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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:APP-MMP9 (FusionGDB2 ID:5697) |
Fusion Gene Summary for APP-MMP9 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: APP-MMP9 | Fusion gene ID: 5697 | Hgene | Tgene | Gene symbol | APP | MMP9 | Gene ID | 351 | 4318 |
| Gene name | amyloid beta precursor protein | matrix metallopeptidase 9 | |
| Synonyms | AAA|ABETA|ABPP|AD1|APPI|CTFgamma|CVAP|PN-II|PN2|preA4 | CLG4B|GELB|MANDP2|MMP-9 | |
| Cytomap | 21q21.3 | 20q13.12 | |
| Type of gene | protein-coding | protein-coding | |
| Description | amyloid-beta precursor proteinalzheimer disease amyloid proteinamyloid beta (A4) precursor proteinamyloid beta A4 proteinamyloid precursor proteinbeta-amyloid peptidebeta-amyloid peptide(1-40)beta-amyloid peptide(1-42)beta-amyloid precursor protei | matrix metalloproteinase-9macrophage gelatinasematrix metallopeptidase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)matrix metalloproteinase 9 (gelatinase B, 92kDa gelatinase, 92kDa type IV collagenase)type V collagenase | |
| Modification date | 20200329 | 20200329 | |
| UniProtAcc | P05067 | P14780 | |
| Ensembl transtripts involved in fusion gene | ENST00000346798, ENST00000348990, ENST00000354192, ENST00000357903, ENST00000358918, ENST00000359726, ENST00000439274, ENST00000440126, ENST00000448388, ENST00000474136, | ENST00000372330, | |
| Fusion gene scores | * DoF score | 31 X 25 X 12=9300 | 5 X 4 X 4=80 |
| # samples | 33 | 5 | |
| ** MAII score | log2(33/9300*10)=-4.81669278663694 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(5/80*10)=-0.678071905112638 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: APP [Title/Abstract] AND MMP9 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | APP(27264034)-MMP9(44643010), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | APP-MMP9 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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 | APP | GO:0001934 | positive regulation of protein phosphorylation | 11404397 |
| Hgene | APP | GO:0008285 | negative regulation of cell proliferation | 22944668 |
| Hgene | APP | GO:1905606 | regulation of presynapse assembly | 19726636 |
| Tgene | MMP9 | GO:0006508 | proteolysis | 2551898|15863497|19022250|24164424 |
| Tgene | MMP9 | GO:0034614 | cellular response to reactive oxygen species | 26514923 |
| Tgene | MMP9 | GO:0043388 | positive regulation of DNA binding | 22984561 |
| Tgene | MMP9 | GO:0071276 | cellular response to cadmium ion | 26514923 |
| Tgene | MMP9 | GO:1900122 | positive regulation of receptor binding | 24164424 |
| Tgene | MMP9 | GO:2001258 | negative regulation of cation channel activity | 24164424 |
| Fusion gene breakpoints across APP (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 MMP9 (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 | BLCA | TCGA-FD-A5BX-01A | APP | chr21 | 27264034 | - | MMP9 | chr20 | 44643010 | + |
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Fusion Gene ORF analysis for APP-MMP9 |
| 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 | ENST00000346798 | ENST00000372330 | APP | chr21 | 27264034 | - | MMP9 | chr20 | 44643010 | + |
| Frame-shift | ENST00000348990 | ENST00000372330 | APP | chr21 | 27264034 | - | MMP9 | chr20 | 44643010 | + |
| Frame-shift | ENST00000354192 | ENST00000372330 | APP | chr21 | 27264034 | - | MMP9 | chr20 | 44643010 | + |
| Frame-shift | ENST00000357903 | ENST00000372330 | APP | chr21 | 27264034 | - | MMP9 | chr20 | 44643010 | + |
| Frame-shift | ENST00000358918 | ENST00000372330 | APP | chr21 | 27264034 | - | MMP9 | chr20 | 44643010 | + |
| Frame-shift | ENST00000359726 | ENST00000372330 | APP | chr21 | 27264034 | - | MMP9 | chr20 | 44643010 | + |
| Frame-shift | ENST00000439274 | ENST00000372330 | APP | chr21 | 27264034 | - | MMP9 | chr20 | 44643010 | + |
| Frame-shift | ENST00000440126 | ENST00000372330 | APP | chr21 | 27264034 | - | MMP9 | chr20 | 44643010 | + |
| Frame-shift | ENST00000448388 | ENST00000372330 | APP | chr21 | 27264034 | - | MMP9 | chr20 | 44643010 | + |
| intron-3CDS | ENST00000474136 | ENST00000372330 | APP | chr21 | 27264034 | - | MMP9 | chr20 | 44643010 | + |
| 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 APP-MMP9 |
