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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:PDGFA-GET4 (FusionGDB2 ID:63421) |
Fusion Gene Summary for PDGFA-GET4 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: PDGFA-GET4 | Fusion gene ID: 63421 | Hgene | Tgene | Gene symbol | PDGFA | GET4 | Gene ID | 5154 | 51608 |
| Gene name | platelet derived growth factor subunit A | guided entry of tail-anchored proteins factor 4 | |
| Synonyms | PDGF-A|PDGF1 | C7orf20|CEE|CGI-20|TRC35 | |
| Cytomap | 7p22.3 | 7p22.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | platelet-derived growth factor subunit APDGF A-chainPDGF subunit Aplatelet-derived growth factor A-chainplatelet-derived growth factor alpha chainplatelet-derived growth factor alpha polypeptide | Golgi to ER traffic protein 4 homologH_NH1244M04.5conserved edge expressed proteinconserved edge proteingolgi to ER traffic protein 4transmembrane domain recognition complex 35 kDa subunittransmembrane domain recognition complex, 35kDa | |
| Modification date | 20200313 | 20200313 | |
| UniProtAcc | . | Q7L5D6 | |
| Ensembl transtripts involved in fusion gene | ENST00000402802, ENST00000354513, ENST00000426681, | ENST00000265857, ENST00000407192, | |
| Fusion gene scores | * DoF score | 7 X 8 X 6=336 | 14 X 5 X 8=560 |
| # samples | 8 | 14 | |
| ** MAII score | log2(8/336*10)=-2.0703893278914 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(14/560*10)=-2 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: PDGFA [Title/Abstract] AND GET4 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | PDGFA(558576)-GET4(925693), # samples:2 | ||
| Anticipated loss of major functional domain due to fusion event. | PDGFA-GET4 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF. | ||
| * 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 | PDGFA | GO:0008284 | positive regulation of cell proliferation | 2439522|2836953|7073684|10806482|16462734|17470632 |
| Hgene | PDGFA | GO:0009611 | response to wounding | 2538439 |
| Hgene | PDGFA | GO:0010512 | negative regulation of phosphatidylinositol biosynthetic process | 2538439 |
| Hgene | PDGFA | GO:0010544 | negative regulation of platelet activation | 2538439 |
| Hgene | PDGFA | GO:0014068 | positive regulation of phosphatidylinositol 3-kinase signaling | 11788434 |
| Hgene | PDGFA | GO:0014910 | regulation of smooth muscle cell migration | 9409235 |
| Hgene | PDGFA | GO:0030335 | positive regulation of cell migration | 11788434|17470632 |
| Hgene | PDGFA | GO:0031954 | positive regulation of protein autophosphorylation | 12070119 |
| Hgene | PDGFA | GO:0035793 | positive regulation of metanephric mesenchymal cell migration by platelet-derived growth factor receptor-beta signaling pathway | 19019919 |
| Hgene | PDGFA | GO:0043406 | positive regulation of MAP kinase activity | 11788434 |
| Hgene | PDGFA | GO:0048008 | platelet-derived growth factor receptor signaling pathway | 2439522|2536956|2836953 |
| Hgene | PDGFA | GO:0048146 | positive regulation of fibroblast proliferation | 2439522|10806482 |
| Hgene | PDGFA | GO:0050919 | negative chemotaxis | 9409235 |
| Hgene | PDGFA | GO:0051897 | positive regulation of protein kinase B signaling | 19019919 |
| Hgene | PDGFA | GO:0070374 | positive regulation of ERK1 and ERK2 cascade | 11788434 |
| Hgene | PDGFA | GO:0072124 | regulation of glomerular mesangial cell proliferation | 11788434 |
| Hgene | PDGFA | GO:2000278 | regulation of DNA biosynthetic process | 11788434|19019919 |
| Tgene | GET4 | GO:0071816 | tail-anchored membrane protein insertion into ER membrane | 25535373 |
| Fusion gene breakpoints across PDGFA (5'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene breakpoints across GET4 (3'-gene) * Click on the image to open the UCSC genome browser with custom track showing this image in a new window. |
| Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0) * 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 | SARC | TCGA-DX-A8BG-01A | PDGFA | chr7 | 558576 | - | GET4 | chr7 | 925693 | + |
| ChimerDB4 | SARC | TCGA-DX-A8BG-01A | PDGFA | chr7 | 558576 | - | GET4 | chr7 | 925693 | + |
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Fusion Gene ORF analysis for PDGFA-GET4 |
| 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 |
| Frame-shift | ENST00000402802 | ENST00000265857 | PDGFA | chr7 | 558576 | - | GET4 | chr7 | 925693 | + |
| 5CDS-5UTR | ENST00000402802 | ENST00000407192 | PDGFA | chr7 | 558576 | - | GET4 | chr7 | 925693 | + |
| Frame-shift | ENST00000354513 | ENST00000265857 | PDGFA | chr7 | 558576 | - | GET4 | chr7 | 925693 | + |
| 5CDS-5UTR | ENST00000354513 | ENST00000407192 | PDGFA | chr7 | 558576 | - | GET4 | chr7 | 925693 | + |
| intron-3CDS | ENST00000426681 | ENST00000265857 | PDGFA | chr7 | 558576 | - | GET4 | chr7 | 925693 | + |
| intron-5UTR | ENST00000426681 | ENST00000407192 | PDGFA | chr7 | 558576 | - | GET4 | chr7 | 925693 | + |
