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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:MET-TES

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: MET-TES
FusionPDB ID: 53037
FusionGDB2.0 ID: 53037
HgeneTgene
Gene symbol

MET

TES

Gene ID

8731

26136

Gene nameRNA guanine-7 methyltransferasetestin LIM domain protein
SynonymsCMT1|CMT1c|MET|Met|RG7MT1|cm1p|hCMT1|hMetTESS|TESS-2
Cytomap

18p11.21

7q31.2

Type of geneprotein-codingprotein-coding
DescriptionmRNA cap guanine-N7 methyltransferaseRNA (guanine-7-) methyltransferasehcm1pmRNA (guanine-7-)methyltransferasemRNA (guanine-N(7)-)-methyltransferasemRNA cap methyltransferasetestintestis derived transcript (3 LIM domains)
Modification date2020032920200313
UniProtAcc

Q9H1A3

Main function of 5'-partner protein:

PRSS21

Main function of 5'-partner protein: 314
Ensembl transtripts involved in fusion geneENST idsENST00000318493, ENST00000397752, 
ENST00000436117, ENST00000495962, 
ENST00000539704, 
ENST00000485009, 
ENST00000393481, ENST00000537767, 
ENST00000358204, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score11 X 10 X 9=9909 X 6 X 7=378
# samples 1610
** MAII scorelog2(16/990*10)=-2.62935662007961
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(10/378*10)=-1.91838623444635
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: MET [Title/Abstract] AND TES [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: MET [Title/Abstract] AND TES [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)MET(116340338)-TES(115874588), # samples:1
TES(115850788)-MET(116339125), # samples:1
TES(115850788)-MET(116371722), # samples:1
Anticipated loss of major functional domain due to fusion event.MET-TES 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.
MET-TES 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.
MET-TES 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.
MET-TES 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.
TES-MET 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.
TES-MET 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.
* 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
HgeneMET

GO:0006370

7-methylguanosine mRNA capping

27422871



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/chr7:116340338/chr7:115874588)
- 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 MET (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 TES (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)
ENST00000397752METchr7116340338+ENST00000358204TESchr7115874588+394014002002638812
ENST00000318493METchr7116340338+ENST00000358204TESchr7115874588+392713871872625812
ENST00000436117METchr7116340338+ENST00000358204TESchr7115874588+3740120002438812

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
ENST00000397752ENST00000358204METchr7116340338+TESchr7115874588+0.0003106440.99968934
ENST00000318493ENST00000358204METchr7116340338+TESchr7115874588+0.0003126040.99968743
ENST00000436117ENST00000358204METchr7116340338+TESchr7115874588+0.0003086520.99969137

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 MET-TES

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
METchr7116340338TESchr71158745881200400HFYGPNHEHCFNRMGLGHEQGFGAPC
METchr7116340338TESchr71158745881387400HFYGPNHEHCFNRMGLGHEQGFGAPC
METchr7116340338TESchr71158745881400400HFYGPNHEHCFNRMGLGHEQGFGAPC

