of blood pressure 0.000000002176 Highly Informative Direct
Biological Process (BP) regulation of cellular ketone metabolic process 0.000000002366 Highly Informative Direct
Biological Process (BP) response to carbohydrate 0.00000002878 Highly Informative Direct
Biological Process (BP) regulation of sequence-specific DNA binding transcription factor activity 0.00000005232 Highly Informative Direct
Biological Process (BP) leukocyte mediated immunity 0.00000006077 Highly Informative Direct
Biological Process (BP) negative regulation of response to external stimulus 0.000000073 Highly Informative Direct
Biological Process (BP) regulation of smooth muscle cell proliferation 0.0000001603 Highly Informative Direct
Biological Process (BP) negative regulation of locomotion 0.000000228 Highly Informative Direct
Biological Process (BP) positive regulation of cell adhesion 0.0000002364 Highly Informative Direct
Biological Process (BP) negative regulation of cellular component movement 0.0000003693 Highly Informative Direct
Biological Process (BP) wound healing 0.0000004181 Highly Informative Direct
Biological Process (BP) MAPK cascade 0.0000005271 Highly Informative Direct
Biological Process (BP) positive regulation of lipid metabolic process 0.0000005636 Highly Informative Direct
Biological Process (BP) humoral immune response 0.000001248 Highly Informative Direct
Biological Process (BP) regulation of vesicle-mediated transport 0.000002922 Highly Informative Direct
Biological Process (BP) regulation of DNA metabolic process 0.00002372 Highly Informative Direct
Biological Process (BP) response to peptide hormone 0.00004759 Highly Informative Direct
Biological Process (BP) response to drug 0.00005352 Highly Informative Direct
Biological Process (BP) hemostasis 0.00007927 Highly Informative Direct
Biological Process (BP) regulation of protein import into nucleus 0.00009076 Highly Informative Direct
Biological Process (BP) positive regulation of cell development 0.0001025 Highly Informative Direct
Biological Process (BP) response to molecule of bacterial origin 0.0001453 Highly Informative Direct
Biological Process (BP) positive regulation of MAPK cascade 0.0002294 Highly Informative Direct
Biological Process (BP) negative regulation of RNA metabolic process 0.0003861 Highly Informative Direct
Biological Process (BP) negative regulation of immune system process 0.000661 Highly Informative Direct
Biological Process (BP) regulation of binding 0.0007078 Highly Informative Direct
Biological Process (BP) protein secretion 0.0008601 Highly Informative Direct
Biological Process (BP) regulation of apoptotic signaling pathway 0.105 Highly Informative Inherited
Biological Process (BP) apoptotic process 1 Highly Informative Inherited
Biological Process (BP) leukocyte cell-cell adhesion 0.00393 Highly Informative Inherited
Biological Process (BP) cellular response to organonitrogen compound 0.001623 Highly Informative Inherited
Biological Process (BP) negative regulation of phosphate metabolic process 0.7277 Highly Informative Inherited
Biological Process (BP) regulation of lymphocyte proliferation 0.001695 Highly Informative Inherited
Biological Process (BP) positive regulation of lymphocyte activation 0.003586 Highly Informative Inherited
Biological Process (BP) negative regulation of cell proliferation 0.01142 Highly Informative Inherited
Biological Process (BP) lymphocyte activation 0.0627 Highly Informative Inherited
Biological Process (BP) negative regulation of intracellular signal transduction 0.4201 Highly Informative Inherited
Biological Process (BP) negative regulation of protein modification process 0.3531 Highly Informative Inherited
Biological Process (BP) positive regulation of proteolysis 1 Highly Informative Inherited
Biological Process (BP) regulation of cysteine-type endopeptidase activity 0.001304 Highly Informative Inherited
Biological Process (BP) positive regulation of adaptive immune response based on somatic recombination of immune receptors b 0.08269 Highly Informative Inherited
Biological Process (BP) positive regulation of immune effector process 0.8666 Highly Informative Inherited
Biological Process (BP) regulation of leukocyte mediated immunity 0.0985 Highly Informative Inherited
Biological Process (BP) regulation of production of molecular mediator of immune response 0.007328 Highly Informative Inherited
Molecular Function (MF) binding 0.002889 Least Informative Inherited
Molecular Function (MF) protein binding 0.000000002643 Moderately Informative Direct
Molecular Function (MF) receptor binding 0 Informative Direct
Molecular Function (MF) cytokine receptor binding 0.000007383 Highly Informative Direct
Cellular Component (CC) cytoplasmic part 1 Least Informative Inherited
Cellular Component (CC) intracellular membrane-bounded organelle 1 Least Informative Inherited
Cellular Component (CC) extracellular region part 0 Moderately Informative Direct
Cellular Component (CC) endoplasmic reticulum 0.0001974 Moderately Informative Direct
Cellular Component (CC) cell surface 0 Informative Direct
Cellular Component (CC) extracellular space 0.0004834 Informative Direct
Cellular Component (CC) extracellular organelle 0.0005475 Informative Direct
Cellular Component (CC) perinuclear region of cytoplasm 0.0000005263 Highly Informative Direct

