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FBXO11 (F-box protein 11)

Written2014-09Shanshan Duan, Michele Pagano
Department of Pathology, NYU Cancer Institute, New York University School of Medicine, 522 First Avenue, SRB 1107, New York, New York 10016, USA

Abstract FBXO11 is a member of the F-box protein family, which is characterized by an approximately 40 amino acid motif, named the F-box domain. It is the substrate binding subunit of the SKP1-CUL1-F-box (SCF) ubiquitin ligase complex. FBXO11 is conserved from nematodes to mammals, and both human FBXO11 and its worm ortholog (DRE-1) form functional SCF ubiquitin ligase complexes. By binding to and mediating the degradation of its substrate proteins, FBXO11 plays important roles in regulating cell cycle regulation, tumorigenesis, and tumor cell metastasis. The gene encoding FBXO11 was found to be deleted or mutated in various types of human tumors.

Keywords F-box, ubiquitin, cell cycle, tumorigenesis, metastasis

(Note : for Links provided by Atlas : click)

Identity

Alias_namesF-box only protein 11
Alias_symbol (synonym)FBX11
UBR6
Other aliasPRMT9
VIT1
HGNC (Hugo) FBXO11
LocusID (NCBI) 80204
Atlas_Id 52605
Location 2p16.3  [Link to chromosome band 2p16]
Location_base_pair Starts at 48034059 and ends at 48132932 bp from pter ( according to hg19-Feb_2009)  [Mapping FBXO11.png]
Fusion genes
(updated 2016)
FBXO11 (2p16.3) / INTS9 (8p21.1)FBXO11 (2p16.3) / MAP2K5 (15q23)MED21 (12p11.23) / FBXO11 (2p16.3)
MSH6 (2p16.3) / FBXO11 (2p16.3)NEBL (10p12.31) / FBXO11 (2p16.3)ZBTB20 (3q13.31) / FBXO11 (2p16.3)

DNA/RNA

 
  Figure 1.
Description The gene is encoded by 23 exons that are located on chrosome 2p16.3 (NM_025133.4). The first ATG occurs in exon 2. There is an alternatively spliced transcript variant encoding an isoform in which the first ATG occurs in exon 1 (NM_001190274).
Transcription 3.8 kb mRNA; 2532 bp open reading frame (for NM_025133.4). 4 kb mRNA; 2784 bp open reading frame (for NM_001190274).

Protein

Description The fbxo11 gene encodes the FBXO11 protein which has 843 amino acids (NP_079409.3), with an estimated molecular weight of 94 kDa. The protein contains from N-term to C-term, an F-box domain, three CASH domains (domain present in carbohydrate binding proteins and sugar hydrolyses), and a Zinc finger domain. Other splice variants were reported (Cook et al., 2006).
Expression Widely expressed.
Localisation Mainly nuclear.
 