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Potential FusionNeoAntigen Information of MET-TES 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.
MET-TES_116340338_115874588.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)
MET-TESchr7116340338chr71158745881387HLA-B18:01HEHCFNRM0.99780.9644614
MET-TESchr7116340338chr71158745881387HLA-B39:01EHCFNRMGL0.99760.812716
MET-TESchr7116340338chr71158745881387HLA-B39:06EHCFNRMGL0.99340.642716
MET-TESchr7116340338chr71158745881387HLA-B38:02EHCFNRMGL0.99230.8711716
MET-TESchr7116340338chr71158745881387HLA-B39:01NHEHCFNRM0.99120.9553514
MET-TESchr7116340338chr71158745881387HLA-B38:01EHCFNRMGL0.99010.8527716
MET-TESchr7116340338chr71158745881387HLA-B38:02NHEHCFNRM0.98720.9483514
MET-TESchr7116340338chr71158745881387HLA-B38:01NHEHCFNRM0.98580.9228514
MET-TESchr7116340338chr71158745881387HLA-B15:10NHEHCFNRM0.84630.5418514
MET-TESchr7116340338chr71158745881387HLA-B15:37NHEHCFNRM0.62110.624514
MET-TESchr7116340338chr71158745881387HLA-B27:04NRMGLGHEQGF10.56271122
MET-TESchr7116340338chr71158745881387HLA-B27:05NRMGLGHEQGF10.57241122
MET-TESchr7116340338chr71158745881387HLA-B15:18NRMGLGHEQGF0.99380.66311122
MET-TESchr7116340338chr71158745881387HLA-B39:12EHCFNRMGL0.99730.8248716
MET-TESchr7116340338chr71158745881387HLA-B39:05EHCFNRMGL0.99170.7916716
MET-TESchr7116340338chr71158745881387HLA-B39:09NHEHCFNRM0.99080.6112514
MET-TESchr7116340338chr71158745881387HLA-B39:05NHEHCFNRM0.98460.9481514
MET-TESchr7116340338chr71158745881387HLA-B73:01NRMGLGHEQ0.93060.92181120
MET-TESchr7116340338chr71158745881387HLA-B14:03EHCFNRMGL0.2630.7089716
MET-TESchr7116340338chr71158745881387HLA-B27:03NRMGLGHEQGF0.99870.59411122
MET-TESchr7116340338chr71158745881387HLA-B39:12NRMGLGHEQGF0.99750.9421122
MET-TESchr7116340338chr71158745881387HLA-B18:05HEHCFNRM0.99780.9644614
MET-TESchr7116340338chr71158745881387HLA-B39:31EHCFNRMGL0.99750.8122716
MET-TESchr7116340338chr71158745881387HLA-B38:05EHCFNRMGL0.99010.8527716
MET-TESchr7116340338chr71158745881387HLA-B38:05NHEHCFNRM0.98580.9228514
MET-TESchr7116340338chr71158745881387HLA-B39:11EHCFNRMGL0.65220.6517716
MET-TESchr7116340338chr71158745881387HLA-B39:11NHEHCFNRM0.54040.7519514
MET-TESchr7116340338chr71158745881387HLA-B27:09NRMGLGHEQGF0.99990.55921122

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Potential FusionNeoAntigen Information of MET-TES 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.

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)

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Fusion breakpoint peptide structures of MET-TES

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
3300HEHCFNRMGLGHEQMETTESchr7116340338chr71158745881387

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of MET-TES

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-B14:023BVN3300HEHCFNRMGLGHEQ-7.15543-7.26883
HLA-B14:023BVN3300HEHCFNRMGLGHEQ-4.77435-5.80965
HLA-B52:013W393300HEHCFNRMGLGHEQ-6.80875-6.92215
HLA-B52:013W393300HEHCFNRMGLGHEQ-4.20386-5.23916
HLA-A11:014UQ23300HEHCFNRMGLGHEQ-7.5194-8.5547
HLA-A11:014UQ23300HEHCFNRMGLGHEQ-6.9601-7.0735
HLA-A24:025HGA3300HEHCFNRMGLGHEQ-7.52403-7.63743
HLA-A24:025HGA3300HEHCFNRMGLGHEQ-5.82433-6.85963
HLA-B27:056PYJ3300HEHCFNRMGLGHEQ-3.28285-4.31815
HLA-B44:053DX83300HEHCFNRMGLGHEQ-5.91172-6.94702
HLA-B44:053DX83300HEHCFNRMGLGHEQ-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of MET-TES

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
MET-TESchr7116340338chr71158745881120NRMGLGHEQAATAGGATGGGCTTAGGTCACGAGCAA
MET-TESchr7116340338chr71158745881122NRMGLGHEQGFAATAGGATGGGCTTAGGTCACGAGCAAGGATTT
MET-TESchr7116340338chr7115874588514NHEHCFNRMAATCATGAGCACTGCTTTAATAGGATG
MET-TESchr7116340338chr7115874588614HEHCFNRMCATGAGCACTGCTTTAATAGGATG
MET-TESchr7116340338chr7115874588716EHCFNRMGLGAGCACTGCTTTAATAGGATGGGCTTA

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

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Information of the samples that have these potential fusion neoantigens of MET-TES

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
THCAMET-TESchr7116340338ENST00000318493chr7115874588ENST00000358204TCGA-ET-A3BU-01A

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Potential target of CAR-T therapy development for MET-TES

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 MET-TES

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 MET-TES

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