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Fusion gene ID: 7455 |
FusionGeneSummary for CLOCK_PDGFRA |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CLOCK_PDGFRA | Fusion gene ID: 7455 | 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 | 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 | 20180519 | 20180523 | |
| UniProtAcc | O15516 | P16234 | |
| Ensembl transtripts involved in fusion gene | ENST00000309964, ENST00000381322, ENST00000513440, ENST00000506923, | ENST00000257290, ENST00000508170, | |
| Fusion gene scores | * DoF score | 6 X 8 X 5=240 | 12 X 13 X 4=624 |
| # samples | 8 | 13 | |
| ** MAII score | log2(8/240*10)=-1.58496250072116 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). 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: CLOCK [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 |
| 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 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 |
| TCGA | RV | LUAD | TCGA-69-7979-01A | CLOCK | chr4 | 56376079 | - | PDGFRA | chr4 | 55153597 | + |
| * 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 |
| 5UTR-3CDS | ENST00000309964 | ENST00000257290 | CLOCK | chr4 | 56376079 | - | PDGFRA | chr4 | 55153597 | + |
| 5UTR-intron | ENST00000309964 | ENST00000508170 | CLOCK | chr4 | 56376079 | - | PDGFRA | chr4 | 55153597 | + |
| 5UTR-3CDS | ENST00000381322 | ENST00000257290 | CLOCK | chr4 | 56376079 | - | PDGFRA | chr4 | 55153597 | + |
| 5UTR-intron | ENST00000381322 | ENST00000508170 | CLOCK | chr4 | 56376079 | - | PDGFRA | chr4 | 55153597 | + |
| 5UTR-3CDS | ENST00000513440 | ENST00000257290 | 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 | + |
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FusionProtFeatures for CLOCK_PDGFRA |
| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| CLOCK | PDGFRA |
| Transcriptional activator which forms a core componentof the circadian clock. The circadian clock, an internal time-keeping system, regulates various physiological processes throughthe generation of approximately 24 hour circadian rhythms in geneexpression, which are translated into rhythms in metabolism andbehavior. It is derived from the Latin roots 'circa' (about) and'diem' (day) and acts as an important regulator of a wide array ofphysiological functions including metabolism, sleep, bodytemperature, blood pressure, endocrine, immune, cardiovascular,and renal function. Consists of two major components: the centralclock, residing in the suprachiasmatic nucleus (SCN) of the brain,and the peripheral clocks that are present in nearly every tissueand organ system. Both the central and peripheral clocks can bereset by environmental cues, also known as Zeitgebers (German for'timegivers'). The predominant Zeitgeber for the central clock islight, which is sensed by retina and signals directly to the SCN.The central clock entrains the peripheral clocks through neuronaland hormonal signals, body temperature and feeding-related cues,aligning all clocks with the external light/dark cycle. Circadianrhythms allow an organism to achieve temporal homeostasis with itsenvironment at the molecular level by regulating gene expressionto create a peak of protein expression once every 24 hours tocontrol when a particular physiological process is most activewith respect to the solar day. Transcription and translation ofcore clock components (CLOCK, NPAS2, ARNTL/BMAL1, ARNTL2/BMAL2,PER1, PER2, PER3, CRY1 and CRY2) plays a critical role in rhythmgeneration, whereas delays imposed by post-translationalmodifications (PTMs) are important for determining the period(tau) of the rhythms (tau refers to the period of a rhythm and isthe length, in time, of one complete cycle). A diurnal rhythm issynchronized with the day/night cycle, while the ultradian andinfradian rhythms have a period shorter and longer than 24 hours,respectively. Disruptions in the circadian rhythms contribute tothe pathology of cardiovascular diseases, cancer, metabolicsyndromes and aging. A transcription/translation feedback loop(TTFL) forms the core of the molecular circadian clock mechanism.Transcription factors, CLOCK or NPAS2 and ARNTL/BMAL1 orARNTL2/BMAL2, form the positive limb of the