  Figure 2.
Function Substrate recognition component of the SCFFBXO11 ubiquitin ligase complex consisting of CUL1, RBX1, SKP1 and FBXO11. Known interactors include p53, BCL6, CDT2, Blimp and Snail (Figure 2).
FBXO11 functions in lymphomagenesis
The SCFFBXO11 complex mediates ubiquitylation and degradation of BCL6, a transcription repressor that is required for normal germinal center development. Constitutive expression of BCL6 occurs in at least 70% patients with diffuse large B-cell lymphoma (DLBCL). The gene encoding FBXO11 was found to be deleted or mutated in multiple DLBCL cell lines, and this inactivation of FBXO11 correlated with increased levels and stability of BCL6 (Duan et al., 2012). Moreover, FBXO11 is deleted or mutated in 12-15% of primary DLBCL.
Fbxo11 in cell cycle regulation
FBXO11 interacts with CDT2 (a DCAF protein that controls cell-cycle progression) and recruits CDT2 to the SCFFBXO11 complex to promote its proteasomal degradation (Abbas et al., 2013; Rossi et al., 2013). CDK-mediated phosphorylation of Thr464 present in the CDT2 degron inhibits recognition by FBXO11 (Rossi et al., 2013). Inhibition of SCFFBXO11-mediated CDT2 degradation result in a delay in cell-cycle exit in response to serum deprivation or TGFβ treatment. The functional interaction between FBXO11 and CDT2 is evolutionary conserved from worms to humans and plays an important role in regulating the timing of cell-cycle exit.
FBXO11 in TGFβ signaling pathway
FBXO11 was implicated in the TGFβ signaling pathway. Mice with inactivated FBXO11 exhibited significant phospho-Smad2 (P-Smad2) nuclear staining in the epithelial cells of palatal shelves, eyelids, and airways of the lung, potentially leading to the developmental defects of these tissues (Tateossian et al., 2009).
SCFFBXO11-mediated degradation of CDT2 was shown to contribute to the stabilization of the CRL4CDT2 substrate p21 and Set8 in response to serum withdraw and TGFβ stimulation (Abbas et al., 2013; Rossi et al., 2013). Depletion of FBXO11 was shown also to inhibit lung adenocarcinoma eptithelial cells migration (Abbas et al., 2013).
FBXO11 in the regulation of cell metastasis
FBXO11 was shown to mediate the ubiquitylation and degradation of SNAIL (Zheng et al., 2014), a transcription factor that promotes epithelial-mesenchymal transition (EMT). The recognition of SNAIL by FBXO11 appears to be dependent on Ser-11 phosphorylation of SNAIL by protein kinase D1 (PDK1). FBXO11 blocks SNAIL-induced EMT, tumor initiation, and metastasis in multiple breast cancer models.
DRE-1/FBXO11 in C. elegans development
The C. elegans ortholog of FBXO11 is DRE-1, whose mutant phenotypes include precocious terminal differentiation of epidermal stem cells and altered temporal patterning of gonadal outgrowth (Fielenbach et al., 2007). DRE-1 forms a functional SCF ubiquitin ligase, and was reported to target the conserved transcription factor BLMP-1 for proteasomal degradation (Horn et al., 2014). The DRE-1 - BLMP-1 axis was important for regulating developmental timing within the heterochronic circuit during late larval development. blmp-1 deletion was shown to suppress dre-1 mutant phenotypes and exhibit developmental timing defects opposite to dre-1.
Other functions
FBXO11 has been shown to act as an adaptor protein to mediate the neddylation of p53, which leads to the suppression of p53 transcriptional activity. SCFFBXO11 does not mediate the ubiquitylation of p53 (Abida et al., 2007).
Homology Human FBXO11 is highly conserved in evolution that shares 100% amino acid identity with Pan troglodytes, 99.8% identity with Canis lupus familiaris, 99.5% identity with Mus musculus, and 61% identity with C. elegans.

Mutations

Somatic FBXO11-inactivating mutations contribute to the pathogenesis of diffuse large B cell lymphoma (DLBCL) through stabilization of BCL6 (Duan et al., 2012). FBXO11 mutations were also identified in other human cancers, such as colon, lung, ovary, and head and neck tumors (Kan et al., 2010; Lohr et al., 2012; Stransky et al., 2011; Yoshida et al., 2011). In mice, a homozygous mutation of Fbxo11 results in cleft palate defects, facial clefting, and perinatal lethality. Moreover, haploinsufficient mutant alleles cause otitis media, a disorder that affects approximately 15% of children (Hardisty-Hughes et al., 2006).

Implicated in

Note
  
Entity Diffuse large B-cell lymphoma
Note FBXO11-inactivating mutations are found in human diffuse large B cell lymphoma (DLBCL), suggesting that FBXO11 may function as a tumor suppressor whose loss of function contributes to the pathogenesis of DLBCL through stabilization of BCL6.
Disease Diffuse Large B-cell lymphoma.
  
  
Entity Otitis Media
Note Genetic studies show a correlation between particular SNP variants of FBXO11 and the development of chronic otitis media (Segade et al., 2006).
Disease Otitis media, inflammation of the middle ear, is the most common cause of hearing impairment in children.
  
  
Entity Vitiligo
Note By comparing RNA isolated from vitiligo melanocyte cultures versus control cultures, VIT1 was found to be downregulated in vitiligo melanocytes, suggesting that it might be associated with this pigmentary disorder (Le Poole et al., 2001).
Disease Vitiligo.
  

