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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:WDR44-PHF21A

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: WDR44-PHF21A
FusionPDB ID: 98986
FusionGDB2.0 ID: 98986
HgeneTgene
Gene symbol

WDR44

PHF21A

Gene ID

54521

51317

Gene nameWD repeat domain 44PHD finger protein 21A
SynonymsRAB11BP|RPH11|SYM-4BHC80|BM-006|IDDBCS|NEDMS
Cytomap

Xq24

11p11.2

Type of geneprotein-codingprotein-coding
DescriptionWD repeat-containing protein 44rabphilin-11PHD finger protein 21ABHC80aBRAF35-HDAC complex protein BHC80BRAF35/HDAC2 complex (80 kDa)
Modification date2020031320200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST idsENST00000254029, ENST00000371822, 
ENST00000371825, ENST00000493448, 
ENST00000527753, ENST00000257821, 
ENST00000323180, ENST00000418153, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score4 X 4 X 4=6413 X 10 X 8=1040
# samples 514
** MAII scorelog2(5/64*10)=-0.356143810225275
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(14/1040*10)=-2.89308479608349
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: WDR44 [Title/Abstract] AND PHF21A [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: WDR44 [Title/Abstract] AND PHF21A [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)WDR44(117566857)-PHF21A(45959863), # samples:1
Anticipated loss of major functional domain due to fusion event.WDR44-PHF21A 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.
WDR44-PHF21A 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.
WDR44-PHF21A 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.
WDR44-PHF21A 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


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/chrX:117566857/chr11:45959863)
- 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 WDR44 (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 PHF21A (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)
ENST00000371822WDR44chrX117566857+ENST00000257821PHF21Achr1145959863-744922074312800789
ENST00000371822WDR44chrX117566857+ENST00000323180PHF21Achr1145959863-420322074312800789
ENST00000371822WDR44chrX117566857+ENST00000418153PHF21Achr1145959863-328822074312800789
ENST00000254029WDR44chrX117566857+ENST00000257821PHF21Achr1145959863-748822463952839814
ENST00000254029WDR44chrX117566857+ENST00000323180PHF21Achr1145959863-424222463952839814
ENST00000254029WDR44chrX117566857+ENST00000418153PHF21Achr1145959863-332722463952839814
ENST00000371825WDR44chrX117566857+ENST00000257821PHF21Achr1145959863-745422123612805814
ENST00000371825WDR44chrX117566857+ENST00000323180PHF21Achr1145959863-420822123612805814
ENST00000371825WDR44chrX117566857+ENST00000418153PHF21Achr1145959863-329322123612805814

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
ENST00000371822ENST00000257821WDR44chrX117566857+PHF21Achr1145959863-0.0015575090.9984425
ENST00000371822ENST00000323180WDR44chrX117566857+PHF21Achr1145959863-0.0012975060.9987025
ENST00000371822ENST00000418153WDR44chrX117566857+PHF21Achr1145959863-0.0027749950.99722505
ENST00000254029ENST00000257821WDR44chrX117566857+PHF21Achr1145959863-0.0019015580.99809843
ENST00000254029ENST00000323180WDR44chrX117566857+PHF21Achr1145959863-0.0016213230.99837863
ENST00000254029ENST00000418153WDR44chrX117566857+PHF21Achr1145959863-0.0030858350.99691415
ENST00000371825ENST00000257821WDR44chrX117566857+PHF21Achr1145959863-0.0018749850.998125
ENST00000371825ENST00000323180WDR44chrX117566857+PHF21Achr1145959863-0.0015622480.9984377
ENST00000371825ENST00000418153WDR44chrX117566857+PHF21Achr1145959863-0.003000640.9969994

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 WDR44-PHF21A

check button +/-13 AA sequence from the breakpoints of the fusion protein sequences.
HgeneHchrHbpTgeneTchrTbpLength(fusion protein)BP in fusion proteinPeptide
WDR44chrX117566857PHF21Achr11459598632207587FCKYKGHTADLLDLSWSKGDIHEDFC
WDR44chrX117566857PHF21Achr11459598632212612FCKYKGHTADLLDLSWSKGDIHEDFC
WDR44chrX117566857PHF21Achr11459598632246612FCKYKGHTADLLDLSWSKGDIHEDFC