| 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) |
| APP | chr21 | 27264033 | - | MMP9 | chr20 | 44643009 | + | 0.0002706 | 0.99972934 |
| APP | chr21 | 27264033 | - | MMP9 | chr20 | 44643009 | + | 0.0002706 | 0.99972934 |
| 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 APP-MMP9 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:27264034/:44643010) - 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 |
| APP | MMP9 |
| FUNCTION: Functions as a cell surface receptor and performs physiological functions on the surface of neurons relevant to neurite growth, neuronal adhesion and axonogenesis. Interaction between APP molecules on neighboring cells promotes synaptogenesis (PubMed:25122912). Involved in cell mobility and transcription regulation through protein-protein interactions. Can promote transcription activation through binding to APBB1-KAT5 and inhibits Notch signaling through interaction with Numb. Couples to apoptosis-inducing pathways such as those mediated by G(O) and JIP. Inhibits G(o) alpha ATPase activity (By similarity). Acts as a kinesin I membrane receptor, mediating the axonal transport of beta-secretase and presenilin 1 (By similarity). By acting as a kinesin I membrane receptor, plays a role in axonal anterograde transport of cargo towards synapes in axons (PubMed:17062754, PubMed:23011729). Involved in copper homeostasis/oxidative stress through copper ion reduction. In vitro, copper-metallated APP induces neuronal death directly or is potentiated through Cu(2+)-mediated low-density lipoprotein oxidation. Can regulate neurite outgrowth through binding to components of the extracellular matrix such as heparin and collagen I and IV. The splice isoforms that contain the BPTI domain possess protease inhibitor activity. Induces a AGER-dependent pathway that involves activation of p38 MAPK, resulting in internalization of amyloid-beta peptide and leading to mitochondrial dysfunction in cultured cortical neurons. Provides Cu(2+) ions for GPC1 which are required for release of nitric oxide (NO) and subsequent degradation of the heparan sulfate chains on GPC1. {ECO:0000250, ECO:0000250|UniProtKB:P12023, ECO:0000269|PubMed:17062754, ECO:0000269|PubMed:23011729, ECO:0000269|PubMed:25122912}.; FUNCTION: Amyloid-beta peptides are lipophilic metal chelators with metal-reducing activity. Bind transient metals such as copper, zinc and iron. In vitro, can reduce Cu(2+) and Fe(3+) to Cu(+) and Fe(2+), respectively. Amyloid-beta protein 42 is a more effective reductant than amyloid-beta protein 40. Amyloid-beta peptides bind to lipoproteins and apolipoproteins E and J in the CSF and to HDL particles in plasma, inhibiting metal-catalyzed oxidation of lipoproteins. APP42-beta may activate mononuclear phagocytes in the brain and elicit inflammatory responses. Promotes both tau aggregation and TPK II-mediated phosphorylation. Interaction with overexpressed HADH2 leads to oxidative stress and neurotoxicity. Also binds GPC1 in lipid rafts.; FUNCTION: Appicans elicit adhesion of neural cells to the extracellular matrix and may regulate neurite outgrowth in the brain. {ECO:0000250}.; FUNCTION: The gamma-CTF peptides as well as the caspase-cleaved peptides, including C31, are potent enhancers of neuronal apoptosis.; FUNCTION: N-APP binds TNFRSF21 triggering caspase activation and degeneration of both neuronal cell bodies (via caspase-3) and axons (via caspase-6). | FUNCTION: May play an essential role in local proteolysis of the extracellular matrix and in leukocyte migration. Could play a role in bone osteoclastic resorption. Cleaves KiSS1 at a Gly-|-Leu bond. Cleaves type IV and type V collagen into large C-terminal three quarter fragments and shorter N-terminal one quarter fragments. Degrades fibronectin but not laminin or Pz-peptide. {ECO:0000269|PubMed:1480034}. |
| 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 APP-MMP9 |
| 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 APP-MMP9 |
| 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 APP-MMP9 |
| 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 APP-MMP9 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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