Bibliography

CRL1-FBXO11 promotes Cdt2 ubiquitylation and degradation and regulates Pr-Set7/Set8-mediated cellular migration.
Abbas T, Mueller AC, Shibata E, Keaton M, Rossi M, Dutta A.
Mol Cell. 2013 Mar 28;49(6):1147-58. doi: 10.1016/j.molcel.2013.02.003. Epub 2013 Mar 7.
PMID 23478445
 
FBXO11 promotes the Neddylation of p53 and inhibits its transcriptional activity.
Abida WM, Nikolaev A, Zhao W, Zhang W, Gu W.
J Biol Chem. 2007 Jan 19;282(3):1797-804. Epub 2006 Nov 9.
PMID 17098746
 
Integrated genomic analyses of ovarian carcinoma.
Cancer Genome Atlas Research Network.
Nature. 2011 Jun 29;474(7353):609-15. doi: 10.1038/nature10166.
PMID 21720365
 
FBXO11/PRMT9, a new protein arginine methyltransferase, symmetrically dimethylates arginine residues.
Cook JR, Lee JH, Yang ZH, Krause CD, Herth N, Hoffmann R, Pestka S.
Biochem Biophys Res Commun. 2006 Apr 7;342(2):472-81. Epub 2006 Feb 8.
PMID 16487488
 
FBXO11 targets BCL6 for degradation and is inactivated in diffuse large B-cell lymphomas.
Duan S, Cermak L, Pagan JK, Rossi M, Martinengo C, di Celle PF, Chapuy B, Shipp M, Chiarle R, Pagano M.
Nature. 2012 Jan 5;481(7379):90-3. doi: 10.1038/nature10688.
PMID 22113614
 
A mutation in the F-box gene, Fbxo11, causes otitis media in the Jeff mouse.
Hardisty-Hughes RE, Tateossian H, Morse SA, Romero MR, Middleton A, Tymowska-Lalanne Z, Hunter AJ, Cheeseman M, Brown SD.
Hum Mol Genet. 2006 Nov 15;15(22):3273-9. Epub 2006 Oct 11.
PMID 17035249
 
DRE-1/FBXO11-dependent degradation of BLMP-1/BLIMP-1 governs C. elegans developmental timing and maturation.
Horn M, Geisen C, Cermak L, Becker B, Nakamura S, Klein C, Pagano M, Antebi A.
Dev Cell. 2014 Mar 31;28(6):697-710. doi: 10.1016/j.devcel.2014.01.028. Epub 2014 Mar 6.
PMID 24613396
 
Diverse somatic mutation patterns and pathway alterations in human cancers.
Kan Z, Jaiswal BS, Stinson J, Janakiraman V, Bhatt D, Stern HM, Yue P, Haverty PM, Bourgon R, Zheng J, Moorhead M, Chaudhuri S, Tomsho LP, Peters BA, Pujara K, Cordes S, Davis DP, Carlton VE, Yuan W, Li L, Wang W, Eigenbrot C, Kaminker JS, Eberhard DA, Waring P, Schuster SC, Modrusan Z, Zhang Z, Stokoe D, de Sauvage FJ, Faham M, Seshagiri S.
Nature. 2010 Aug 12;466(7308):869-73. doi: 10.1038/nature09208. Epub 2010 Jul 28.
PMID 20668451
 
'VIT1', a novel gene associated with vitiligo.
Le Poole IC, Sarangarajan R, Zhao Y, Stennett LS, Brown TL, Sheth P, Miki T, Boissy RE.
Pigment Cell Res. 2001 Dec;14(6):475-84.
PMID 11775060
 
Discovery and prioritization of somatic mutations in diffuse large B-cell lymphoma (DLBCL) by whole-exome sequencing.
Lohr JG, Stojanov P, Lawrence MS, Auclair D, Chapuy B, Sougnez C, Cruz-Gordillo P, Knoechel B, Asmann YW, Slager SL, Novak AJ, Dogan A, Ansell SM, Link BK, Zou L, Gould J, Saksena G, Stransky N, Rangel-Escareno C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Hernandez-Lemus E, Schwarz-Cruz y Celis A, Imaz-Rosshandler I, Ojesina AI, Jung J, Pedamallu CS, Lander ES, Habermann TM, Cerhan JR, Shipp MA, Getz G, Golub TR.
Proc Natl Acad Sci U S A. 2012 Mar 6;109(10):3879-84. doi: 10.1073/pnas.1121343109. Epub 2012 Feb 17.
PMID 22343534
 
