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Fusion gene ID: 26467 |
FusionGeneSummary for PDGFRB_NDE1 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: PDGFRB_NDE1 | Fusion gene ID: 26467 | Hgene | Tgene | Gene symbol | PDGFRB | NDE1 | Gene ID | 5159 | 54820 |
| Gene name | platelet derived growth factor receptor beta | nudE neurodevelopment protein 1 | |
| Synonyms | CD140B|IBGC4|IMF1|JTK12|KOGS|PDGFR|PDGFR-1|PDGFR1|PENTT | HOM-TES-87|LIS4|MHAC|NDE|NUDE|NUDE1 | |
| Cytomap | 5q32 | 16p13.11 | |
| Type of gene | protein-coding | protein-coding | |
| Description | platelet-derived growth factor receptor betaActivated tyrosine kinase PDGFRBCD140 antigen-like family member BNDEL1-PDGFRBPDGF-R-betaPDGFR-betabeta-type platelet-derived growth factor receptorplatelet-derived growth factor receptor 1platelet-deriv | nuclear distribution protein nudE homolog 1LIS1-interacting protein NUDE1, rat homolognudE nuclear distribution E homolog 1nudE nuclear distribution gene E homolog 1 | |
| Modification date | 20180523 | 20180523 | |
| UniProtAcc | P09619 | Q9NXR1 | |
| Ensembl transtripts involved in fusion gene | ENST00000261799, ENST00000523456, | ENST00000396353, ENST00000396355, ENST00000396354, ENST00000342673, ENST00000571896, | |
| Fusion gene scores | * DoF score | 3 X 3 X 2=18 | 13 X 17 X 2=442 |
| # samples | 3 | 19 | |
| ** MAII score | log2(3/18*10)=0.736965594166206 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(19/442*10)=-1.21804695106048 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: PDGFRB [Title/Abstract] AND NDE1 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Functional or gene categories assigned by FusionGDB annotation | |||
| * DoF score (Degree of Frequency) = # partners X # break points X # cancer types ** MAII score (Major Active Isofusion Index) = log2(# samples/DoF score*10) |
| Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez |
| Partner | Gene | GO ID | GO term | PubMed ID |
| Hgene | PDGFRB | GO:0007165 | signal transduction | 10821867 |
| Hgene | PDGFRB | GO:0010863 | positive regulation of phospholipase C activity | 1653029 |
| Hgene | PDGFRB | GO:0018108 | peptidyl-tyrosine phosphorylation | 1653029|2536956|2850496 |
| Hgene | PDGFRB | GO:0030335 | positive regulation of cell migration | 17470632 |
| Hgene | PDGFRB | GO:0032516 | positive regulation of phosphoprotein phosphatase activity | 7691811 |
| Hgene | PDGFRB | GO:0038091 | positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway | 17470632 |
| Hgene | PDGFRB | GO:0043552 | positive regulation of phosphatidylinositol 3-kinase activity | 1314164 |
| Hgene | PDGFRB | GO:0046777 | protein autophosphorylation | 1314164|2536956|2850496 |
| Hgene | PDGFRB | GO:0048008 | platelet-derived growth factor receptor signaling pathway | 1314164|2536956 |
| Hgene | PDGFRB | GO:0060326 | cell chemotaxis | 2554309|17991872 |
| Fusion gene information from three resources (ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018)) * All genome coordinats were lifted-over on hg19. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| Data type | Source | Cancer type | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChiTaRS3.1 | DQ317513 | PDGFRB | chr5 | 149508606 | + | NDE1 | chr16 | 15784639 | - |
| * LD: Li Ding group's fusion gene list RV: Roel Verhaak group's fusion gene list ChiTaRs fusion database |
| Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure. * Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser. |
| ORF | Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| intron-intron | ENST00000261799 | ENST00000396353 | PDGFRB | chr5 | 149508606 | + | NDE1 | chr16 | 15784639 | - |
| intron-intron | ENST00000261799 | ENST00000396355 | PDGFRB | chr5 | 149508606 | + | NDE1 | chr16 | 15784639 | - |
| intron-intron | ENST00000261799 | ENST00000396354 | PDGFRB | chr5 | 149508606 | + | NDE1 | chr16 | 15784639 | - |
| intron-intron | ENST00000261799 | ENST00000342673 | PDGFRB | chr5 | 149508606 | + | NDE1 | chr16 | 15784639 | - |
