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Center for Computational Systems Medicine
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Fusion Gene and Fusion Protein Summary

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Fusion Amino Acid Sequences (multiple BPs and multiple gene isoforms)

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Fusion Protein Breakpoint Sequences - (for the Screening of the FusionNeoAntigens)

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Potential FusionNeoAntigens in HLA I - (netMHCpan v4.1 + deepHLApan v1.1)

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Potential FusionNeoAntigens in HLA II - (netMHCIIpan v4.1)

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Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D - (Glide)

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Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

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Potential target of CAR-T therapy development

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Information on the samples that have these potential fusion neoantigens

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Fusion Protein Targeting Drugs - (Manual Curation)

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Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:TYR-MMP20

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: TYR-MMP20
FusionPDB ID: 95681
FusionGDB2.0 ID: 95681
HgeneTgene
Gene symbol

TYR

MMP20

Gene ID

7299

64386

Gene nametyrosinasematrix metallopeptidase 25
SynonymsATN|CMM8|OCA1|OCA1A|OCAIA|SHEP3MMP-25|MMP20|MMP20A|MMPL1|MT-MMP 6|MT-MMP6|MT6-MMP|MT6MMP|MTMMP6
Cytomap

11q14.3

16p13.3

Type of geneprotein-codingprotein-coding
DescriptiontyrosinaseLB24-ABSK29-ABmonophenol monooxygenaseoculocutaneous albinism IAtumor rejection antigen ABmatrix metalloproteinase-25leukolysinmatrix metallopeptidase-like 1matrix metalloproteinase 20matrix metalloproteinase-like 1membrane-type 6 matrix metalloproteinasemembrane-type matrix metalloproteinase 6
Modification date2020032220200313
UniProtAcc

TDP2

Main function of 5'-partner protein: 362
.
Ensembl transtripts involved in fusion geneENST idsENST00000526139, ENST00000263321, 
ENST00000260228, ENST00000544938, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score5 X 1 X 2=102 X 5 X 5=50
# samples 57
** MAII scorelog2(5/10*10)=2.32192809488736
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(7/50*10)=0.485426827170242
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Fusion gene context

PubMed: TYR [Title/Abstract] AND MMP20 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: TYR [Title/Abstract] AND MMP20 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)TYR(88924586)-MMP20(102480761), # samples:2
Anticipated loss of major functional domain due to fusion event.TYR-MMP20 seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
TYR-MMP20 seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
TYR-MMP20 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
TYR-MMP20 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
TYR-MMP20 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
TYR-MMP20 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)

check button Gene ontology of each fusion partner gene with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneTYR

GO:0042438

melanin biosynthetic process

8126111



check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/chr11:88924586/chr11:102480761)
- 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.
FGviewer

check buttonRetention analysis results 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, are available here.

check buttonFusion gene breakpoints across TYR (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across MMP20 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Amino Acid Sequences


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)
BP loci
(transcript)
Predicted start
(transcript)
Predicted stop
(transcript)
Seq length
(amino acids)
ENST00000263321TYRchr1188924586+ENST00000260228MMP20chr11102480761-295815385022466654

check buttonDeepORF 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.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandNo-coding scoreCoding score
ENST00000263321ENST00000260228TYRchr1188924586+MMP20chr11102480761-0.0008703940.9991296

check button Predicted full-length fusion amino acid sequences. For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among all the predicted ones.

Get the fusion protein sequences from here.

Fusion protein sequence information is available in the fasta format.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

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Fusion Protein Breakpoint Sequences for TYR-MMP20

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
TYRchr1188924586MMP20chr111024807611538345DKAANFSFRNTLEDHGDSYPFDGPRG

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Potential FusionNeoAntigen Information of TYR-MMP20 in HLA I

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
TYR-MMP20_88924586_102480761.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCpan v4.1 (%rank<0.5) and deepHLApan v1.1 (immunogenic score>0.5)
Fusion geneHchrHbpTgeneTchrTbpHLA IFusionNeoAntigen peptideBinding scoreImmunogenic scoreNeoantigen start (at BP 13)Neoantigen end (at BP 13)
TYR-MMP20chr1188924586chr111024807611538HLA-B18:01LEDHGDSY0.98660.71291119
TYR-MMP20chr1188924586chr111024807611538HLA-B35:08TLEDHGDSY0.76190.74491019
TYR-MMP20chr1188924586chr111024807611538HLA-B15:02TLEDHGDSY0.70550.79411019
TYR-MMP20chr1188924586chr111024807611538HLA-B15:21TLEDHGDSY0.70970.7641019
TYR-MMP20chr1188924586chr111024807611538HLA-B15:05TLEDHGDSY0.66180.72631019
TYR-MMP20chr1188924586chr111024807611538HLA-B15:31TLEDHGDSY0.58230.73241019
TYR-MMP20chr1188924586chr111024807611538HLA-B18:05LEDHGDSY0.98660.71291119
TYR-MMP20chr1188924586chr111024807611538HLA-B18:11LEDHGDSY0.97010.67911119
TYR-MMP20chr1188924586chr111024807611538HLA-B15:12TLEDHGDSY0.77950.72581019
TYR-MMP20chr1188924586chr111024807611538HLA-B15:11TLEDHGDSY0.720.72261019
TYR-MMP20chr1188924586chr111024807611538HLA-B15:08TLEDHGDSY0.69840.72211019
TYR-MMP20chr1188924586chr111024807611538HLA-B15:20TLEDHGDSY0.67450.78771019
TYR-MMP20chr1188924586chr111024807611538HLA-B35:28TLEDHGDSY0.56090.78571019
TYR-MMP20chr1188924586chr111024807611538HLA-B35:20TLEDHGDSY0.53940.79091019