Regulation of the CRL4(Cdt2) ubiquitin ligase and cell-cycle exit by the SCF(Fbxo11) ubiquitin ligase.
Rossi M, Duan S, Jeong YT, Horn M, Saraf A, Florens L, Washburn MP, Antebi A, Pagano M.
Mol Cell. 2013 Mar 28;49(6):1159-66. doi: 10.1016/j.molcel.2013.02.004. Epub 2013 Mar 7.
PMID 23478441
 
Association of the FBXO11 gene with chronic otitis media with effusion and recurrent otitis media: the Minnesota COME/ROM Family Study.
Segade F, Daly KA, Allred D, Hicks PJ, Cox M, Brown M, Hardisty-Hughes RE, Brown SD, Rich SS, Bowden DW.
Arch Otolaryngol Head Neck Surg. 2006 Jul;132(7):729-33.
PMID 16847180
 
The mutational landscape of head and neck squamous cell carcinoma.
Stransky N, Egloff AM, Tward AD, Kostic AD, Cibulskis K, Sivachenko A, Kryukov GV, Lawrence MS, Sougnez C, McKenna A, Shefler E, Ramos AH, Stojanov P, Carter SL, Voet D, Cortes ML, Auclair D, Berger MF, Saksena G, Guiducci C, Onofrio RC, Parkin M, Romkes M, Weissfeld JL, Seethala RR, Wang L, Rangel-Escareno C, Fernandez-Lopez JC, Hidalgo-Miranda A, Melendez-Zajgla J, Winckler W, Ardlie K, Gabriel SB, Meyerson M, Lander ES, Getz G, Golub TR, Garraway LA, Grandis JR.
Science. 2011 Aug 26;333(6046):1157-60. doi: 10.1126/science.1208130. Epub 2011 Jul 28.
PMID 21798893
 
Regulation of TGF-beta signalling by Fbxo11, the gene mutated in the Jeff otitis media mouse mutant.
Tateossian H, Hardisty-Hughes RE, Morse S, Romero MR, Hilton H, Dean C, Brown SD.
Pathogenetics. 2009 Jul 6;2(1):5. doi: 10.1186/1755-8417-2-5.
PMID 19580641
 
Frequent pathway mutations of splicing machinery in myelodysplasia.
Yoshida K, Sanada M, Shiraishi Y, Nowak D, Nagata Y, Yamamoto R, Sato Y, Sato-Otsubo A, Kon A, Nagasaki M, Chalkidis G, Suzuki Y, Shiosaka M, Kawahata R, Yamaguchi T, Otsu M, Obara N, Sakata-Yanagimoto M, Ishiyama K, Mori H, Nolte F, Hofmann WK, Miyawaki S, Sugano S, Haferlach C, Koeffler HP, Shih LY, Haferlach T, Chiba S, Nakauchi H, Miyano S, Ogawa S.
Nature. 2011 Sep 11;478(7367):64-9. doi: 10.1038/nature10496.
PMID 21909114
 
PKD1 phosphorylation-dependent degradation of SNAIL by SCF-FBXO11 regulates epithelial-mesenchymal transition and metastasis.
Zheng H, Shen M, Zha YL, Li W, Wei Y, Blanco MA, Ren G, Zhou T, Storz P, Wang HY, Kang Y.
Cancer Cell. 2014 Sep 8;26(3):358-73. doi: 10.1016/j.ccr.2014.07.022.
PMID 25203322
 

Citation

This paper should be referenced as such :
Duan S, Pagano M
FBXO11 (F-box protein 11);
Atlas Genet Cytogenet Oncol Haematol. in press
On line version : http://AtlasGeneticsOncology.org/Genes/FBXO11ID52605ch2p16.html


