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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:EPCAM-MSH2 (FusionGDB2 ID:26923) |
Fusion Gene Summary for EPCAM-MSH2 |
 Fusion gene summary |
| Fusion gene information | Fusion gene name: EPCAM-MSH2 | Fusion gene ID: 26923 | Hgene | Tgene | Gene symbol | EPCAM | MSH2 | Gene ID | 4072 | 4436 |
| Gene name | epithelial cell adhesion molecule | mutS homolog 2 | |
| Synonyms | DIAR5|EGP-2|EGP314|EGP40|ESA|HNPCC8|KS1/4|KSA|M4S1|MIC18|MK-1|TACSTD1|TROP1 | COCA1|FCC1|HNPCC|HNPCC1|LCFS2|hMSH2 | |
| Cytomap | 2p21 | 2p21-p16.3 | |
| Type of gene | protein-coding | protein-coding | |
| Description | epithelial cell adhesion moleculeadenocarcinoma-associated antigencell surface glycoprotein Trop-1epithelial glycoprotein 314human epithelial glycoprotein-2major gastrointestinal tumor-associated protein GA733-2membrane component, chromosome 4, surf | DNA mismatch repair protein Msh2DNA mismatch repair protein Msh2 transcriptmutS homolog 2, colon cancer, nonpolyposis type 1 | |
| Modification date | 20200322 | 20200322 | |
| UniProtAcc | P16422 | P43246 | |
| Ensembl transtripts involved in fusion gene | ENST00000263735, ENST00000405271, | ENST00000233146, ENST00000406134, ENST00000461394, ENST00000543555, | |
| Fusion gene scores | * DoF score | 11 X 12 X 4=528 | 9 X 9 X 4=324 |
| # samples | 11 | 9 | |
| ** MAII score | log2(11/528*10)=-2.26303440583379 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | log2(9/324*10)=-1.84799690655495 possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs). DoF>8 and MAII<0 | |
| Context | PubMed: EPCAM [Title/Abstract] AND MSH2 [Title/Abstract] AND fusion [Title/Abstract] | ||
| Most frequent breakpoint | MSH2(47630541)-EPCAM(47612305), # samples:3 MSH2(47643568)-EPCAM(47612305), # samples:3 | ||
| Anticipated loss of major functional domain due to fusion event. | MSH2-EPCAM seems lost the major protein functional domain in Hgene partner, which is a CGC due to the frame-shifted ORF. MSH2-EPCAM seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF. MSH2-EPCAM 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 | EPCAM | GO:0008284 | positive regulation of cell proliferation | 15195135 |
| Hgene | EPCAM | GO:0045944 | positive regulation of transcription by RNA polymerase II | 15195135|15922867 |
| Hgene | EPCAM | GO:2000048 | negative regulation of cell-cell adhesion mediated by cadherin | 9382878 |
| Tgene | MSH2 | GO:0006281 | DNA repair | 8942985 |
| Tgene | MSH2 | GO:0006298 | mismatch repair | 7923193|11555625 |
| Tgene | MSH2 | GO:0006301 | postreplication repair | 7923193 |
| Tgene | MSH2 | GO:0045910 | negative regulation of DNA recombination | 17715146 |
| Tgene | MSH2 | GO:0051096 | positive regulation of helicase activity | 17715146 |
| Fusion gene breakpoints across EPCAM (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 MSH2 (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 |
| ChimerKB4 | . | . | EPCAM | chr2 | 47604152 | + | MSH2 | chr2 | 47604152 | + |
| ChimerKB4 | . | . | EPCAM | chr2 | 47606907 | + | MSH2 | chr2 | 47606907 | + |
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Fusion Gene ORF analysis for EPCAM-MSH2 |
| 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 |
| intron-intron | ENST00000263735 | ENST00000233146 | EPCAM | chr2 | 47604152 | + | MSH2 | chr2 | 47604152 | + |
| intron-intron | ENST00000263735 | ENST00000233146 | EPCAM | chr2 | 47606907 | + | MSH2 | chr2 | 47606907 | + |
| intron-intron | ENST00000263735 | ENST00000406134 | EPCAM | chr2 | 47604152 | + | MSH2 | chr2 | 47604152 | + |
| intron-intron | ENST00000263735 | ENST00000406134 | EPCAM | chr2 | 47606907 | + | MSH2 | chr2 | 47606907 | + |
| intron-intron | ENST00000263735 | ENST00000461394 | EPCAM | chr2 | 47604152 | + | MSH2 | chr2 | 47604152 | + |
| intron-intron | ENST00000263735 | ENST00000461394 | EPCAM | chr2 | 47606907 | + | MSH2 | chr2 | 47606907 | + |
| intron-intron | ENST00000263735 | ENST00000543555 | EPCAM | chr2 | 47604152 | + | MSH2 | chr2 | 47604152 | + |