| 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 PDGFA-GET4 |
| 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) |
| PDGFA | chr7 | 558575 | - | GET4 | chr7 | 925692 | + | 0.06307167 | 0.93692833 |
| PDGFA | chr7 | 558575 | - | GET4 | chr7 | 925692 | + | 0.06307167 | 0.93692833 |
| Distribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page. |
| 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 PDGFA-GET4 |
| Go to FGviewer for the breakpoints of :-: - FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels. |
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| Main function of each fusion partner protein. (from UniProt) |
| Hgene | Tgene |
| . | GET4 |
| FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes. | FUNCTION: As part of a cytosolic protein quality control complex, the BAG6/BAT3 complex, maintains misfolded and hydrophobic patches-containing proteins in a soluble state and participates in their proper delivery to the endoplasmic reticulum or alternatively can promote their sorting to the proteasome where they undergo degradation (PubMed:20676083, PubMed:21636303, PubMed:21743475, PubMed:28104892). The BAG6/BAT3 complex is involved in the post-translational delivery of tail-anchored/type II transmembrane proteins to the endoplasmic reticulum membrane. Recruited to ribosomes, it interacts with the transmembrane region of newly synthesized tail-anchored proteins and together with SGTA and ASNA1 mediates their delivery to the endoplasmic reticulum (PubMed:20676083, PubMed:28104892, PubMed:25535373). Client proteins that cannot be properly delivered to the endoplasmic reticulum are ubiquitinated and sorted to the proteasome (PubMed:28104892). Similarly, the BAG6/BAT3 complex also functions as a sorting platform for proteins of the secretory pathway that are mislocalized to the cytosol either delivering them to the proteasome for degradation or to the endoplasmic reticulum (PubMed:21743475). The BAG6/BAT3 complex also plays a role in the endoplasmic reticulum-associated degradation (ERAD), a quality control mechanism that eliminates unwanted proteins of the endoplasmic reticulum through their retrotranslocation to the cytosol and their targeting to the proteasome. It maintains these retrotranslocated proteins in an unfolded yet soluble state condition in the cytosol to ensure their proper delivery to the proteasome (PubMed:21636303). {ECO:0000269|PubMed:20676083, ECO:0000269|PubMed:21636303, ECO:0000269|PubMed:21743475, ECO:0000269|PubMed:25535373, ECO:0000269|PubMed:28104892}. |
| 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 PDGFA-GET4 |
| 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 PDGFA-GET4 |
| 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 PDGFA-GET4 |
| 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 |
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Related Diseases for PDGFA-GET4 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
| Hgene | PDGFA | C0007097 | Carcinoma | 2 | CTD_human |
| Hgene | PDGFA | C0024667 | Animal Mammary Neoplasms | 2 | CTD_human |
| Hgene | PDGFA | C0024668 | Mammary Neoplasms, Experimental | 2 | CTD_human |
| Hgene | PDGFA | C0205696 | Anaplastic carcinoma | 2 | CTD_human |
| Hgene | PDGFA | C0205697 | Carcinoma, Spindle-Cell | 2 | CTD_human |
| Hgene | PDGFA | C0205698 | Undifferentiated carcinoma | 2 | CTD_human |
| Hgene | PDGFA | C0205699 | Carcinomatosis | 2 | CTD_human |
| Hgene | PDGFA | C1257925 | Mammary Carcinoma, Animal | 2 | CTD_human |
| Hgene | PDGFA | C0005942 | Bone Diseases, Endocrine | 1 | CTD_human |
| Hgene | PDGFA | C0006142 | Malignant neoplasm of breast | 1 | CTD_human |
| Hgene | PDGFA | C0023893 | Liver Cirrhosis, Experimental | 1 | CTD_human |
| Hgene | PDGFA | C0024115 | Lung diseases | 1 | CTD_human |
| Hgene | PDGFA | C0025500 | Mesothelioma | 1 | CTD_human |
| Hgene | PDGFA | C0034069 | Pulmonary Fibrosis | 1 | CTD_human |
| Hgene | PDGFA | C0040028 | Thrombocythemia, Essential | 1 | CTD_human |
| Hgene | PDGFA | C0040136 | Thyroid Neoplasm | 1 | CTD_human |
| Hgene | PDGFA | C0151468 | Thyroid Gland Follicular Adenoma | 1 | CTD_human |
| Hgene | PDGFA | C0549473 | Thyroid carcinoma | 1 | CTD_human |
| Hgene | PDGFA | C0678222 | Breast Carcinoma | 1 | CTD_human |
| Hgene | PDGFA | C1257931 | Mammary Neoplasms, Human | 1 | CTD_human |
| Hgene | PDGFA | C1458155 | Mammary Neoplasms | 1 | CTD_human |
| Hgene | PDGFA | C1862939 | AMYOTROPHIC LATERAL SCLEROSIS 1 | 1 | CTD_human |
| Hgene | PDGFA | C1862941 | Amyotrophic Lateral Sclerosis, Sporadic | 1 | CTD_human |
| Hgene | PDGFA | C3489628 | Thrombocytosis, Autosomal Dominant | 1 | CTD_human |
| Hgene | PDGFA | C4551993 | Amyotrophic Lateral Sclerosis, Familial | 1 | CTD_human |
| Hgene | PDGFA | C4704874 | Mammary Carcinoma, Human | 1 | CTD_human |
| Hgene | PDGFA | C4721507 | Alveolitis, Fibrosing | 1 | CTD_human |
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