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Potential FusionNeoAntigen Information of TYR-MMP20 in HLA II

check button Multiple sequence alignments of the potential FusionNeoAntigens per fusion breakpoints. If the MSA is empty, then it means that there were predicted fusion neoantigens in this fusion breakpoint, but those predicted fusion neoantigens were not across the breakpoint, which is not fusion-specific.
TYR-MMP20_88924586_102480761.msa

check button Potential FusionNeoAntigen Information
* We used NetMHCIIpan v4.1 (%rank<0.5).
Fusion geneHchrHbpTgeneTchrTbpHLA IIFusionNeoAntigen peptideNeoantigen start (at BP 13)Neoantigen end (at BP 13)
TYR-MMP20chr1188924586chr111024807611538DRB1-0801AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0801KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0801ANFSFRNTLEDHGDS318
TYR-MMP20chr1188924586chr111024807611538DRB1-0801DKAANFSFRNTLEDH015
TYR-MMP20chr1188924586chr111024807611538DRB1-0803AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0803KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0803ANFSFRNTLEDHGDS318
TYR-MMP20chr1188924586chr111024807611538DRB1-0803DKAANFSFRNTLEDH015
TYR-MMP20chr1188924586chr111024807611538DRB1-0805AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0808AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0808KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0811AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0811KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0814AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0814KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0814ANFSFRNTLEDHGDS318
TYR-MMP20chr1188924586chr111024807611538DRB1-0814DKAANFSFRNTLEDH015
TYR-MMP20chr1188924586chr111024807611538DRB1-0816AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0816KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0816ANFSFRNTLEDHGDS318
TYR-MMP20chr1188924586chr111024807611538DRB1-0816DKAANFSFRNTLEDH015
TYR-MMP20chr1188924586chr111024807611538DRB1-0818AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0823AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0823KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0823ANFSFRNTLEDHGDS318
TYR-MMP20chr1188924586chr111024807611538DRB1-0823DKAANFSFRNTLEDH015
TYR-MMP20chr1188924586chr111024807611538DRB1-0826AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0826KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0826ANFSFRNTLEDHGDS318
TYR-MMP20chr1188924586chr111024807611538DRB1-0826DKAANFSFRNTLEDH015
TYR-MMP20chr1188924586chr111024807611538DRB1-0827AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0827KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0827ANFSFRNTLEDHGDS318
TYR-MMP20chr1188924586chr111024807611538DRB1-0827DKAANFSFRNTLEDH015
TYR-MMP20chr1188924586chr111024807611538DRB1-0833AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0833KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0833ANFSFRNTLEDHGDS318
TYR-MMP20chr1188924586chr111024807611538DRB1-0833DKAANFSFRNTLEDH015
TYR-MMP20chr1188924586chr111024807611538DRB1-0835AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0835KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0835ANFSFRNTLEDHGDS318
TYR-MMP20chr1188924586chr111024807611538DRB1-0835DKAANFSFRNTLEDH015
TYR-MMP20chr1188924586chr111024807611538DRB1-0836AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0836KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0836ANFSFRNTLEDHGDS318
TYR-MMP20chr1188924586chr111024807611538DRB1-0836DKAANFSFRNTLEDH015
TYR-MMP20chr1188924586chr111024807611538DRB1-0837AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0837KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0838AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0838KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0838ANFSFRNTLEDHGDS318
TYR-MMP20chr1188924586chr111024807611538DRB1-0838DKAANFSFRNTLEDH015
TYR-MMP20chr1188924586chr111024807611538DRB1-0839AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-0839KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-0839ANFSFRNTLEDHGDS318
TYR-MMP20chr1188924586chr111024807611538DRB1-0839DKAANFSFRNTLEDH015
TYR-MMP20chr1188924586chr111024807611538DRB1-1313AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-1313KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-1355AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-1355KAANFSFRNTLEDHG116
TYR-MMP20chr1188924586chr111024807611538DRB1-1463AANFSFRNTLEDHGD217
TYR-MMP20chr1188924586chr111024807611538DRB1-1485AANFSFRNTLEDHGD217