| intron-intron | ENST00000261799 | ENST00000571896 | PDGFRB | chr5 | 149508606 | + | NDE1 | chr16 | 15784639 | - |
| intron-intron | ENST00000523456 | ENST00000396353 | PDGFRB | chr5 | 149508606 | + | NDE1 | chr16 | 15784639 | - |
| intron-intron | ENST00000523456 | ENST00000396355 | PDGFRB | chr5 | 149508606 | + | NDE1 | chr16 | 15784639 | - |
| intron-intron | ENST00000523456 | ENST00000396354 | PDGFRB | chr5 | 149508606 | + | NDE1 | chr16 | 15784639 | - |
| intron-intron | ENST00000523456 | ENST00000342673 | PDGFRB | chr5 | 149508606 | + | NDE1 | chr16 | 15784639 | - |
| intron-intron | ENST00000523456 | ENST00000571896 | PDGFRB | chr5 | 149508606 | + | NDE1 | chr16 | 15784639 | - |
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FusionProtFeatures for PDGFRB_NDE1 |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| PDGFRB | NDE1 |
| Tyrosine-protein kinase that acts as cell-surfacereceptor for homodimeric PDGFB and PDGFD and for heterodimersformed by PDGFA and PDGFB, and plays an essential role in theregulation of embryonic development, cell proliferation, survival,differentiation, chemotaxis and migration. Plays an essential rolein blood vessel development by promoting proliferation, migrationand recruitment of pericytes and smooth muscle cells toendothelial cells. Plays a role in the migration of vascularsmooth muscle cells and the formation of neointima at vascularinjury sites. Required for normal development of thecardiovascular system. Required for normal recruitment ofpericytes (mesangial cells) in the kidney glomerulus, and fornormal formation of a branched network of capillaries in kidneyglomeruli. Promotes rearrangement of the actin cytoskeleton andthe formation of membrane ruffles. Binding of its cognate ligands- homodimeric PDGFB, heterodimers formed by PDGFA and PDGFB orhomodimeric PDGFD -leads to the activation of several signalingcascades; the response depends on the nature of the bound ligandand is modulated by the formation of heterodimers between PDGFRAand PDGFRB. Phosphorylates PLCG1, PIK3R1, PTPN11, RASA1/GAP, CBL,SHC1 and NCK1. Activation of PLCG1 leads to the production of thecellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate, mobilization of cytosolic Ca(2+) and the activationof protein kinase C. Phosphorylation of PIK3R1, the regulatorysubunit of phosphatidylinositol 3-kinase, leads to the activationof the AKT1 signaling pathway. Phosphorylation of SHC1, or of theC-terminus of PTPN11, creates a binding site for GRB2, resultingin the activation of HRAS, RAF1 and down-stream MAP kinases,including MAPK1/ERK2 and/or MAPK3/ERK1. Promotes phosphorylationand activation of SRC family kinases. Promotes phosphorylation ofPDCD6IP/ALIX and STAM. Receptor signaling is down-regulated byprotein phosphatases that dephosphorylate the receptor and itsdown-stream effectors, and by rapid internalization of theactivated receptor. {ECO:0000269|PubMed:11297552,ECO:0000269|PubMed:11331881, ECO:0000269|PubMed:1314164,ECO:0000269|PubMed:1396585, ECO:0000269|PubMed:1653029,ECO:0000269|PubMed:1709159, ECO:0000269|PubMed:1846866,ECO:0000269|PubMed:20494825, ECO:0000269|PubMed:20529858,ECO:0000269|PubMed:21098708, ECO:0000269|PubMed:21679854,ECO:0000269|PubMed:21733313, ECO:0000269|PubMed:2554309,ECO:0000269|PubMed:26599395, ECO:0000269|PubMed:2835772,ECO:0000269|PubMed:2850496, ECO:0000269|PubMed:7685273,ECO:0000269|PubMed:7691811, ECO:0000269|PubMed:7692233,ECO:0000269|PubMed:8195171}. | Required for centrosome duplication and formation andfunction of the mitotic spindle. Essential for the development ofthe cerebral cortex. May regulate the production of neurons bycontrolling the orientation of the mitotic spindle during divisionof cortical neuronal progenitors of the proliferative ventricularzone of the brain. Orientation of the division plane perpendicularto the layers of the cortex gives rise to two proliferativeneuronal progenitors whereas parallel orientation of the divisionplane yields one proliferative neuronal progenitor and a post-mitotic neuron. A premature shift towards a neuronal fate withinthe progenitor population may result in an overall reduction inthe final number of neurons and an increase in the number ofneurons in the deeper layers of the cortex.{ECO:0000269|PubMed:17600710, ECO:0000269|PubMed:21529752}. |
| Retention analysis result of each fusion partner protein across 39 protein features of UniProt such as six molecule processing features, 13 region features, four site features, six amino acid modification features, two natural variation features, five experimental info features, and 3 secondary structure features. Here, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at . * Minus value of BPloci means that the break pointn is located before the CDS. |
| - In-frame and retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
| - In-frame and not-retained protein feature among the 13 regional features. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Protein feature | Protein feature note |
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FusionGeneSequence for PDGFRB_NDE1 |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. (nt: nucleotides, aa: amino acids) |
| * Fusion amino acid sequences. |
| * Fusion transcript sequences (only coding sequence (CDS) region). |
| * Fusion transcript sequences (Full-length transcript). |
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FusionGenePPI for PDGFRB_NDE1 |
| Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in . |
| Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160) |
| Hgene | Hgene's interactors | Tgene | Tgene's interactors |
| - Retained PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Still interaction with |
| - Lost PPIs in in-frame fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
| - Retained PPIs, but lost function due to frame-shift fusion. |
| Partner | Gene | Hbp | Tbp | ENST | Strand | BPexon | TotalExon | Protein feature loci | *BPloci | TotalLen | Interaction lost with |
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RelatedDrugs for PDGFRB_NDE1 |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.0 2018-04-02) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Hgene | PDGFRB | P09619 | DB00619 | Imatinib | Platelet-derived growth factor receptor beta | small molecule | approved |
| Hgene | PDGFRB | P09619 | DB06589 | Pazopanib | Platelet-derived growth factor receptor beta | small molecule | approved |
| Hgene | PDGFRB | P09619 | DB08896 | Regorafenib | Platelet-derived growth factor receptor beta | small molecule | approved |
| Hgene | PDGFRB | P09619 | DB00102 | Becaplermin | Platelet-derived growth factor receptor beta | biotech | approved|investigational |
| Hgene | PDGFRB | P09619 | DB00398 | Sorafenib | Platelet-derived growth factor receptor beta | small molecule | approved|investigational |
| Hgene | PDGFRB | P09619 | DB01254 | Dasatinib | Platelet-derived growth factor receptor beta | small molecule | approved|investigational |
| Hgene | PDGFRB | P09619 | DB01268 | Sunitinib | Platelet-derived growth factor receptor beta | small molecule | approved|investigational |
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RelatedDiseases for PDGFRB_NDE1 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | PDGFRB | C3554321 | BASAL GANGLIA CALCIFICATION, IDIOPATHIC, 4 | 3 | UNIPROT |
| Hgene | PDGFRB | C0023893 | Liver Cirrhosis, Experimental | 2 | CTD_human |
| Hgene | PDGFRB | C0036341 | Schizophrenia | 2 | PSYGENET |
| Hgene | PDGFRB | C0432284 | Infantile myofibromatosis | 2 | ORPHANET;UNIPROT |
| Hgene | PDGFRB | C0004782 | Basal Ganglia Diseases | 1 | CTD_human |
| Hgene | PDGFRB | C0006663 | Calcinosis | 1 | CTD_human |
| Hgene | PDGFRB | C0036337 | Schizoaffective Disorder | 1 | PSYGENET |
| Hgene | PDGFRB | C1866182 | Penttinen-Aula syndrome | 1 | ORPHANET;UNIPROT |
| Hgene | PDGFRB | C4225270 | KOSAKI OVERGROWTH SYNDROME | 1 | UNIPROT |
| Tgene | NDE1 | C0036341 | Schizophrenia | 4 | PSYGENET |
| Tgene | NDE1 | C0033975 | Psychotic Disorders | 1 | PSYGENET |
| Tgene | NDE1 | C0349204 | Nonorganic psychosis | 1 | PSYGENET |
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