Document: GO annotation of SCOP domains

Disease Ontology (DO)

(show details)
DO termFDR (all)SDDO levelAnnotation (direct or inherited)
Disease Ontology (DO)immune system disease0.01833Least InformativeInherited
Disease Ontology (DO)nervous system disease0.123Least InformativeInherited
Disease Ontology (DO)organ system cancer0.5612Least InformativeInherited
Disease Ontology (DO)connective tissue disease0.0000000002199Moderately InformativeDirect
Disease Ontology (DO)artery disease0.00008931Moderately InformativeDirect
Disease Ontology (DO)blood coagulation disease0.00009023Moderately InformativeDirect
Disease Ontology (DO)urinary system disease0.0003469Moderately InformativeDirect
Disease Ontology (DO)disease of metabolism0.005489Moderately InformativeInherited
Disease Ontology (DO)hematologic cancer0.006958Moderately InformativeInherited
Disease Ontology (DO)endocrine system disease0.009032Moderately InformativeInherited
Disease Ontology (DO)sensory system disease0.2131Moderately InformativeInherited
Disease Ontology (DO)hypersensitivity reaction type II disease0.2763Moderately InformativeInherited
Disease Ontology (DO)neurodegenerative disease0.4135Moderately InformativeInherited
Disease Ontology (DO)skin disease0.7645Moderately InformativeInherited
Disease Ontology (DO)atherosclerosis0.000001795InformativeDirect
Disease Ontology (DO)hemorrhagic disease0.000001957InformativeDirect
Disease Ontology (DO)arthritis0.000002027InformativeDirect
Disease Ontology (DO)myeloma0.0000268InformativeDirect
Disease Ontology (DO)multiple sclerosis0.0000517InformativeDirect
Disease Ontology (DO)myocardial infarction0.0002009InformativeDirect
Disease Ontology (DO)intrinsic cardiomyopathy0.0003397InformativeDirect
Disease Ontology (DO)alopecia0.000516InformativeDirect
Disease Ontology (DO)retinal disease0.0006148InformativeDirect
Disease Ontology (DO)scleroderma0.0006852InformativeDirect
Disease Ontology (DO)Kawasaki disease0.0009914InformativeDirect
Disease Ontology (DO)primary immunodeficiency disease0.01642InformativeInherited
Disease Ontology (DO)bullous skin disease0.03264InformativeInherited
Disease Ontology (DO)lysosomal storage disease0.1082InformativeInherited
Disease Ontology (DO)lymphoma0.1253InformativeInherited
Disease Ontology (DO)pancreas disease0.1444InformativeInherited
Disease Ontology (DO)glucose metabolism disease1InformativeInherited
Disease Ontology (DO)rheumatoid arthritis0.00000008921Highly InformativeDirect
Disease Ontology (DO)pemphigus0.00001345Highly InformativeDirect
Disease Ontology (DO)primary open angle glaucoma0.00002418Highly InformativeDirect
Disease Ontology (DO)dilated cardiomyopathy0.00003388Highly InformativeDirect
Disease Ontology (DO)agammaglobulinemia0.0001949Highly InformativeDirect
Disease Ontology (DO)Burkitt lymphoma0.0002707Highly InformativeDirect
Disease Ontology (DO)thrombocytopenia0.0006039Highly InformativeDirect
Disease Ontology (DO)meningitis0.0008431Highly InformativeDirect
Disease Ontology (DO)endocrine pancreas disease0.04108Highly InformativeInherited

