FusionNeoAntigen Logo

Home

Download

Statistics

Examples

Help

Contact

Terms of Use

Center for Computational Systems Medicine
leaf

Fusion Gene and Fusion Protein Summary

leaf

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

leaf

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

leaf

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

leaf

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

leaf

Fusion Breakpoint 14 AA Peptide Structure - (RoseTTAFold)

leaf

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

leaf

Vaccine Design for the FusionNeoAntigens (RNA/protein sequences)

leaf

Potential target of CAR-T therapy development

leaf

Information on the samples that have these potential fusion neoantigens

leaf

Fusion Protein Targeting Drugs - (Manual Curation)

leaf

Fusion Protein Related diseases - (Manual Curation)

Fusion Protein:PTGDS-CLU

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PTGDS-CLU
FusionPDB ID: 69940
FusionGDB2.0 ID: 69940
HgeneTgene
Gene symbol

PTGDS

CLU

Gene ID

5730

1191

Gene nameprostaglandin D2 synthaseclusterin
SynonymsL-PGDS|LPGDS|PDS|PGD2|PGDS|PGDS2AAG4|APO-J|APOJ|CLI|CLU1|CLU2|KUB1|NA1/NA2|SGP-2|SGP2|SP-40|TRPM-2|TRPM2
Cytomap

9q34.3

8p21.1

Type of geneprotein-codingprotein-coding
Descriptionprostaglandin-H2 D-isomerasePGD2 synthasebeta-trace proteincerebrin-28glutathione-independent PGD synthaseglutathione-independent PGD synthetaselipocalin-type prostaglandin D synthaseprostaglandin D synthaseprostaglandin D2 synthase 21kDa (brain)clusterinaging-associated protein 4apolipoprotein Jcomplement cytolysis inhibitorcomplement lysis inhibitorcomplement-associated protein SP-40,40epididymis secretory sperm binding proteinku70-binding protein 1sulfated glycoprotein 2testosterone-r
Modification date2020031320200327
UniProtAcc.

Q15846

Main function of 5'-partner protein:
Ensembl transtripts involved in fusion geneENST idsENST00000224167, ENST00000371625, 
ENST00000460340, 
ENST00000523500, 
ENST00000546343, ENST00000560366, 
ENST00000316403, ENST00000405140, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score17 X 10 X 6=102023 X 24 X 12=6624
# samples 1930
** MAII scorelog2(19/1020*10)=-2.42449782852791
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(30/6624*10)=-4.46466826700344
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: PTGDS [Title/Abstract] AND CLU [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: PTGDS [Title/Abstract] AND CLU [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PTGDS(139872144)-CLU(27455767), # samples:1
Anticipated loss of major functional domain due to fusion event.PTGDS-CLU 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.
PTGDS-CLU 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.
PTGDS-CLU seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
PTGDS-CLU seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PTGDS-CLU seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor 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
HgenePTGDS

GO:0001516

prostaglandin biosynthetic process

20667974

TgeneCLU

GO:0000902

cell morphogenesis

15857407

TgeneCLU

GO:0001774

microglial cell activation

15857407

TgeneCLU

GO:0017038

protein import

24446231

TgeneCLU

GO:0031333

negative regulation of protein complex assembly

22179788|23106396

TgeneCLU

GO:0031334

positive regulation of protein complex assembly

22179788

TgeneCLU

GO:0032760

positive regulation of tumor necrosis factor production

15857407

TgeneCLU

GO:0045429

positive regulation of nitric oxide biosynthetic process

15857407

TgeneCLU

GO:0050821

protein stabilization

11123922|12176985

TgeneCLU

GO:0051131

chaperone-mediated protein complex assembly

17412999

TgeneCLU

GO:0051788

response to misfolded protein

19996109

TgeneCLU

GO:0061077

chaperone-mediated protein folding

11123922

TgeneCLU

GO:0061518

microglial cell proliferation

15857407

TgeneCLU

GO:1900221

regulation of amyloid-beta clearance

24446231

TgeneCLU

GO:1901214

regulation of neuron death

17412999

TgeneCLU

GO:1901216

positive regulation of neuron death

15857407

TgeneCLU

GO:1902430

negative regulation of amyloid-beta formation

12047389|17412999

TgeneCLU

GO:1905907

negative regulation of amyloid fibril formation

22179788



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/chr9:139872144/chr8:27455767)
- 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 PTGDS (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 CLU (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


Top

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)
ENST00000224167PTGDSchr9139872144+ENST00000316403CLUchr827455767-1523189971657104
ENST00000224167PTGDSchr9139872144+ENST00000405140CLUchr827455767-6321893247981
ENST00000371625PTGDSchr9139872144+ENST00000316403CLUchr827455767-1522188970656104
ENST00000371625PTGDSchr9139872144+ENST00000405140CLUchr827455767-6311883237881

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
ENST00000224167ENST00000316403PTGDSchr9139872144+CLUchr827455767-0.691635670.30836433
ENST00000224167ENST00000405140PTGDSchr9139872144+CLUchr827455767-0.261685580.7383144
ENST00000371625ENST00000316403PTGDSchr9139872144+CLUchr827455767-0.72665880.27334118
ENST00000371625ENST00000405140PTGDSchr9139872144+CLUchr827455767-0.273852470.72614753

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

Top

Fusion Protein Breakpoint Sequences for PTGDS-CLU

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

Top

Potential FusionNeoAntigen Information of PTGDS-CLU 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.