| intron-intron | ENST00000263735 | ENST00000543555 | EPCAM | chr2 | 47606907 | + | MSH2 | chr2 | 47606907 | + |
| intron-intron | ENST00000405271 | ENST00000233146 | EPCAM | chr2 | 47604152 | + | MSH2 | chr2 | 47604152 | + |
| intron-intron | ENST00000405271 | ENST00000233146 | EPCAM | chr2 | 47606907 | + | MSH2 | chr2 | 47606907 | + |
| intron-intron | ENST00000405271 | ENST00000406134 | EPCAM | chr2 | 47604152 | + | MSH2 | chr2 | 47604152 | + |
| intron-intron | ENST00000405271 | ENST00000406134 | EPCAM | chr2 | 47606907 | + | MSH2 | chr2 | 47606907 | + |
| intron-intron | ENST00000405271 | ENST00000461394 | EPCAM | chr2 | 47604152 | + | MSH2 | chr2 | 47604152 | + |
| intron-intron | ENST00000405271 | ENST00000461394 | EPCAM | chr2 | 47606907 | + | MSH2 | chr2 | 47606907 | + |
| intron-intron | ENST00000405271 | ENST00000543555 | EPCAM | chr2 | 47604152 | + | MSH2 | chr2 | 47604152 | + |
| intron-intron | ENST00000405271 | ENST00000543555 | EPCAM | chr2 | 47606907 | + | MSH2 | chr2 | 47606907 | + |
| 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 EPCAM-MSH2 |
| 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 EPCAM-MSH2 |
| Four levels of functional features of fusion genes Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:47630541/:47612305) - 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 |
| EPCAM | MSH2 |
| FUNCTION: May act as a physical homophilic interaction molecule between intestinal epithelial cells (IECs) and intraepithelial lymphocytes (IELs) at the mucosal epithelium for providing immunological barrier as a first line of defense against mucosal infection. Plays a role in embryonic stem cells proliferation and differentiation. Up-regulates the expression of FABP5, MYC and cyclins A and E. {ECO:0000269|PubMed:15195135, ECO:0000269|PubMed:15922867, ECO:0000269|PubMed:19785009, ECO:0000269|PubMed:20064925}. | FUNCTION: Component of the post-replicative DNA mismatch repair system (MMR). Forms two different heterodimers: MutS alpha (MSH2-MSH6 heterodimer) and MutS beta (MSH2-MSH3 heterodimer) which binds to DNA mismatches thereby initiating DNA repair. When bound, heterodimers bend the DNA helix and shields approximately 20 base pairs. MutS alpha recognizes single base mismatches and dinucleotide insertion-deletion loops (IDL) in the DNA. MutS beta recognizes larger insertion-deletion loops up to 13 nucleotides long. After mismatch binding, MutS alpha or beta forms a ternary complex with the MutL alpha heterodimer, which is thought to be responsible for directing the downstream MMR events, including strand discrimination, excision, and resynthesis. Recruits DNA helicase MCM9 to chromatin which unwinds the mismatch containing DNA strand (PubMed:26300262). ATP binding and hydrolysis play a pivotal role in mismatch repair functions. The ATPase activity associated with MutS alpha regulates binding similar to a molecular switch: mismatched DNA provokes ADP-->ATP exchange, resulting in a discernible conformational transition that converts MutS alpha into a sliding clamp capable of hydrolysis-independent diffusion along the DNA backbone. This transition is crucial for mismatch repair. MutS alpha may also play a role in DNA homologous recombination repair. In melanocytes may modulate both UV-B-induced cell cycle regulation and apoptosis. {ECO:0000269|PubMed:10078208, ECO:0000269|PubMed:10660545, ECO:0000269|PubMed:15064730, ECO:0000269|PubMed:17611581, ECO:0000269|PubMed:21120944, ECO:0000269|PubMed:26300262, ECO:0000269|PubMed:9564049, ECO:0000269|PubMed:9822679, ECO:0000269|PubMed:9822680}. |
| 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 EPCAM-MSH2 |
| 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 EPCAM-MSH2 |
| 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 EPCAM-MSH2 |
| 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 EPCAM-MSH2 |
| Diseases associated with fusion partners. (DisGeNet 4.0) |
| Partner | Gene | Disease ID | Disease name | # pubmeds | Source |
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