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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:PHF20-SPAG4

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PHF20-SPAG4
FusionPDB ID: 64827
FusionGDB2.0 ID: 64827
HgeneTgene
Gene symbol

PHF20

SPAG4

Gene ID

51230

6676

Gene namePHD finger protein 20sperm associated antigen 4
SynonymsC20orf104|GLEA2|HCA58|NZF|TDRD20A|TZPCT127|SUN4
Cytomap

20q11.22-q11.23

20q11.22

Type of geneprotein-codingprotein-coding
DescriptionPHD finger protein 20glioma-expressed antigen 2hepatocellular carcinoma-associated antigen 58novel zinc finger proteintranscription factor TZPtudor domain containing 20Asperm-associated antigen 4 proteinSUN domain-containing protein 4Sad1 and UNC84 domain containing 4acrosomal protein ACR55cancer/testis antigen 127outer dense fiber-associated protein SPAG4sperm tail protein
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000439301, ENST00000481202, 
ENST00000374012, 
ENST00000374273, 
ENST00000462896, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score19 X 17 X 11=35534 X 3 X 3=36
# samples 297
** MAII scorelog2(29/3553*10)=-3.61491288331629
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/36*10)=0.959358015502654
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Fusion gene context

PubMed: PHF20 [Title/Abstract] AND SPAG4 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PHF20 [Title/Abstract] AND SPAG4 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PHF20(34487570)-SPAG4(34207117), # samples:3
Anticipated loss of major functional domain due to fusion event.PHF20-SPAG4 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.
PHF20-SPAG4 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.
PHF20-SPAG4 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.
PHF20-SPAG4 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
HgenePHF20

GO:0043981

histone H4-K5 acetylation

20018852

HgenePHF20

GO:0043982

histone H4-K8 acetylation

20018852

HgenePHF20

GO:0043984

histone H4-K16 acetylation

20018852



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/chr20:34487570/chr20:34207117)
- 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 PHF20 (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 SPAG4 (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)
ENST00000374012PHF20chr2034487570+ENST00000374273SPAG4chr2034207117+223816901232210695
ENST00000374012PHF20chr2034487570+ENST00000374273SPAG4chr2034207116+223816901232210695

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
ENST00000374012ENST00000374273PHF20chr2034487570+SPAG4chr2034207117+0.0007546780.9992454
ENST00000374012ENST00000374273PHF20chr2034487570+SPAG4chr2034207116+0.0007546780.9992454

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 PHF20-SPAG4

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
PHF20chr2034487570SPAG4chr20342071161690521QETLTRKRVSASSPRASIDLQKTSHD
PHF20chr2034487570SPAG4chr20342071171690521QETLTRKRVSASSPRASIDLQKTSHD

