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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:CASP4-USP28 (FusionGDB2 ID:13221) |
Fusion Gene Summary for CASP4-USP28 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: CASP4-USP28 | Fusion gene ID: 13221 | Hgene | Tgene | Gene symbol | CASP4 | USP28 | Gene ID | 837 | 57646 |
| Gene name | caspase 4 | ubiquitin specific peptidase 28 | |
| Synonyms | ICE(rel)II|ICEREL-II|ICH-2|Mih1|Mih1/TX|TX | - | |
| Cytomap | 11q22.3 | 11q23.2 | |
| Type of gene | protein-coding | protein-coding | |
| Description | caspase-4CASP-4ICE and Ced-3 homolog 2ICE(rel)-IIapoptotic cysteine protease Mih1/TXcaspase 4, apoptosis-related cysteine peptidasecaspase 4, apoptosis-related cysteine proteaseprotease ICH-2protease TX | ubiquitin carboxyl-terminal hydrolase 28deubiquitinating enzyme 28ubiquitin carboxyl-terminal hydrolase 28 variant 1ubiquitin thioesterase 28ubiquitin thiolesterase 28ubiquitin-specific-processing protease 28 | |
| Modification date | 20200320 | 20200313 | |
| UniProtAcc | P49662 | . | |
| Ensembl transtripts involved in fusion gene | ENST00000444739, ENST00000531333, ENST00000393150, | ENST00000542033, ENST00000003302, ENST00000260188, ENST00000537706, ENST00000544967, ENST00000545540, | |
| Fusion gene scores | * DoF score | 1 X 1 X 1=1 | 8 X 8 X 6=384 |
| # samples | 1 | 9 | |
| ** MAII score | log2(1/1*10)=3.32192809488736 | log2(9/384*10)=-2.09310940439148 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: CASP4 [Title/Abstract] AND USP28 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | CASP4(104839246)-USP28(113688559), # samples:1 | ||
| Anticipated loss of major functional domain due to fusion event. | CASP4-USP28 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF. CASP4-USP28 seems lost the major protein functional domain in Hgene 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 | CASP4 | GO:1903265 | positive regulation of tumor necrosis factor-mediated signaling pathway | 16920334 |
| Tgene | USP28 | GO:0006974 | cellular response to DNA damage stimulus | 17873522 |
| Tgene | USP28 | GO:0010212 | response to ionizing radiation | 16901786 |
| Tgene | USP28 | GO:0016579 | protein deubiquitination | 16901786|17558397|18662541 |
| Tgene | USP28 | GO:0034644 | cellular response to UV | 17873522 |
| Tgene | USP28 | GO:0042771 | intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator | 16901786 |
| Fusion gene breakpoints across CASP4 (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 USP28 (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 | LUAD | TCGA-55-7570-01A | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
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Fusion Gene ORF analysis for CASP4-USP28 |
| 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 |
| 5CDS-intron | ENST00000444739 | ENST00000542033 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| 5UTR-3CDS | ENST00000531333 | ENST00000003302 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| 5UTR-3CDS | ENST00000531333 | ENST00000260188 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| 5UTR-3CDS | ENST00000531333 | ENST00000537706 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| 5UTR-3CDS | ENST00000531333 | ENST00000544967 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| 5UTR-3CDS | ENST00000531333 | ENST00000545540 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| 5UTR-intron | ENST00000531333 | ENST00000542033 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| Frame-shift | ENST00000444739 | ENST00000003302 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| Frame-shift | ENST00000444739 | ENST00000260188 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| Frame-shift | ENST00000444739 | ENST00000537706 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| Frame-shift | ENST00000444739 | ENST00000544967 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| Frame-shift | ENST00000444739 | ENST00000545540 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| intron-3CDS | ENST00000393150 | ENST00000003302 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| intron-3CDS | ENST00000393150 | ENST00000260188 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| intron-3CDS | ENST00000393150 | ENST00000537706 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| intron-3CDS | ENST00000393150 | ENST00000544967 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| intron-3CDS | ENST00000393150 | ENST00000545540 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| intron-intron | ENST00000393150 | ENST00000542033 | CASP4 | chr11 | 104839246 | - | USP28 | chr11 | 113688559 | - |
| 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 CASP4-USP28 |
| 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) |
| 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 CASP4-USP28 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:104839246/:113688559) - 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 |
| CASP4 | . |
| FUNCTION: Inflammatory caspase that acts as an essential effector of NLRP3 inflammasome-dependent CASP1 activation and IL1B and IL18 secretion in response to non-canonical activators, such as UVB radiation, cholera enterotoxin subunit B and cytosolic LPS (PubMed:23516580, PubMed:24879791, PubMed:25119034, PubMed:22246630, PubMed:26174085, PubMed:26173988, PubMed:26508369, PubMed:25964352). Thiol protease that cleaves a tetrapeptide after an Asp residue at position P1 (PubMed:7797510, PubMed:23516580). Independently of NLRP3 inflammasome and CASP1, promotes pyroptosis, through GSDMD cleavage and activation, followed by IL1A, IL18 and HMGB1 release in response to non-canonical inflammasome activators (PubMed:26375003, PubMed:32109412). Plays a crucial role in the restriction of Salmonella typhimurium replication in colonic epithelial cells during infection: in later stages of the infection, LPS from cytosolic Salmonella triggers CASP4 activation, which catalyzes cleavage of GSDMD, resulting in pyroptosis of infected cells and their extrusion into the gut lumen, as well as in IL18 secretion (PubMed:25121752, PubMed:26375003, PubMed:25964352, PubMed:32109412). Cleavage of GSDMD is not strictly dependent on the consensus cleavage site but depends on an exosite interface on CASP4 that recognizes and binds the Gasdermin-D, C-terminal (GSDMD-CT) part (PubMed:32109412). Pyroptosis limits bacterial replication, while cytokine secretion promotes the recruitment and activation of immune cells and triggers mucosal inflammation (PubMed:25121752, PubMed:26375003, PubMed:25964352). Involved in LPS-induced IL6 secretion; this activity may not require caspase enzymatic activity (PubMed:26508369). Involved in cell death induced by endoplasmic reticulum stress and by treatment with cytotoxic APP peptides found Alzheimer's patient brains (PubMed:15123740, PubMed:22246630, PubMed:23661706). Activated by direct binding to LPS without the need of an upstream sensor (PubMed:25119034). Does not directly process IL1B (PubMed:7743998, PubMed:7797510, PubMed:7797592). During non-canonical inflammasome activation, cuts CGAS and may play a role in the regulation of antiviral innate immune activation (PubMed:28314590). {ECO:0000269|PubMed:15123740, ECO:0000269|PubMed:22246630, ECO:0000269|PubMed:23516580, ECO:0000269|PubMed:23661706, ECO:0000269|PubMed:24879791, ECO:0000269|PubMed:25119034, ECO:0000269|PubMed:25121752, ECO:0000269|PubMed:25964352, ECO:0000269|PubMed:26173988, ECO:0000269|PubMed:26174085, ECO:0000269|PubMed:26375003, ECO:0000269|PubMed:26508369, ECO:0000269|PubMed:28314590, ECO:0000269|PubMed:32109412, ECO:0000269|PubMed:7743998, ECO:0000269|PubMed:7797510, ECO:0000269|PubMed:7797592}. | 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}. |
| 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 CASP4-USP28 |
| 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 CASP4-USP28 |
| 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 CASP4-USP28 |
| 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 CASP4-USP28 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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