Document: DO annotation of SCOP domains

Human Phenotype (HP)

(show details)
HP termFDR (all)SDHP levelAnnotation (direct or inherited)
Phenotypic Abnormality (PA)Abnormality of the immune system0.06301Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the digestive system0.09303Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the cardiovascular system0.2342Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the face0.2971Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of metabolism/homeostasis0.42Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skeletal morphology0.5425Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the integument0.573Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of nervous system morphology0.8369Least InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the genitourinary system0.9228Least InformativeInherited
Phenotypic Abnormality (PA)Abnormal inflammatory response0.0008023Moderately InformativeDirect
Phenotypic Abnormality (PA)Abnormality of humoral immunity0.00241Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the abdominal organs0.07478Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of blood and blood-forming tissues0.08013Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal joint morphology0.09241Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the vasculature0.1762Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of skin morphology0.2706Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormal respiratory system morphology0.2797Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the urinary system physiology0.2813Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the upper urinary tract0.4206Moderately InformativeInherited
Phenotypic Abnormality (PA)Abnormality of the nose0.428Moderately InformativeInherited
Phenotypic Abnormality (PA)Complement deficiency0.0001299InformativeDirect
Phenotypic Abnormality (PA)Nephritis0.0002476InformativeDirect
Phenotypic Abnormality (PA)CNS infection0.0007987InformativeDirect
Phenotypic Abnormality (PA)Abnormal vascular morphology0.0008523InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the glomerulus0.0008725InformativeDirect
Phenotypic Abnormality (PA)Abnormality of the upper respiratory tract0.02927InformativeInherited
Phenotypic Abnormality (PA)Respiratory tract infection0.03135InformativeInherited
Phenotypic Abnormality (PA)Abnormality of lymphocytes0.04188InformativeInherited
Phenotypic Abnormality (PA)Recurrent infections0.1226InformativeInherited
Phenotypic Abnormality (PA)Abnormality of cell physiology0.1553InformativeInherited
Phenotypic Abnormality (PA)Dermatological manifestations of systemic disorders0.214InformativeInherited
Phenotypic Abnormality (PA)Chronic active hepatitis0.000004716Highly InformativeDirect
Phenotypic Abnormality (PA)Vasculitis0.00000503Highly InformativeDirect
Phenotypic Abnormality (PA)Discoid lupus erythematosus0.00001252Highly InformativeDirect
Phenotypic Abnormality (PA)Recurrent bronchitis0.00008825Highly InformativeDirect
Phenotypic Abnormality (PA)Abnormality of T cell physiology0.0004074Highly InformativeDirect
Phenotypic Abnormality (PA)Arthralgia0.0005738Highly InformativeDirect

Document: HP annotation of SCOP domains

Mouse Phenotype (MP)

(show details)
MP termFDR (all)SDMP levelAnnotation (direct or inherited)
Mammalian Phenotype (MP)hematopoietic system phenotype0.008176Least InformativeInherited
Mammalian Phenotype (MP)immune system phenotype0.01182Least InformativeInherited
Mammalian Phenotype (MP)abnormal immune system organ morphology0.0178Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal eye morphology0.02669Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal immune serum protein physiology0.04696Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal professional antigen presenting cell physiology0.2009Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal inflammatory response0.3728Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal leukocyte physiology0.5972Moderately InformativeInherited
Mammalian Phenotype (MP)abnormal gland morphology0.8908Moderately InformativeInherited
Mammalian Phenotype (MP)autoimmune response0.000002479InformativeDirect
Mammalian Phenotype (MP)abnormal Peyer's patch morphology0.00007841InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node morphology0.0002142InformativeDirect
Mammalian Phenotype (MP)joint inflammation0.004108InformativeInherited
Mammalian Phenotype (MP)abnormal spleen morphology0.0136InformativeInherited
Mammalian Phenotype (MP)abnormal interferon secretion0.01387InformativeInherited
Mammalian Phenotype (MP)abnormal retinal neuronal layer morphology0.01531InformativeInherited
Mammalian Phenotype (MP)abnormal humoral immune response0.01673InformativeInherited
Mammalian Phenotype (MP)abnormal thymus morphology0.02988InformativeInherited
Mammalian Phenotype (MP)abnormal interleukin secretion0.177InformativeInherited
Mammalian Phenotype (MP)abnormal lymph organ size0.2964InformativeInherited
Mammalian Phenotype (MP)abnormal IgG2a level0.0000005292Highly InformativeDirect
Mammalian Phenotype (MP)abnormal mesenteric lymph node morphology0.000004809Highly InformativeDirect
Mammalian Phenotype (MP)abnormal spleen germinal center morphology0.00003465Highly InformativeDirect
Mammalian Phenotype (MP)lymph node hypoplasia0.00004167Highly InformativeDirect
Mammalian Phenotype (MP)arthritis0.00007018Highly InformativeDirect
Mammalian Phenotype (MP)decreased interleukin-10 secretion0.000107Highly InformativeDirect
Mammalian Phenotype (MP)abnormal lymph node B cell domain morphology0.0001263Highly InformativeDirect
Mammalian Phenotype (MP)thin retinal outer nuclear layer0.0006482Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus epithelium morphology0.0007101Highly InformativeDirect
Mammalian Phenotype (MP)thin retinal inner nuclear layer0.0007336Highly InformativeDirect
Mammalian Phenotype (MP)abnormal response to transplant0.0008264Highly InformativeDirect
Mammalian Phenotype (MP)abnormal thymus medulla morphology0.001655Highly InformativeInherited
Mammalian Phenotype (MP)abnormal peripheral lymph node morphology0.01447Highly InformativeInherited
Mammalian Phenotype (MP)abnormal Peyer's patch size0.3772Highly InformativeInherited

Document: MP annotation of SCOP domains

Zebrafish Anatomy (ZA)

(show details) Document: ZA annotation of SCOP domains

Xenopus Anatomy (XA)

(show details) Document: XA annotation of SCOP domains

DrugBank ATC (DB)

(show details)
DB termFDR (all)SDDB levelAnnotation (direct or inherited)
Drugbank ATC_code (DB)antineoplastic and immunomodulating agents0Least InformativeDirect
Drugbank ATC_code (DB)blood and blood forming organs0.001009Least InformativeInherited
Drugbank ATC_code (DB)antiinfectives for systemic use0.02647Least InformativeInherited
Drugbank ATC_code (DB)immunosuppressants0Moderately InformativeDirect
Drugbank ATC_code (DB)antithrombotic agents1Moderately InformativeInherited
Drugbank ATC_code (DB)interleukin inhibitors0.2296InformativeInherited
Drugbank ATC_code (DB)palivizumab0.000000792Highly InformativeDirect
Drugbank ATC_code (DB)rituximab0.000000792Highly InformativeDirect
Drugbank ATC_code (DB)bevacizumab0.000000792Highly InformativeDirect
Drugbank ATC_code (DB)cetuximab0.000001078Highly InformativeDirect
Drugbank ATC_code (DB)daclizumab0.000001078Highly InformativeDirect
Drugbank ATC_code (DB)trastuzumab0.000001456Highly InformativeDirect
Drugbank ATC_code (DB)basiliximab0.000001456Highly InformativeDirect
Drugbank ATC_code (DB)abciximab0.000001897Highly InformativeDirect

Document: DB annotation of SCOP domains

UniProtKB KeyWords (KW)

(show details)
KW termFDR (all)SDKW levelAnnotation (direct or inherited)
Biological processImmunity0Moderately InformativeDirect
Biological processApoptosis0.0000000002363Moderately InformativeDirect
Biological processDifferentiation0.0000001167Moderately InformativeDirect
Biological processAngiogenesis0.000000000000006823InformativeDirect
Biological processCell adhesion0.000000009307InformativeDirect
Biological processInnate immunity0.06798InformativeInherited
Biological processComplement pathway0.00000000001272Highly InformativeDirect
Cellular componentMembrane6.533e-16Least InformativeDirect
Cellular componentSecreted0Moderately InformativeDirect
Cellular componentCell junction0.0004994Moderately InformativeDirect
Cellular componentCell membrane0.0009908Moderately InformativeDirect
Cellular componentSynapse0.0000001735InformativeDirect
Cellular componentLysosome0.0000003589InformativeDirect
DiseaseDisease mutation0.0005887Least InformativeDirect
DomainSignal0.0000000000000193Least InformativeDirect
DomainTransmembrane0.0003899Least InformativeDirect
DomainSignal-anchor0InformativeDirect
DomainCollagen0Highly InformativeDirect
Post-translational modificationCytokine0Highly InformativeDirect
Post-translational modificationHormone0.00000000000000267Highly InformativeDirect
Post-translational modificationGlycoprotein0Least InformativeDirect
Post-translational modificationDisulfide bond0Least InformativeDirect
Post-translational modificationHydroxylation0InformativeDirect
Post-translational modificationMyristate0InformativeDirect

Document: KW annotation of SCOP domains

InterPro annotation
Cross references IPR008983 SSF49842 Protein matches
Abstract

The tumour necrosis factor (TNF)-like domains are found in both TNF and C1q protein families. Structurally these domains self-associate to make a compact bell-shaped homotrimer, each monomer being composed of an anti-parallel beta-sheet sandwich with a jellyroll topology. Both TNF and C1q family members can be expressed as soluble plasma proteins or as type II membrane-bound proteins.

TNF family members bind extracellularly to cysteine-rich receptors, thereby inducing a clustering of the receptors, which subsequently triggers the intracellular apoptotic cascade. The TNF proteins are important mediators in inflammation, immune responses and cytotoxicity through their interaction with the TNF-R55 and the TNF-R75 cell-surface receptors [PubMed9442056]. Other TNF family members include the CD40 ligand (C-terminal TNF-like domain) which is involved in the immune response via the CD40 receptor [PubMed8589998], TRAIL which selectively induces apoptosis in tumour cells via DR4 and DR5 receptors [PubMed10651627], the RANK ligand which triggers osteoclastogenesis via the RANK receptor [PubMed11733492], and TALL-1 (soluble domain) which is involved in the immune response via the TACI, BCMA, and BAFF-R receptors [PubMed11862220].

C1q proteins also contain TNF-like domains. C1q family members include the serum protein ACRP30 (C-terminal TNF-like domain) which may be involved in energy homeostasis and obesity, and X-NC1 (C-terminal TNF-like domain) which is crucial for collagen X assembly in bone tissue [PubMed11839302].


InterPro database


PDBeMotif information about ligands, sequence and structure motifs
Cross references PDB entries
Ligand binding statistics
Nucleic-acid binding statistics
Occurrence of secondary structure elements
Occurrence of small 3D structural motifs

PDBeMotif resource

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Internal database links

Browse genome assignments for this superfamily. The SUPERFAMILY hidden Markov model library has been used to carry out SCOP domain assignments to all genomes at the superfamily level.


Alignments of sequences to 19 models in this superfamily are available by clicking on the 'Alignments' icon above. PDB sequences less than 40% identical are shown by default, but any other sequence(s) may be aligned. Select PDB sequences, genome sequences, or paste in or upload your own sequences.


Browse and view proteins in genomes which have different domain combinations including a TNF-like domain.


Examine the distribution of domain superfamilies, or families, across the major taxonomic kingdoms or genomes within a kingdom. This gives an immediate impression of how superfamilies, or families, are restricted to certain kingdoms of life.


Explore domain occurrence network where nodes represent genomes and edges are domain architectures (shared between genomes) containing the superfamily of interest.

There are 19 hidden Markov models representing the TNF-like superfamily. Information on how the models are built, and plots showing hydrophobicity, match emmission probabilities and insertion/deletion probabilities can be inspected.


Jump to [ Top of page · SCOP classification · InterPro annotation · PDBeMotif links · Functional annotation · Gene Ontology (high-coverage) · Disease Ontology (DO) · Human Phenotype (HP) · Mouse Phenotype (MP) · Zebrafish Anatomy (ZA) · Xenopus Anatomy (XA) · DrugBank ATC (DB) · UniProtKB KeyWords (KW) · Internal database links ]