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Fusion breakpoint peptide structures of TYR-MMP20

check button3D structures of the fusion breakpoint peptide of 14AA sequence that have potential fusion neoantigens
* The minimum length of the amino acid sequence in RoseTTAFold is 14AA. Here, we predicted the 14AA fusion protein breakpoint sequence not the fusion neoantigen peptide, which is shorter than 14 AA.
File nameBPseqHgeneTgeneHchrHbpTchrTbpAAlen
8563SFRNTLEDHGDSYPTYRMMP20chr1188924586chr111024807611538

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of TYR-MMP20

check buttonVirtual screening between 25 HLAs (from PDB) and FusionNeoAntigens
* We used Glide to predict the interaction between HLAs and neoantigens.
HLA allelePDB IDFile nameBPseqDocking scoreGlide score
HLA-B14:023BVN8563SFRNTLEDHGDSYP-6.77781-6.89121
HLA-B14:023BVN8563SFRNTLEDHGDSYP-3.08719-4.12249
HLA-B52:013W398563SFRNTLEDHGDSYP-6.66315-6.77655
HLA-B52:013W398563SFRNTLEDHGDSYP-2.65785-3.69315
HLA-A24:025HGA8563SFRNTLEDHGDSYP-7.20627-7.31967
HLA-A24:025HGA8563SFRNTLEDHGDSYP-6.50211-7.53741
HLA-B44:053DX88563SFRNTLEDHGDSYP-7.75024-7.86364
HLA-B44:053DX88563SFRNTLEDHGDSYP-6.53073-7.56603
HLA-A02:016TDR8563SFRNTLEDHGDSYP-4.4528-5.4881

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Vaccine Design for the FusionNeoAntigens of TYR-MMP20

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-Is.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptide sequenceFusionNeoAntigen RNA sequence
TYR-MMP20chr1188924586chr111024807611019TLEDHGDSYCACTGGAAGATCACGGGGATTCCTATC
TYR-MMP20chr1188924586chr111024807611119LEDHGDSYTGGAAGATCACGGGGATTCCTATC

check button mRNA and peptide sequences of FusionNeoAntigens that have potential interaction with HLA-IIs.
Fusion geneHchrHbpTchrTbpStart in +/-13AAEnd in +/-13AAFusionNeoAntigen peptideFusionNEoAntigen RNA sequence
TYR-MMP20chr1188924586chr11102480761015DKAANFSFRNTLEDHATAAAGCTGCCAATTTCAGCTTTAGAAATACACTGGAAGATCACG
TYR-MMP20chr1188924586chr11102480761116KAANFSFRNTLEDHGAAGCTGCCAATTTCAGCTTTAGAAATACACTGGAAGATCACGGGG
TYR-MMP20chr1188924586chr11102480761217AANFSFRNTLEDHGDCTGCCAATTTCAGCTTTAGAAATACACTGGAAGATCACGGGGATT
TYR-MMP20chr1188924586chr11102480761318ANFSFRNTLEDHGDSCCAATTTCAGCTTTAGAAATACACTGGAAGATCACGGGGATTCCT

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Information of the samples that have these potential fusion neoantigens of TYR-MMP20

check button These samples were reported as having these fusion breakpoints. For individual breakpoints, we checked the open reading frames considering multiple gene isoforms and chose the in-frame fusion genes only. Then, we made fusion protein sequences and predicted the fusion neoantigens. These fusion-positive samples may have these potential fusion neoantigens.
Cancer typeFusion geneHchrHbpHenstTchrTbpTenstSample
SKCMTYR-MMP20chr1188924586ENST00000263321chr11102480761ENST00000260228TCGA-EB-A57M-01A

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Potential target of CAR-T therapy development for TYR-MMP20

check button Predicted 3D structure. We used RoseTTAFold.

check buttonRetention 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, to provide the retention of the transmembrane domain, we only show the protein feature retention information of those transmembrane features


* Minus value of BPloci means that the break point is located before the CDS.
- In-frame and retained 'Transmembrane'.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

check button Subcellular localization prediction of the transmembrane domain retained fusion proteins
* We used DeepLoc 1.0. The order of the X-axis of the barplot is as follows: Entry_ID, Localization, Type, Nucleus, Cytoplasm, Extracellular, Mitochondrion, Cell_membrane, Endoplasmic_reticulum, Plastid, Golgi.apparatus, Lysosome.Vacuole, Peroxisome. Y-axis is the output score of DeepLoc. Clicking the image will open a new tab with a large image.
HgeneHchrHbpHenstTgeneTchrTbpTenstDeepLoc result

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Related Drugs to TYR-MMP20

check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to TYR-MMP20

check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource