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Fusion gene ID: 23573 |
FusionGeneSummary for NCDN_PDGFRA |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: NCDN_PDGFRA | Fusion gene ID: 23573 | Hgene | Tgene | Gene symbol | NCDN | PDGFRA | Gene ID | 23154 | 5156 |
| Gene name | neurochondrin | platelet derived growth factor receptor alpha | |
| Synonyms | - | CD140A|PDGFR-2|PDGFR2 | |
| Cytomap | 1p34.3 | 4q12 | |
| Type of gene | protein-coding | protein-coding | |
| Description | neurochondrin | platelet-derived growth factor receptor alphaCD140 antigen-like family member ACD140a antigenPDGF-R-alphaalpha-type platelet-derived growth factor receptorplatelet-derived growth factor receptor 2platelet-derived growth factor receptor, alpha polype | |
| Modification date | 20180519 | 20180523 | |
| UniProtAcc | Q9UBB6 | P16234 | |
| Ensembl transtripts involved in fusion gene | ENST00000373253, ENST00000356090, ENST00000373243, ENST00000459931, | ENST00000257290, ENST00000508170, | |
| Fusion gene scores | * DoF score | 3 X 3 X 1=9 | 12 X 13 X 4=624 |
| # samples | 3 | 13 | |
| ** MAII score | log2(3/9*10)=1.73696559416621 effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs). DoF>8 and MAII>0 | log2(13/624*10)=-2.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: NCDN [Title/Abstract] AND PDGFRA [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 |
| Tgene | PDGFRA | GO:0008284 | positive regulation of cell proliferation | 10806482 |
| Tgene | PDGFRA | GO:0010544 | negative regulation of platelet activation | 8188664 |
| Tgene | PDGFRA | GO:0018108 | peptidyl-tyrosine phosphorylation | 1646396|2536956|8188664 |
| Tgene | PDGFRA | GO:0030335 | positive regulation of cell migration | 17470632 |
| Tgene | PDGFRA | GO:0034614 | cellular response to reactive oxygen species | 24190966 |
| Tgene | PDGFRA | GO:0038091 | positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway | 17470632 |
| Tgene | PDGFRA | GO:0046777 | protein autophosphorylation | 1646396|2536956|8188664 |
| Tgene | PDGFRA | GO:0048008 | platelet-derived growth factor receptor signaling pathway | 2536956|10806482 |
| Tgene | PDGFRA | GO:0048146 | positive regulation of fibroblast proliferation | 10806482 |
| 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 | BU682470 | NCDN | chr1 | 36032249 | - | PDGFRA | chr4 | 55164280 | + |
| * 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 |
| 3UTR-3UTR | ENST00000373253 | ENST00000257290 | NCDN | chr1 | 36032249 | - | PDGFRA | chr4 | 55164280 | + |
| 3UTR-intron | ENST00000373253 | ENST00000508170 | NCDN | chr1 | 36032249 | - | PDGFRA | chr4 | 55164280 | + |
| 3UTR-3UTR | ENST00000356090 | ENST00000257290 | NCDN | chr1 | 36032249 | - | PDGFRA | chr4 | 55164280 | + |
| 3UTR-intron | ENST00000356090 | ENST00000508170 | NCDN | chr1 | 36032249 | - | PDGFRA | chr4 | 55164280 | + |
| 3UTR-3UTR | ENST00000373243 | ENST00000257290 | NCDN | chr1 | 36032249 | - | PDGFRA | chr4 | 55164280 | + |
| 3UTR-intron | ENST00000373243 | ENST00000508170 | NCDN | chr1 | 36032249 | - | PDGFRA | chr4 | 55164280 | + |
| intron-3UTR | ENST00000459931 | ENST00000257290 | NCDN | chr1 | 36032249 | - | PDGFRA | chr4 | 55164280 | + |
| intron-intron | ENST00000459931 | ENST00000508170 | NCDN | chr1 | 36032249 | - | PDGFRA | chr4 | 55164280 | + |
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FusionProtFeatures for NCDN_PDGFRA |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| NCDN | PDGFRA |
| Probably involved in signal transduction, in the nervoussystem, via increasing cell surface localization of GRM5 andpositively regulating its signaling (By similarity). Required forthe spatial learning process. Acts as a negative regulator ofCa(2+)-calmodulin-dependent protein kinase 2 (CaMK2)phosphorylation. May play a role in modulating melanin-concentrating hormone-mediated functions via its interaction withMCHR1 that interferes with G protein-coupled signal transduction.May be involved in bone metabolism. May also be involved inneurite outgrowth. {ECO:0000250, ECO:0000269|PubMed:16945926}. | Tyrosine-protein kinase that acts as a cell-surfacereceptor for PDGFA, PDGFB and PDGFC and