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)

Top

Potential FusionNeoAntigen Information of PTGDS-CLU 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)

Top

Fusion breakpoint peptide structures of PTGDS-CLU

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.

Top

Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of PTGDS-CLU

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

Top

Vaccine Design for the FusionNeoAntigens of PTGDS-CLU

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

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

Top

Information of the samples that have these potential fusion neoantigens of PTGDS-CLU

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

Top

Potential target of CAR-T therapy development for PTGDS-CLU

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

Top

Related Drugs to PTGDS-CLU

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

Top

Related Diseases to PTGDS-CLU

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
TgeneCLUC0022660Kidney Failure, Acute6CTD_human
TgeneCLUC1565662Acute Kidney Insufficiency6CTD_human
TgeneCLUC2609414Acute kidney injury6CTD_human
TgeneCLUC0002395Alzheimer's Disease3CTD_human
TgeneCLUC0011265Presenile dementia3CTD_human
TgeneCLUC0022658Kidney Diseases3CTD_human
TgeneCLUC0276496Familial Alzheimer Disease (FAD)3CTD_human
TgeneCLUC0494463Alzheimer Disease, Late Onset3CTD_human
TgeneCLUC0546126Acute Confusional Senile Dementia3CTD_human
TgeneCLUC0750900Alzheimer's Disease, Focal Onset3CTD_human
TgeneCLUC0750901Alzheimer Disease, Early Onset3CTD_human
TgeneCLUC0013221Drug toxicity2CTD_human
TgeneCLUC0029408Degenerative polyarthritis2CTD_human
TgeneCLUC0041755Adverse reaction to drug2CTD_human
TgeneCLUC0086743Osteoarthrosis Deformans2CTD_human
TgeneCLUC0019193Hepatitis, Toxic1CTD_human
TgeneCLUC0022333Jacksonian Seizure1CTD_human
TgeneCLUC0024141Lupus Erythematosus, Systemic1CTD_human
TgeneCLUC0025202melanoma1CTD_human
TgeneCLUC0027686Pathologic Neovascularization1CTD_human
TgeneCLUC0033578Prostatic Neoplasms1CTD_human
TgeneCLUC0036341Schizophrenia1PSYGENET
TgeneCLUC0036572Seizures1CTD_human
TgeneCLUC0087031Juvenile-Onset Still Disease1CTD_human
TgeneCLUC0149958Complex partial seizures1CTD_human
TgeneCLUC0234533Generalized seizures1CTD_human
TgeneCLUC0234535Clonic Seizures1CTD_human
TgeneCLUC0234985Mental deterioration1CTD_human
TgeneCLUC0242380Libman-Sacks Disease1CTD_human
TgeneCLUC0270824Visual seizure1CTD_human
TgeneCLUC0270844Tonic Seizures1CTD_human
TgeneCLUC0270846Epileptic drop attack1CTD_human
TgeneCLUC0333641Atrophic1CTD_human
TgeneCLUC0338656Impaired cognition1CTD_human
TgeneCLUC0376358Malignant neoplasm of prostate1CTD_human
TgeneCLUC0422850Seizures, Somatosensory1CTD_human
TgeneCLUC0422852Seizures, Auditory1CTD_human
TgeneCLUC0422853Olfactory seizure1CTD_human
TgeneCLUC0422854Gustatory seizure1CTD_human
TgeneCLUC0422855Vertiginous seizure1CTD_human
TgeneCLUC0494475Tonic - clonic seizures1CTD_human
TgeneCLUC0751056Non-epileptic convulsion1CTD_human
TgeneCLUC0751110Single Seizure1CTD_human
TgeneCLUC0751123Atonic Absence Seizures1CTD_human
TgeneCLUC0751494Convulsive Seizures1CTD_human
TgeneCLUC0751495Seizures, Focal1CTD_human
TgeneCLUC0751496Seizures, Sensory1CTD_human
TgeneCLUC0860207Drug-Induced Liver Disease1CTD_human
TgeneCLUC1262760Hepatitis, Drug-Induced1CTD_human
TgeneCLUC1270972Mild cognitive disorder1CTD_human
TgeneCLUC1862939AMYOTROPHIC LATERAL SCLEROSIS 11CTD_human
TgeneCLUC1862941Amyotrophic Lateral Sclerosis, Sporadic1CTD_human
TgeneCLUC3495559Juvenile arthritis1CTD_human
TgeneCLUC3495874Nonepileptic Seizures1CTD_human
TgeneCLUC3658290Drug-Induced Acute Liver Injury1CTD_human
TgeneCLUC3714758Juvenile psoriatic arthritis1CTD_human
TgeneCLUC4048158Convulsions1CTD_human
TgeneCLUC4277682Chemical and Drug Induced Liver Injury1CTD_human
TgeneCLUC4279912Chemically-Induced Liver Toxicity1CTD_human
TgeneCLUC4316903Absence Seizures1CTD_human
TgeneCLUC4317109Epileptic Seizures1CTD_human
TgeneCLUC4317123Myoclonic Seizures1CTD_human
TgeneCLUC4505436Generalized Absence Seizures1CTD_human
TgeneCLUC4551993Amyotrophic Lateral Sclerosis, Familial1CTD_human
TgeneCLUC4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
TgeneCLUC4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human