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Potential FusionNeoAntigen Information of PHF20-SPAG4 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.
PHF20-SPAG4_34487570_34207116.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)
PHF20-SPAG4chr2034487570chr20342071161690HLA-B27:05KRVSASSPR0.99880.691615
PHF20-SPAG4chr2034487570chr20342071161690HLA-A30:08RVSASSPRA0.97830.7363716
PHF20-SPAG4chr2034487570chr20342071161690HLA-B52:01SASSPRASI0.9770.8149918
PHF20-SPAG4chr2034487570chr20342071161690HLA-B27:05SPRASIDLQK0.93540.63711222
PHF20-SPAG4chr2034487570chr20342071161690HLA-B27:05SSPRASIDLQK0.99470.67571122
PHF20-SPAG4chr2034487570chr20342071161690HLA-C03:07SASSPRASI0.99940.9729918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C15:06SASSPRASI0.99880.9135918
PHF20-SPAG4chr2034487570chr20342071161690HLA-B27:14KRVSASSPR0.99870.7002615
PHF20-SPAG4chr2034487570chr20342071161690HLA-C03:19SASSPRASI0.9980.9818918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C03:08SASSPRASI0.99780.9184918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C02:06SASSPRASI0.99080.9709918
PHF20-SPAG4chr2034487570chr20342071161690HLA-B07:12SASSPRASI0.99030.5853918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C06:03SASSPRASI0.97920.9919918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C12:04SASSPRASI0.97750.9933918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C01:17SASSPRASI0.97540.9619918
PHF20-SPAG4chr2034487570chr20342071161690HLA-B51:07SASSPRASI0.97060.6576918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C12:12SASSPRASI0.96760.8993918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C08:04SASSPRASI0.95810.9604918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C08:13SASSPRASI0.95810.9604918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C01:30SASSPRASI0.9460.9688918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C01:17SSPRASIDL0.85940.94451120
PHF20-SPAG4chr2034487570chr20342071161690HLA-C08:03SASSPRASI0.76370.9786918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C01:30SSPRASIDL0.72810.95371120
PHF20-SPAG4chr2034487570chr20342071161690HLA-B27:14SPRASIDLQK0.89850.56981222
PHF20-SPAG4chr2034487570chr20342071161690HLA-B27:14SSPRASIDLQK0.98950.61531122
PHF20-SPAG4chr2034487570chr20342071161690HLA-B67:01SPRASIDL0.50270.52231220
PHF20-SPAG4chr2034487570chr20342071161690HLA-C15:02SASSPRASI0.9990.8598918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C15:05SASSPRASI0.99890.8981918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C03:05SASSPRASI0.99890.9372918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C03:17SASSPRASI0.9980.9704918
PHF20-SPAG4chr2034487570chr20342071161690HLA-B27:10KRVSASSPR0.99790.7967615
PHF20-SPAG4chr2034487570chr20342071161690HLA-C03:04SASSPRASI0.99640.9879918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C03:03SASSPRASI0.99640.9879918
PHF20-SPAG4chr2034487570chr20342071161690HLA-B07:13SASSPRASI0.99220.8867918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C16:04SASSPRASI0.98860.9724918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C01:02SASSPRASI0.98330.9616918
PHF20-SPAG4chr2034487570chr20342071161690HLA-A30:01RVSASSPRA0.97860.8502716
PHF20-SPAG4chr2034487570chr20342071161690HLA-C16:02SASSPRASI0.97640.9956918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C03:06SASSPRASI0.95260.9873918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C12:02SASSPRASI0.94520.9642918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C12:03SASSPRASI0.94140.9762918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C16:01SASSPRASI0.88960.9848918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C01:02SSPRASIDL0.8730.94331120
PHF20-SPAG4chr2034487570chr20342071161690HLA-C01:03SASSPRASI0.86430.9492918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C01:03SSPRASIDL0.83790.92691120
PHF20-SPAG4chr2034487570chr20342071161690HLA-C08:01SASSPRASI0.76370.9786918
PHF20-SPAG4chr2034487570chr20342071161690HLA-C17:01SASSPRASI0.74710.9524918

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Potential FusionNeoAntigen Information of PHF20-SPAG4 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 PHF20-SPAG4

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
4587KRVSASSPRASIDLPHF20SPAG4chr2034487570chr20342071161690

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PHF20-SPAG4

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-B14:023BVN4587KRVSASSPRASIDL-7.15543-7.26883
HLA-B14:023BVN4587KRVSASSPRASIDL-4.77435-5.80965
HLA-B52:013W394587KRVSASSPRASIDL-6.80875-6.92215
HLA-B52:013W394587KRVSASSPRASIDL-4.20386-5.23916
HLA-A11:014UQ24587KRVSASSPRASIDL-7.5194-8.5547
HLA-A11:014UQ24587KRVSASSPRASIDL-6.9601-7.0735
HLA-A24:025HGA4587KRVSASSPRASIDL-7.52403-7.63743
HLA-A24:025HGA4587KRVSASSPRASIDL-5.82433-6.85963
HLA-B27:056PYJ4587KRVSASSPRASIDL-3.28285-4.31815
HLA-B44:053DX84587KRVSASSPRASIDL-5.91172-6.94702
HLA-B44:053DX84587KRVSASSPRASIDL-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of PHF20-SPAG4

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
PHF20-SPAG4chr2034487570chr20342071161120SSPRASIDLCCCCAAGAGCCTCCATCGACCTGCAGA
PHF20-SPAG4chr2034487570chr20342071161122SSPRASIDLQKCCCCAAGAGCCTCCATCGACCTGCAGAAGACAT
PHF20-SPAG4chr2034487570chr20342071161220SPRASIDLCAAGAGCCTCCATCGACCTGCAGA
PHF20-SPAG4chr2034487570chr20342071161222SPRASIDLQKCAAGAGCCTCCATCGACCTGCAGAAGACAT
PHF20-SPAG4chr2034487570chr2034207116615KRVSASSPRGGGTCTCTGCCAGTTCCCCAAGAGCCT
PHF20-SPAG4chr2034487570chr2034207116716RVSASSPRATCTCTGCCAGTTCCCCAAGAGCCTCCA
PHF20-SPAG4chr2034487570chr2034207116918SASSPRASICCAGTTCCCCAAGAGCCTCCATCGACC

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 PHF20-SPAG4

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
ACCPHF20-SPAG4chr2034487570ENST00000374012chr2034207116ENST00000374273TCGA-OR-A5JT

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Potential target of CAR-T therapy development for PHF20-SPAG4

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 PHF20-SPAG4

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 PHF20-SPAG4

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