feedback loop, act inthe form of a heterodimer and activate the transcription of coreclock genes and clock-controlled genes (involved in key metabolicprocesses), harboring E-box elements (5'-CACGTG-3') within theirpromoters. The core clock genes: PER1/2/3 and CRY1/2 which aretranscriptional repressors form the negative limb of the feedbackloop and interact with the CLOCK|NPAS2-ARNTL/BMAL1|ARNTL2/BMAL2heterodimer inhibiting its activity and thereby negativelyregulating their own expression. This heterodimer also activatesnuclear receptors NR1D1/2 and RORA/B/G, which form a secondfeedback loop and which activate and repress ARNTL/BMAL1transcription, respectively. Regulates the circadian expression ofICAM1, VCAM1, CCL2, THPO and MPL and also acts as an enhancer ofthe transactivation potential of NF-kappaB. Plays an importantrole in the homeostatic regulation of sleep. The CLOCK-ARNTL/BMAL1heterodimer regulates the circadian expression of SERPINE1/PAI1,VWF, B3, CCRN4L/NOC, NAMPT, DBP, MYOD1, PPARGC1A, PPARGC1B, SIRT1,GYS2, F7, NGFR, GNRHR, BHLHE40/DEC1, ATF4, MTA1, KLF10 and alsogenes implicated in glucose and lipid metabolism. Promotesrhythmic chromatin opening, regulating the DNA accessibility ofother transcription factors. The CLOCK-ARNTL2/BMAL2 heterodimeractivates the transcription of SERPINE1/PAI1 and BHLHE40/DEC1. Thepreferred binding motif for the CLOCK-ARNTL/BMAL1 heterodimer is5'-CACGTGA-3', which contains a flanking Ala residue in additionto the canonical 6-nucleotide E-box sequence (PubMed:23229515).CLOCK specifically binds to the half-site 5'-CAC-3', while ARNTLbinds to the half-site 5'-GTGA-3' (PubMed:23229515). The CLOCK-ARNTL/BMAL1 heterodimer also recognizes the non-canonical E-boxmotifs 5'-AACGTGA-3' and 5'-CATGTGA-3' (PubMed:23229515). CLOCKhas an intrinsic acetyltransferase activity, which enablescircadian chromatin remodeling by acetylating histones andnonhistone proteins, including its own partner ARNTL/BMAL1.Represses glucocorticoid receptor NR3C1/GR-induced transcriptionalactivity by reducing the association of NR3C1/GR to glucocorticoidresponse elements (GREs) via the acetylation of multiple lysineresidues located in its hinge region (PubMed:21980503). Theacetyltransferase activity of CLOCK is as important as itstranscription activity in circadian control. Acetylates metabolicenzymes IMPDH2 and NDUFA9 in a circadian manner. Facilitated byBMAL1, rhythmically interacts and acetylates argininosuccinatesynthase 1 (ASS1) leading to enzymatic inhibition of ASS1 as wellas the circadian oscillation of arginine biosynthesis andsubsequent ureagenesis (PubMed:28985504).{ECO:0000269|PubMed:14645221, ECO:0000269|PubMed:18587630,ECO:0000269|PubMed:21659603, ECO:0000269|PubMed:21980503,ECO:0000269|PubMed:22284746, ECO:0000269|PubMed:23229515,ECO:0000269|PubMed:23785138, ECO:0000269|PubMed:24005054,ECO:0000269|PubMed:28985504}. | 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 CLOCK_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 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 |
| CLOCK | ARNTL, ARNTL2, EP300, KAT2B, RXRA, RARA, SIRT1, TFAP4, SOX2, CIPC, CRY1, CRY2, DEC1, BHLHE41, NPAS2, PPP2R5D, PPP2R5E, CSNK2B, PPP2R1B, NR1D2, PER2, PPP1CA, PPP1CB, PPP1CC, RORB, CSNK1E, DBP, RORC, SRGAP3, TEKT4, CREBBP, EXOC1, PKN3, NCKAP5L, TFPT, CCHCR1, YEATS4, TUFT1, RABGAP1L, GOLGA5, PSMD9, VPS53, DZIP3, GRIPAP1, RCOR1, HMG20A, CCDC132, CCDC93, OIP5, PHF21A, PTRF, PHLDB3, GIT2, HAUS6, RPRD1A, MAX, RABGEF1, NUF2, THAP11, VPS51, TSSC1, KDM1A, RABEP1 | PDGFRA | CBL, PDGFA, PDGFB, PDGFC, PDGFRB, PDGFRA, CRKL, CRK, GRB2, PLCG1, SLC9A3R1, ITGB3, CAV1, CAV3, SNX6, SNX2, SNX4, PTEN, PIK3R1, KIT, FBXO25, ULBP2, TGFBR2, SRPK1, CCDC155, EGFR, NTRK1, CLU, DSG2, H3F3A, MYO1C, NRD1, THOC5, TFRC, TNK1, FARP1, FLOT1, RNPS1, SCFD1, PPIL2, PACSIN3, WDR74, PRKRIP1, RAB11FIP1, MAK16, PHLDB2, STAT3, STAT1, SMURF1, DNM2, PTPN11, BRCA1, MTOR, TOP1, VHL, RRM2, CDK9, SHF, RASA1, PIK3CA |
| - 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 CLOCK_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 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 | 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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