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 | Fusion Gene Summary |
| Fusion Gene ORF analysis |
| Fusion Genomic Features |
| Fusion Protein Features |
| Fusion Gene Sequence |
| Fusion Gene PPI analysis |
| Related Drugs |
| Related Diseases |
Fusion gene:CLOCK-PDGFRA (FusionGDB2 ID:HG9575TG5156) |
Fusion Gene Summary for CLOCK-PDGFRA |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CLOCK-PDGFRA | Fusion gene ID: hg9575tg5156 | Hgene | Tgene | Gene symbol | CLOCK | PDGFRA | Gene ID | 9575 | 5156 |
| Gene name | clock circadian regulator | platelet derived growth factor receptor alpha | |
| Synonyms | KAT13D|bHLHe8 | CD140A|PDGFR-2|PDGFR2 | |
| Cytomap | ('CLOCK')('PDGFRA') 4q12 | 4q12 | |
| Type of gene | protein-coding | protein-coding | |
| Description | circadian locomoter output cycles protein kaputcircadian locomoter output cycles kaput proteinclass E basic helix-loop-helix protein 8clock homolog | 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 | 20200313 | 20200329 | |
| UniProtAcc | . | P16234 | |
| Ensembl transtripts involved in fusion gene | ENST00000309964, ENST00000381322, ENST00000513440, ENST00000506923, | ||
| Fusion gene scores | * DoF score | 10 X 13 X 6=780 | 18 X 27 X 8=3888 |
| # samples | 14 | 17 | |
| ** MAII score | log2(14/780*10)=-2.47804729680464 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(17/3888*10)=-4.51542156746808 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: CLOCK [Title/Abstract] AND PDGFRA [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | CLOCK(56376079)-PDGFRA(55153597), # samples:3 | ||
| Anticipated loss of major functional domain due to fusion event. | |||
| * 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 | CLOCK | GO:0006473 | protein acetylation | 28985504 |
| Hgene | CLOCK | GO:0032922 | circadian regulation of gene expression | 24005054 |
| Hgene | CLOCK | GO:0045893 | positive regulation of transcription, DNA-templated | 23785138 |
| Hgene | CLOCK | GO:0051775 | response to redox state | 11441146 |
| Hgene | CLOCK | GO:0071479 | cellular response to ionizing radiation | 21659603 |
| 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 * 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. |
| Source | Disease | Sample | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand |
| ChimerDB4 | LUAD | TCGA-69-7979-01A | CLOCK | chr4 | 56376079 | - | PDGFRA | chr4 | 55153597 | + |
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Fusion Gene ORF analysis for CLOCK-PDGFRA |
| 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 |
| 5UTR-3CDS | ENST00000309964 | ENST00000257290 | CLOCK | chr4 | 56376079 | - | PDGFRA | chr4 | 55153597 | + |
| 5UTR-3CDS | ENST00000381322 | ENST00000257290 | CLOCK | chr4 | 56376079 | - | PDGFRA | chr4 | 55153597 | + |
| 5UTR-3CDS | ENST00000513440 | ENST00000257290 | CLOCK | chr4 | 56376079 | - | PDGFRA | chr4 | 55153597 | + |
| 5UTR-intron | ENST00000309964 | ENST00000508170 | CLOCK | chr4 | 56376079 | - | PDGFRA | chr4 | 55153597 | + |
| 5UTR-intron | ENST00000381322 | ENST00000508170 | CLOCK | chr4 | 56376079 | - | PDGFRA | chr4 | 55153597 | + |
| 5UTR-intron | ENST00000513440 | ENST00000508170 | CLOCK | chr4 | 56376079 | - | PDGFRA | chr4 | 55153597 | + |
| intron-3CDS | ENST00000506923 | ENST00000257290 | CLOCK | chr4 | 56376079 | - | PDGFRA | chr4 | 55153597 | + |
| intron-intron | ENST00000506923 | ENST00000508170 | CLOCK | chr4 | 56376079 | - | PDGFRA | chr4 | 55153597 | + |
| ORFfinder result based on the fusion transcript sequence of in-frame fusion genes. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | Seq length (transcript) | BP loci (transcript) | Predicted start (transcript) | Predicted stop (transcript) | Seq length (amino acids) |
| DeepORF prediction of the coding potential based on the fusion transcript sequence of in-frame fusion genes. DeepORF is a coding potential classifier based on convolutional neural network by comparing the real Ribo-seq data. If the no-coding score < 0.5 and coding score > 0.5, then the in-frame fusion transcript is predicted as being likely translated. |
| Henst | Tenst | Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | No-coding score | Coding score |
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Fusion Genomic Features for CLOCK-PDGFRA |
| FusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints. |
| Hgene | Hchr | Hbp | Hstrand | Tgene | Tchr | Tbp | Tstrand | 1-p | p (fusion gene breakpoint) |
| CLOCK | chr4 | 56376078 | - | PDGFRA | chr4 | 55153596 | + | 1.08E-05 | 0.99998915 |
| CLOCK | chr4 | 56376078 | - | PDGFRA | chr4 | 55153596 | + | 1.08E-05 | 0.99998915 |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page. |
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Fusion Protein Features for CLOCK-PDGFRA |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:56376079/:55153597) - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. - How to search 1. Put your fusion gene symbol. 2. Press the tab key until there will be shown the breakpoint information filled. 4. Go down and press 'Search' tab twice. 4. Go down to have the hyperlink of the search result. 5. Click the hyperlink. 6. See the FGviewer result for your fusion gene. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| . | PDGFRA |
| FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}. | FUNCTION: Tyrosine-protein kinase that acts as a cell-surface receptor for PDGFA, PDGFB and PDGFC and plays an essential role in the regulation of embryonic development, cell proliferation, survival and chemotaxis. Depending on the context, promotes or inhibits cell proliferation and cell migration. Plays an important role in the differentiation of bone marrow-derived mesenchymal stem cells. Required for normal skeleton development and cephalic closure during embryonic development. Required for normal development of the mucosa lining the gastrointestinal tract, and for recruitment of mesenchymal cells and normal development of intestinal villi. Plays a role in cell migration and chemotaxis in wound healing. Plays a role in platelet activation, secretion of agonists from platelet granules, and in thrombin-induced platelet aggregation. Binding of its cognate ligands - homodimeric PDGFA, homodimeric PDGFB, heterodimers formed by PDGFA and PDGFB or homodimeric PDGFC -leads to the activation of several signaling cascades; the response depends on the nature of the bound ligand and is modulated by the formation of heterodimers between PDGFRA and PDGFRB. Phosphorylates PIK3R1, PLCG1, and PTPN11. Activation of PLCG1 leads to the production of the cellular signaling molecules diacylglycerol and inositol 1,4,5-trisphosphate, mobilization of cytosolic Ca(2+) and the activation of protein kinase C. Phosphorylates PIK3R1, the regulatory subunit of phosphatidylinositol 3-kinase, and thereby mediates activation of the AKT1 signaling pathway. Mediates activation of HRAS and of the MAP kinases MAPK1/ERK2 and/or MAPK3/ERK1. Promotes activation of STAT family members STAT1, STAT3 and STAT5A and/or STAT5B. Receptor signaling is down-regulated by protein phosphatases that dephosphorylate the receptor and its down-stream effectors, and by rapid 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:17087943, 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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Fusion Gene Sequence for CLOCK-PDGFRA |
| For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones. |
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Fusion Gene PPI Analysis for CLOCK-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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Related Drugs for CLOCK-PDGFRA |
| Drugs targeting genes involved in this fusion gene. (DrugBank Version 5.1.8 2021-05-08) |
| Partner | Gene | UniProtAcc | DrugBank ID | Drug name | Drug activity | Drug type | Drug status |
| Tgene | PDGFRA | P16234 | DB00619 | Imatinib | Antagonist | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB00619 | Imatinib | Antagonist | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB00619 | Imatinib | Antagonist | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB06589 | Pazopanib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB06589 | Pazopanib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB06589 | Pazopanib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB08896 | Regorafenib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB08896 | Regorafenib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB08896 | Regorafenib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB09079 | Nintedanib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB09079 | Nintedanib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB09079 | Nintedanib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB10772 | Foreskin keratinocyte (neonatal) | Agonist | Biotech | Approved |
| Tgene | PDGFRA | P16234 | DB10772 | Foreskin keratinocyte (neonatal) | Agonist | Biotech | Approved |
| Tgene | PDGFRA | P16234 | DB10772 | Foreskin keratinocyte (neonatal) | Agonist | Biotech | Approved |
| Tgene | PDGFRA | P16234 | DB14840 | Ripretinib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB14840 | Ripretinib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB14840 | Ripretinib | Inhibitor | Small molecule | Approved |
| Tgene | PDGFRA | P16234 | DB00102 | Becaplermin | Biotech | Approved|Investigational | |
| Tgene | PDGFRA | P16234 | DB00102 | Becaplermin | Biotech | Approved|Investigational | |
| Tgene | PDGFRA | P16234 | DB00102 | Becaplermin | Biotech | Approved|Investigational | |
| Tgene | PDGFRA | P16234 | DB01268 | Sunitinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB01268 | Sunitinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB01268 | Sunitinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB06043 | Olaratumab | Antagonist | Biotech | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB06043 | Olaratumab | Antagonist | Biotech | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB06043 | Olaratumab | Antagonist | Biotech | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB06595 | Midostaurin | Antagonist|Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB06595 | Midostaurin | Antagonist|Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB06595 | Midostaurin | Antagonist|Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB08901 | Ponatinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB08901 | Ponatinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB08901 | Ponatinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB09078 | Lenvatinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB09078 | Lenvatinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB09078 | Lenvatinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB12010 | Fostamatinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB12010 | Fostamatinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB12010 | Fostamatinib | Inhibitor | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB12147 | Erdafitinib | Substrate | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB12147 | Erdafitinib | Substrate | Small molecule | Approved|Investigational |
| Tgene | PDGFRA | P16234 | DB12147 | Erdafitinib | Substrate | Small molecule | Approved|Investigational |
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Related Diseases for CLOCK-PDGFRA |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | CLOCK | C0005586 | Bipolar Disorder | 5 | PSYGENET |
| Hgene | CLOCK | C0011570 | Mental Depression | 5 | PSYGENET |
| Hgene | CLOCK | C0011581 | Depressive disorder | 5 | PSYGENET |
| Hgene | CLOCK | C0041696 | Unipolar Depression | 5 | PSYGENET |
| Hgene | CLOCK | C0525045 | Mood Disorders | 5 | PSYGENET |
| Hgene | CLOCK | C1269683 | Major Depressive Disorder | 5 | PSYGENET |
| Hgene | CLOCK | C0085159 | Seasonal Affective Disorder | 3 | PSYGENET |
| Hgene | CLOCK | C3496069 | cocaine use | 2 | PSYGENET |
| Hgene | CLOCK | C0001957 | Alcohol Withdrawal Delirium | 1 | PSYGENET |
| Hgene | CLOCK | C0001973 | Alcoholic Intoxication, Chronic | 1 | PSYGENET |
| Hgene | CLOCK | C0036341 | Schizophrenia | 1 | PSYGENET |
| Hgene | CLOCK | C0600427 | Cocaine Dependence | 1 | PSYGENET |
| Tgene | C0238198 | Gastrointestinal Stromal Tumors | 10 | CGI;CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT | |
| Tgene | C3179349 | Gastrointestinal Stromal Sarcoma | 9 | CLINGEN;CTD_human;ORPHANET | |
| Tgene | C0346421 | Chronic eosinophilic leukemia | 4 | ORPHANET | |
| Tgene | C0206141 | Idiopathic Hypereosinophilic Syndrome | 3 | CTD_human;GENOMICS_ENGLAND | |
| Tgene | C0006413 | Burkitt Lymphoma | 2 | ORPHANET | |
| Tgene | C0206142 | Eosinophilic leukemia | 2 | CTD_human | |
| Tgene | C0206143 | Loeffler's Endocarditis | 2 | CTD_human | |
| Tgene | C1292769 | Precursor B-cell lymphoblastic leukemia | 2 | ORPHANET | |
| Tgene | C1540912 | Hypereosinophilic syndrome | 2 | CGI;CTD_human | |
| Tgene | C0008925 | Cleft Palate | 1 | CTD_human | |
| Tgene | C0015923 | Fetal Alcohol Syndrome | 1 | PSYGENET | |
| Tgene | C0018801 | Heart failure | 1 | CTD_human | |
| Tgene | C0018802 | Congestive heart failure | 1 | CTD_human | |
| Tgene | C0023212 | Left-Sided Heart Failure | 1 | CTD_human | |
| Tgene | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human | |
| Tgene | C0024115 | Lung diseases | 1 | CTD_human | |
| Tgene | C0025149 | Medulloblastoma | 1 | CTD_human | |
| Tgene | C0035238 | Congenital abnormality of respiratory system | 1 | CTD_human | |
| Tgene | C0038219 | Status Dysraphicus | 1 | CTD_human | |
| Tgene | C0080178 | Spina Bifida | 1 | CTD_human | |
| Tgene | C0205833 | Medullomyoblastoma | 1 | CTD_human | |
| Tgene | C0206637 | Mesenchymal Chondrosarcoma | 1 | CTD_human | |
| Tgene | C0235527 | Heart Failure, Right-Sided | 1 | CTD_human | |
| Tgene | C0266508 | Rachischisis | 1 | CTD_human | |
| Tgene | C0278510 | Childhood Medulloblastoma | 1 | CTD_human | |
| Tgene | C0278876 | Adult Medulloblastoma | 1 | CTD_human | |
| Tgene | C0376634 | Craniofacial Abnormalities | 1 | CTD_human | |
| Tgene | C0751291 | Desmoplastic Medulloblastoma | 1 | CTD_human | |
| Tgene | C1275668 | Melanotic medulloblastoma | 1 | CTD_human | |
| Tgene | C1837218 | Cleft palate, isolated | 1 | CTD_human | |
| Tgene | C1959583 | Myocardial Failure | 1 | CTD_human | |
| Tgene | C1961112 | Heart Decompensation | 1 | CTD_human | |
| Tgene | C2718076 | Fetal Mummification | 1 | CTD_human | |
| Tgene | C2985290 | Fetal Alcohol Spectrum Disorders | 1 | PSYGENET | |
| Tgene | C4545381 | Myeloid and/or lymphoid neoplasm associated with platelet derived growth factor receptor alpha rearrangement | 1 | ORPHANET |
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