Atlas of Genetics and Cytogenetics in Oncology and Haematology


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TNFSF11 (tumor necrosis factor superfamily member 11)

Identity

Alias_namestumor necrosis factor (ligand) superfamily
Alias_symbol (synonym)TRANCE
RANKL
OPGL
ODF
CD254
Other aliasOPTB2
TNLG6B
hRANKL2
sOdf
HGNC (Hugo) TNFSF11
LocusID (NCBI) 8600
Atlas_Id 42633
Location 13q14.11  [Link to chromosome band 13q14]
Location_base_pair Starts at 43148291 and ends at 43182149 bp from pter ( according to hg19-Feb_2009)
Fusion genes
(updated 2016)
APLP2 (11q24.3) / TNFSF11 (13q14.11)

Note

Non-annotated gene. Preliminary data : if you are an author
who wish to write a full paper/card on this gene, go to  How to contribute

DNA/RNA

 


Other Leukemias implicated (Data extracted from papers in the Atlas) [ 1 ]
  Multiple Myeloma in 2017


Other Solid tumors implicated (Data extracted from papers in the Atlas) [ 1 ]
  Lung: Translocations in Adenocarcinoma


External links

Nomenclature
HGNC (Hugo)TNFSF11   11926
Cards
Entrez_Gene (NCBI)TNFSF11  8600  tumor necrosis factor superfamily member 11
AliasesCD254; ODF; OPGL; OPTB2; 
RANKL; TNLG6B; TRANCE; hRANKL2; sOdf
GeneCards (Weizmann)TNFSF11
Ensembl hg19 (Hinxton)ENSG00000120659 [Gene_View]  chr13:43148291-43182149 [Contig_View]  TNFSF11 [Vega]
Ensembl hg38 (Hinxton)ENSG00000120659 [Gene_View]  chr13:43148291-43182149 [Contig_View]  TNFSF11 [Vega]
ICGC DataPortalENSG00000120659
TCGA cBioPortalTNFSF11
AceView (NCBI)TNFSF11
Genatlas (Paris)TNFSF11
WikiGenes8600
SOURCE (Princeton)TNFSF11
Genetics Home Reference (NIH)TNFSF11
Genomic and cartography
GoldenPath hg19 (UCSC)TNFSF11  -     chr13:43148291-43182149 +  13q14.11   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)TNFSF11  -     13q14.11   [Description]    (hg38-Dec_2013)
EnsemblTNFSF11 - 13q14.11 [CytoView hg19]  TNFSF11 - 13q14.11 [CytoView hg38]
Mapping of homologs : NCBITNFSF11 [Mapview hg19]  TNFSF11 [Mapview hg38]
OMIM259710   602642   
Gene and transcription
Genbank (Entrez)AA504211 AB037599 AB061227 AB064268 AB064269
RefSeq transcript (Entrez)NM_003701 NM_033012
RefSeq genomic (Entrez)NC_000013 NC_018924 NG_008990 NT_024524 NW_004929388
Consensus coding sequences : CCDS (NCBI)TNFSF11
Cluster EST : UnigeneHs.333791 [ NCBI ]
CGAP (NCI)Hs.333791
Alternative Splicing GalleryENSG00000120659
Gene ExpressionTNFSF11 [ NCBI-GEO ]   TNFSF11 [ EBI - ARRAY_EXPRESS ]   TNFSF11 [ SEEK ]   TNFSF11 [ MEM ]
Gene Expression Viewer (FireBrowse)TNFSF11 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)8600
GTEX Portal (Tissue expression)TNFSF11
Protein : pattern, domain, 3D structure
UniProt/SwissProtO14788   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtO14788  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProO14788
Splice isoforms : SwissVarO14788
PhosPhoSitePlusO14788
Domaine pattern : Prosite (Expaxy)TNF_2 (PS50049)   
Domains : Interpro (EBI)TNF_dom    TNF_ligand_10/11    Tumour_necrosis_fac-like_dom   
Domain families : Pfam (Sanger)TNF (PF00229)   
Domain families : Pfam (NCBI)pfam00229   
Domain families : Smart (EMBL)TNF (SM00207)  
Conserved Domain (NCBI)TNFSF11
DMDM Disease mutations8600
Blocks (Seattle)TNFSF11
PDB (SRS)3URF    5BNQ   
PDB (PDBSum)3URF    5BNQ   
PDB (IMB)3URF    5BNQ   
PDB (RSDB)3URF    5BNQ   
Structural Biology KnowledgeBase3URF    5BNQ   
SCOP (Structural Classification of Proteins)3URF    5BNQ   
CATH (Classification of proteins structures)3URF    5BNQ   
SuperfamilyO14788
Human Protein AtlasENSG00000120659
Peptide AtlasO14788
HPRD04031
IPIIPI00023732   IPI00219810   IPI00219811   
Protein Interaction databases
DIP (DOE-UCLA)O14788
IntAct (EBI)O14788
FunCoupENSG00000120659
BioGRIDTNFSF11
STRING (EMBL)TNFSF11
ZODIACTNFSF11
Ontologies - Pathways
QuickGOO14788
Ontology : AmiGOossification  osteoclast proliferation  monocyte chemotaxis  cytokine activity  cytokine activity  tumor necrosis factor receptor binding  extracellular region  extracellular region  extracellular space  cytoplasm  plasma membrane  integral component of plasma membrane  immune response  activation of JUN kinase activity  organ morphogenesis  cytokine-mediated signaling pathway  osteoclast differentiation  osteoclast differentiation  osteoclast differentiation  tumor necrosis factor receptor superfamily binding  tumor necrosis factor-mediated signaling pathway  tumor necrosis factor-mediated signaling pathway  mammary gland epithelial cell proliferation  positive regulation of homotypic cell-cell adhesion  paracrine signaling  positive regulation of I-kappaB kinase/NF-kappaB signaling  positive regulation of MAP kinase activity  bone resorption  positive regulation of osteoclast differentiation  positive regulation of bone resorption  positive regulation of transcription from RNA polymerase II promoter  positive regulation of T cell activation  positive regulation of sequence-specific DNA binding transcription factor activity  positive regulation of NF-kappaB transcription factor activity  protein homooligomerization  positive regulation of corticotropin-releasing hormone secretion  positive regulation of protein kinase B signaling  calcium ion homeostasis  mammary gland alveolus development  ERK1 and ERK2 cascade  positive regulation of fever generation by positive regulation of prostaglandin secretion  TNFSF11-mediated signaling pathway  positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling  positive regulation of intracellular signal transduction  positive regulation of osteoclast development  
Ontology : EGO-EBIossification  osteoclast proliferation  monocyte chemotaxis  cytokine activity  cytokine activity  tumor necrosis factor receptor binding  extracellular region  extracellular region  extracellular space  cytoplasm  plasma membrane  integral component of plasma membrane  immune response  activation of JUN kinase activity  organ morphogenesis  cytokine-mediated signaling pathway  osteoclast differentiation  osteoclast differentiation  osteoclast differentiation  tumor necrosis factor receptor superfamily binding  tumor necrosis factor-mediated signaling pathway  tumor necrosis factor-mediated signaling pathway  mammary gland epithelial cell proliferation  positive regulation of homotypic cell-cell adhesion  paracrine signaling  positive regulation of I-kappaB kinase/NF-kappaB signaling  positive regulation of MAP kinase activity  bone resorption  positive regulation of osteoclast differentiation  positive regulation of bone resorption  positive regulation of transcription from RNA polymerase II promoter  positive regulation of T cell activation  positive regulation of sequence-specific DNA binding transcription factor activity  positive regulation of NF-kappaB transcription factor activity  protein homooligomerization  positive regulation of corticotropin-releasing hormone secretion  positive regulation of protein kinase B signaling  calcium ion homeostasis  mammary gland alveolus development  ERK1 and ERK2 cascade  positive regulation of fever generation by positive regulation of prostaglandin secretion  TNFSF11-mediated signaling pathway  positive regulation of ERK1 and ERK2 cascade via TNFSF11-mediated signaling  positive regulation of intracellular signal transduction  positive regulation of osteoclast development  
Pathways : BIOCARTABone Remodelling [Genes]   
Pathways : KEGGCytokine-cytokine receptor interaction    NF-kappa B signaling pathway    Osteoclast differentiation    Prolactin signaling pathway    Rheumatoid arthritis   
NDEx NetworkTNFSF11
Atlas of Cancer Signalling NetworkTNFSF11
Wikipedia pathwaysTNFSF11
Orthology - Evolution
OrthoDB8600
GeneTree (enSembl)ENSG00000120659
Phylogenetic Trees/Animal Genes : TreeFamTNFSF11
HOVERGENO14788
HOGENOMO14788
Homologs : HomoloGeneTNFSF11
Homology/Alignments : Family Browser (UCSC)TNFSF11
Gene fusions - Rearrangements
Fusion : MitelmanAPLP2/TNFSF11 [11q24.3/13q14.11]  [t(11;13)(q24;q14)]  
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerTNFSF11 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)TNFSF11
dbVarTNFSF11
ClinVarTNFSF11
1000_GenomesTNFSF11 
Exome Variant ServerTNFSF11
ExAC (Exome Aggregation Consortium)TNFSF11 (select the gene name)
Genetic variants : HAPMAP8600
Genomic Variants (DGV)TNFSF11 [DGVbeta]
DECIPHER (Syndromes)13:43148291-43182149  ENSG00000120659
CONAN: Copy Number AnalysisTNFSF11 
Mutations
ICGC Data PortalTNFSF11 
TCGA Data PortalTNFSF11 
Broad Tumor PortalTNFSF11
OASIS PortalTNFSF11 [ Somatic mutations - Copy number]
Somatic Mutations in Cancer : COSMICTNFSF11  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDTNFSF11
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD - Leiden Open Variation Database
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch TNFSF11
DgiDB (Drug Gene Interaction Database)TNFSF11
DoCM (Curated mutations)TNFSF11 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)TNFSF11 (select a term)
intoGenTNFSF11
Cancer3DTNFSF11(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM259710    602642   
Orphanet2530   
MedgenTNFSF11
Genetic Testing Registry TNFSF11
NextProtO14788 [Medical]
TSGene8600
GENETestsTNFSF11
Huge Navigator TNFSF11 [HugePedia]
snp3D : Map Gene to Disease8600
BioCentury BCIQTNFSF11
ClinGenTNFSF11
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD8600
Chemical/Pharm GKB GenePA36619
Clinical trialTNFSF11
Miscellaneous
canSAR (ICR)TNFSF11 (select the gene name)
Probes
Litterature
PubMed478 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineTNFSF11
EVEXTNFSF11
GoPubMedTNFSF11
iHOPTNFSF11
Genes in titleautomatic search in PubMed
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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indexed on : Tue Mar 14 13:31:42 CET 2017

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