External links

Nomenclature
HGNC (Hugo)FBXO11   13590
Cards
AtlasFBXO11ID52605ch2p16
Entrez_Gene (NCBI)FBXO11  80204  F-box protein 11
AliasesFBX11; PRMT9; UBR6; UG063H01; 
VIT1
GeneCards (Weizmann)FBXO11
Ensembl hg19 (Hinxton)ENSG00000138081 [Gene_View]  chr2:48034059-48132932 [Contig_View]  FBXO11 [Vega]
Ensembl hg38 (Hinxton)ENSG00000138081 [Gene_View]  chr2:48034059-48132932 [Contig_View]  FBXO11 [Vega]
ICGC DataPortalENSG00000138081
TCGA cBioPortalFBXO11
AceView (NCBI)FBXO11
Genatlas (Paris)FBXO11
WikiGenes80204
SOURCE (Princeton)FBXO11
Genetics Home Reference (NIH)FBXO11
Genomic and cartography
GoldenPath hg19 (UCSC)FBXO11  -     chr2:48034059-48132932 -  2p16.3   [Description]    (hg19-Feb_2009)
GoldenPath hg38 (UCSC)FBXO11  -     2p16.3   [Description]    (hg38-Dec_2013)
EnsemblFBXO11 - 2p16.3 [CytoView hg19]  FBXO11 - 2p16.3 [CytoView hg38]
Mapping of homologs : NCBIFBXO11 [Mapview hg19]  FBXO11 [Mapview hg38]
OMIM607871   
Gene and transcription
Genbank (Entrez)AF174599 AF176706 AF264714 AF351618 AI879484
RefSeq transcript (Entrez)NM_001190274 NM_012167 NM_018693 NM_025133
RefSeq genomic (Entrez)NC_000002 NC_018913 NG_008397 NT_022184 NW_004929300
Consensus coding sequences : CCDS (NCBI)FBXO11
Cluster EST : UnigeneHs.352677 [ NCBI ]
CGAP (NCI)Hs.352677
Alternative Splicing GalleryENSG00000138081
Gene ExpressionFBXO11 [ NCBI-GEO ]   FBXO11 [ EBI - ARRAY_EXPRESS ]   FBXO11 [ SEEK ]   FBXO11 [ MEM ]
Gene Expression Viewer (FireBrowse)FBXO11 [ Firebrowse - Broad ]
SOURCE (Princeton)Expression in : [Datasets]   [Normal Tissue Atlas]  [carcinoma Classsification]  [NCI60]
GenevisibleExpression in : [tissues]  [cell-lines]  [cancer]  [perturbations]  
BioGPS (Tissue expression)80204
GTEX Portal (Tissue expression)FBXO11
Protein : pattern, domain, 3D structure
UniProt/SwissProtQ86XK2   [function]  [subcellular_location]  [family_and_domains]  [pathology_and_biotech]  [ptm_processing]  [expression]  [interaction]
NextProtQ86XK2  [Sequence]  [Exons]  [Medical]  [Publications]
With graphics : InterProQ86XK2
Splice isoforms : SwissVarQ86XK2
PhosPhoSitePlusQ86XK2
Domaine pattern : Prosite (Expaxy)FBOX (PS50181)    ZF_UBR (PS51157)   
Domains : Interpro (EBI)Carb-bd_sugar_hydrolysis-dom    F-box_dom    FBX11/DRE-1    NosD_dom    Para_beta_helix_rpt-2    PbH1    Pectin_lyas_fold    Pectin_lyase_fold/virulence    Znf_UBR   
Domain families : Pfam (Sanger)F-box-like (PF12937)    NosD (PF05048)    zf-UBR (PF02207)   
Domain families : Pfam (NCBI)pfam12937    pfam05048    pfam02207   
Domain families : Smart (EMBL)CASH (SM00722)  FBOX (SM00256)  PbH1 (SM00710)  
Conserved Domain (NCBI)FBXO11
DMDM Disease mutations80204
Blocks (Seattle)FBXO11
SuperfamilyQ86XK2
Human Protein AtlasENSG00000138081
Peptide AtlasQ86XK2
HPRD06985
IPIIPI00328209   IPI00980427   IPI00005896   IPI00386876   IPI00894244   IPI00914054   IPI00377003   IPI00827549   IPI00893849   
Protein Interaction databases
DIP (DOE-UCLA)Q86XK2
IntAct (EBI)Q86XK2
FunCoupENSG00000138081
BioGRIDFBXO11
STRING (EMBL)FBXO11
ZODIACFBXO11
Ontologies - Pathways
QuickGOQ86XK2