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Potential FusionNeoAntigen Information of WDR44-PHF21A 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.
WDR44-PHF21A_117566857_45959863.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)
WDR44-PHF21AchrX117566857chr11459598632246HLA-B39:01GHTADLLDL0.99190.9133514
WDR44-PHF21AchrX117566857chr11459598632246HLA-B58:01TADLLDLSW0.98610.9834716
WDR44-PHF21AchrX117566857chr11459598632246HLA-B38:02GHTADLLDL0.98540.956514
WDR44-PHF21AchrX117566857chr11459598632246HLA-B38:01GHTADLLDL0.98490.9569514
WDR44-PHF21AchrX117566857chr11459598632246HLA-B57:01TADLLDLSW0.97070.9906716
WDR44-PHF21AchrX117566857chr11459598632246HLA-B58:02TADLLDLSW0.93530.9723716
WDR44-PHF21AchrX117566857chr11459598632246HLA-B53:01TADLLDLSW0.9250.7968716
WDR44-PHF21AchrX117566857chr11459598632246HLA-B35:08TADLLDLSW0.80590.9308716
WDR44-PHF21AchrX117566857chr11459598632246HLA-B57:03TADLLDLSW0.72080.9957716
WDR44-PHF21AchrX117566857chr11459598632246HLA-B57:01HTADLLDLSW0.99960.9853616
WDR44-PHF21AchrX117566857chr11459598632246HLA-B58:01HTADLLDLSW0.99930.97616
WDR44-PHF21AchrX117566857chr11459598632246HLA-B58:02HTADLLDLSW0.99830.9607616
WDR44-PHF21AchrX117566857chr11459598632246HLA-B15:17HTADLLDLSW0.99740.959616
WDR44-PHF21AchrX117566857chr11459598632246HLA-B15:16HTADLLDLSW0.99580.9266616
WDR44-PHF21AchrX117566857chr11459598632246HLA-B57:03HTADLLDLSW0.96150.9942616
WDR44-PHF21AchrX117566857chr11459598632246HLA-B53:01HTADLLDLSW0.94180.7275616
WDR44-PHF21AchrX117566857chr11459598632246HLA-A32:13HTADLLDLSW0.84750.9716616
WDR44-PHF21AchrX117566857chr11459598632246HLA-B57:01GHTADLLDLSW0.99980.9579516
WDR44-PHF21AchrX117566857chr11459598632246HLA-B58:01GHTADLLDLSW0.99790.9429516
WDR44-PHF21AchrX117566857chr11459598632246HLA-B39:05GHTADLLDL0.98660.9034514
WDR44-PHF21AchrX117566857chr11459598632246HLA-B38:05GHTADLLDL0.98490.9569514
WDR44-PHF21AchrX117566857chr11459598632246HLA-B57:04TADLLDLSW0.98140.889716
WDR44-PHF21AchrX117566857chr11459598632246HLA-B57:10TADLLDLSW0.97070.9906716
WDR44-PHF21AchrX117566857chr11459598632246HLA-B57:02TADLLDLSW0.92640.9726716
WDR44-PHF21AchrX117566857chr11459598632246HLA-B53:02TADLLDLSW0.85810.7708716
WDR44-PHF21AchrX117566857chr11459598632246HLA-B15:09GHTADLLDL0.83330.8841514
WDR44-PHF21AchrX117566857chr11459598632246HLA-B15:13TADLLDLSW0.72090.9003716
WDR44-PHF21AchrX117566857chr11459598632246HLA-B39:11GHTADLLDL0.64650.8904514
WDR44-PHF21AchrX117566857chr11459598632246HLA-B51:06TADLLDLSW0.09260.7204716
WDR44-PHF21AchrX117566857chr11459598632246HLA-B57:04HTADLLDLSW0.99970.8881616
WDR44-PHF21AchrX117566857chr11459598632246HLA-B57:10HTADLLDLSW0.99960.9853616
WDR44-PHF21AchrX117566857chr11459598632246HLA-B57:02HTADLLDLSW0.99770.9791616
WDR44-PHF21AchrX117566857chr11459598632246HLA-B58:06HTADLLDLSW0.99610.9107616
WDR44-PHF21AchrX117566857chr11459598632246HLA-B15:13HTADLLDLSW0.98020.8943616
WDR44-PHF21AchrX117566857chr11459598632246HLA-B15:24HTADLLDLSW0.96350.9601616
WDR44-PHF21AchrX117566857chr11459598632246HLA-A32:01HTADLLDLSW0.95820.9792616
WDR44-PHF21AchrX117566857chr11459598632246HLA-A25:01HTADLLDLSW0.91640.9618616
WDR44-PHF21AchrX117566857chr11459598632246HLA-B53:02HTADLLDLSW0.77780.709616
WDR44-PHF21AchrX117566857chr11459598632246HLA-B57:10GHTADLLDLSW0.99980.9579516
WDR44-PHF21AchrX117566857chr11459598632246HLA-B57:04GHTADLLDLSW0.99960.8383516

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Potential FusionNeoAntigen Information of WDR44-PHF21A 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 WDR44-PHF21A

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
3513HTADLLDLSWSKGDWDR44PHF21AchrX117566857chr11459598632246

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Filtering FusionNeoAntigens Through Checking the Interaction with HLAs in 3D of WDR44-PHF21A

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-B14:023BVN3513HTADLLDLSWSKGD-7.15543-7.26883
HLA-B14:023BVN3513HTADLLDLSWSKGD-4.77435-5.80965
HLA-B52:013W393513HTADLLDLSWSKGD-6.80875-6.92215
HLA-B52:013W393513HTADLLDLSWSKGD-4.20386-5.23916
HLA-A11:014UQ23513HTADLLDLSWSKGD-7.5194-8.5547
HLA-A11:014UQ23513HTADLLDLSWSKGD-6.9601-7.0735
HLA-A24:025HGA3513HTADLLDLSWSKGD-7.52403-7.63743
HLA-A24:025HGA3513HTADLLDLSWSKGD-5.82433-6.85963
HLA-B27:056PYJ3513HTADLLDLSWSKGD-3.28285-4.31815
HLA-B44:053DX83513HTADLLDLSWSKGD-5.91172-6.94702
HLA-B44:053DX83513HTADLLDLSWSKGD-4.24346-4.35686

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Vaccine Design for the FusionNeoAntigens of WDR44-PHF21A

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
WDR44-PHF21AchrX117566857chr1145959863514GHTADLLDLCTCCTTGATCTTTCATGGTCTAAAGGT
WDR44-PHF21AchrX117566857chr1145959863516GHTADLLDLSWCTCCTTGATCTTTCATGGTCTAAAGGTGATATT
WDR44-PHF21AchrX117566857chr1145959863616HTADLLDLSWCTTGATCTTTCATGGTCTAAAGGTGATATT
WDR44-PHF21AchrX117566857chr1145959863716TADLLDLSWGATCTTTCATGGTCTAAAGGTGATATT

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 WDR44-PHF21A

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
OVWDR44-PHF21AchrX117566857ENST00000254029chr1145959863ENST00000257821TCGA-29-1694

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Potential target of CAR-T therapy development for WDR44-PHF21A

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 WDR44-PHF21A

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 WDR44-PHF21A

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