plays an essential role inthe regulation of embryonic development, cell proliferation,survival and chemotaxis. Depending on the context, promotes orinhibits cell proliferation and cell migration. Plays an importantrole in the differentiation of bone marrow-derived mesenchymalstem cells. Required for normal skeleton development and cephalicclosure during embryonic development. Required for normaldevelopment of the mucosa lining the gastrointestinal tract, andfor recruitment of mesenchymal cells and normal development ofintestinal villi. Plays a role in cell migration and chemotaxis inwound healing. Plays a role in platelet activation, secretion ofagonists from platelet granules, and in thrombin-induced plateletaggregation. Binding of its cognate ligands - homodimeric PDGFA,homodimeric PDGFB, heterodimers formed by PDGFA and PDGFB orhomodimeric PDGFC -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 PIK3R1, PLCG1, and PTPN11. Activationof PLCG1 leads to the production of the cellular signalingmolecules diacylglycerol and inositol 1,4,5-trisphosphate,mobilization of cytosolic Ca(2+) and the activation of proteinkinase C. Phosphorylates PIK3R1, the regulatory subunit ofphosphatidylinositol 3-kinase, and thereby mediates activation ofthe AKT1 signaling pathway. Mediates activation of HRAS and of theMAP kinases MAPK1/ERK2 and/or MAPK3/ERK1. Promotes activation ofSTAT family members STAT1, STAT3 and STAT5A and/or STAT5B.Receptor signaling is down-regulated by protein phosphatases thatdephosphorylate the receptor and its down-stream effectors, and byrapid internalization of the activated receptor.{ECO:0000269|PubMed:10734113, ECO:0000269|PubMed:10947961,ECO:0000269|PubMed:11297552, ECO:0000269|PubMed:12522257,ECO:0000269|PubMed:1646396, ECO:0000269|PubMed:1709159,ECO:0000269|PubMed:17141222, ECO:0000269|PubMed:20972453,ECO:0000269|PubMed:21224473, ECO:0000269|PubMed:21596750,ECO:0000269|PubMed:2554309, ECO:0000269|PubMed:8188664,ECO:0000269|PubMed:8760137, ECO:0000269|PubMed:8943348}. |
| 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 NCDN_PDGFRA |
| 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 NCDN_PDGFRA |
| 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 NCDN_PDGFRA |
| 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 |
| Tgene | PDGFRA | P16234 | DB00619 | Imatinib | Platelet-derived growth factor receptor alpha | small molecule | approved |
| Tgene | PDGFRA | P16234 | DB06589 | Pazopanib | Platelet-derived growth factor receptor alpha | small molecule | approved |
| Tgene | PDGFRA | P16234 | DB08896 | Regorafenib | Platelet-derived growth factor receptor alpha | small molecule | approved |
| Tgene | PDGFRA | P16234 | DB00102 | Becaplermin | Platelet-derived growth factor receptor alpha | biotech | approved|investigational |
| Tgene | PDGFRA | P16234 | DB01268 | Sunitinib | Platelet-derived growth factor receptor alpha | small molecule | approved|investigational |
| Tgene | PDGFRA | P16234 | DB08901 | Ponatinib | Platelet-derived growth factor receptor alpha | small molecule | approved|investigational |
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RelatedDiseases for NCDN_PDGFRA |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Tgene | PDGFRA | C0238198 | Gastrointestinal Stromal Tumors | 2 | CTD_human;HPO;ORPHANET;UNIPROT |
| Tgene | PDGFRA | C0008925 | Cleft Palate | 1 | CTD_human |
| Tgene | PDGFRA | C0015923 | Fetal Alcohol Syndrome | 1 | PSYGENET |
| Tgene | PDGFRA | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| Tgene | PDGFRA | C0024115 | Lung diseases | 1 | CTD_human |
| Tgene | PDGFRA | C0025149 | Medulloblastoma | 1 | CTD_human |
| Tgene | PDGFRA | C0035238 | Congenital abnormality of respiratory system | 1 | CTD_human |
| Tgene | PDGFRA | C0080178 | Spina Bifida | 1 | CTD_human |
| Tgene | PDGFRA | C0206637 | Chondrosarcoma, Mesenchymal | 1 | CTD_human |
| Tgene | PDGFRA | C0376634 | Craniofacial Abnormalities | 1 | CTD_human |
| Tgene | PDGFRA | C1540912 | Hypereosinophilic syndrome | 1 | CTD_human |
| Tgene | PDGFRA | C2985290 | Fetal Alcohol Spectrum Disorders | 1 | PSYGENET |
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