Ontology : AmiGOubiquitin ligase complex  ubiquitin-protein transferase activity  protein binding  nucleus  chromosome  nucleolus  cytoplasm  cellular protein modification process  ubiquitin-dependent protein catabolic process  sensory perception of sound  zinc ion binding  protein-arginine N-methyltransferase activity  protein ubiquitination  protein ubiquitination  peptidyl-arginine N-methylation  
Ontology : EGO-EBIubiquitin ligase complex  ubiquitin-protein transferase activity  protein binding  nucleus  chromosome  nucleolus  cytoplasm  cellular protein modification process  ubiquitin-dependent protein catabolic process  sensory perception of sound  zinc ion binding  protein-arginine N-methyltransferase activity  protein ubiquitination  protein ubiquitination  peptidyl-arginine N-methylation  
NDEx NetworkFBXO11
Atlas of Cancer Signalling NetworkFBXO11
Wikipedia pathwaysFBXO11
Orthology - Evolution
OrthoDB80204
GeneTree (enSembl)ENSG00000138081
Phylogenetic Trees/Animal Genes : TreeFamFBXO11
HOVERGENQ86XK2
HOGENOMQ86XK2
Homologs : HomoloGeneFBXO11
Homology/Alignments : Family Browser (UCSC)FBXO11
Gene fusions - Rearrangements
Fusion : MitelmanFBXO11/INTS9 [2p16.3/8p21.1]  
Fusion : MitelmanNEBL/FBXO11 [10p12.31/2p16.3]  [t(2;10)(p16;p12)]  
Fusion: TCGAFBXO11 2p16.3 INTS9 8p21.1 PRAD
Fusion: TCGANEBL 10p12.31 FBXO11 2p16.3 BRCA
Polymorphisms : SNP and Copy number variants
NCBI Variation ViewerFBXO11 [hg38]
dbSNP Single Nucleotide Polymorphism (NCBI)FBXO11
dbVarFBXO11
ClinVarFBXO11
1000_GenomesFBXO11 
Exome Variant ServerFBXO11
ExAC (Exome Aggregation Consortium)FBXO11 (select the gene name)
Genetic variants : HAPMAP80204
Genomic Variants (DGV)FBXO11 [DGVbeta]
DECIPHER (Syndromes)2:48034059-48132932  ENSG00000138081
CONAN: Copy Number AnalysisFBXO11 
Mutations
ICGC Data PortalFBXO11 
TCGA Data PortalFBXO11 
Broad Tumor PortalFBXO11
OASIS PortalFBXO11 [ Somatic mutations - Copy number]
Cancer Gene: CensusFBXO11 
Somatic Mutations in Cancer : COSMICFBXO11  [overview]  [genome browser]  [tissue]  [distribution]  
Mutations and Diseases : HGMDFBXO11
intOGen PortalFBXO11
LOVD (Leiden Open Variation Database)Whole genome datasets
LOVD (Leiden Open Variation Database)LOVD 3.0 shared installation
BioMutasearch FBXO11
DgiDB (Drug Gene Interaction Database)FBXO11
DoCM (Curated mutations)FBXO11 (select the gene name)
CIViC (Clinical Interpretations of Variants in Cancer)FBXO11 (select a term)
intoGenFBXO11
NCG5 (London)FBXO11
Cancer3DFBXO11(select the gene name)
Impact of mutations[PolyPhen2] [SIFT Human Coding SNP] [Buck Institute : MutDB] [Mutation Assessor] [Mutanalyser]
Diseases
OMIM607871   
Orphanet
MedgenFBXO11
Genetic Testing Registry FBXO11
NextProtQ86XK2 [Medical]
TSGene80204
GENETestsFBXO11
Huge Navigator FBXO11 [HugePedia]
snp3D : Map Gene to Disease80204
BioCentury BCIQFBXO11
ClinGenFBXO11
Clinical trials, drugs, therapy
Chemical/Protein Interactions : CTD80204
Chemical/Pharm GKB GenePA28031
Clinical trialFBXO11
Miscellaneous
canSAR (ICR)FBXO11 (select the gene name)
Probes
Litterature
PubMed41 Pubmed reference(s) in Entrez
GeneRIFsGene References Into Functions (Entrez)
CoreMineFBXO11
EVEXFBXO11
GoPubMedFBXO11
iHOPFBXO11
REVIEW articlesautomatic search in PubMed
Last year publicationsautomatic search in PubMed

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