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:YAP1-BIRC2

Fusion Gene and Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: YAP1-BIRC2
FusionPDB ID: 99877
FusionGDB2.0 ID: 99877
HgeneTgene
Gene symbol

YAP1

BIRC2

Gene ID

10413

329

Gene nameYes1 associated transcriptional regulatorbaculoviral IAP repeat containing 2
SynonymsCOB1|YAP|YAP2|YAP65|YKIAPI1|HIAP2|Hiap-2|MIHB|RNF48|c-IAP1|cIAP1
Cytomap

11q22.1

11q22.2

Type of geneprotein-codingprotein-coding
Descriptiontranscriptional coactivator YAP165 kDa Yes-associated proteinYes associated protein 1protein yorkie homologyes-associated protein 1yes-associated protein 2yes-associated protein YAP65 homologyorkie homologbaculoviral IAP repeat-containing protein 2IAP homolog BIAP-2NFR2-TRAF signalling complex proteinRING finger protein 48RING-type E3 ubiquitin transferase BIRC2TNFR2-TRAF-signaling complex protein 2apoptosis inhibitor 1cellular inhibitor of apoptos
Modification date2020032920200320
UniProtAcc.

Q13490

Main function of 5'-partner protein: FUNCTION: Multi-functional protein which regulates not only caspases and apoptosis, but also modulates inflammatory signaling and immunity, mitogenic kinase signaling, and cell proliferation, as well as cell invasion and metastasis. Acts as an E3 ubiquitin-protein ligase regulating NF-kappa-B signaling and regulates both canonical and non-canonical NF-kappa-B signaling by acting in opposite directions: acts as a positive regulator of the canonical pathway and suppresses constitutive activation of non-canonical NF-kappa-B signaling. The target proteins for its E3 ubiquitin-protein ligase activity include: RIPK1, RIPK2, RIPK3, RIPK4, CASP3, CASP7, CASP8, TRAF2, DIABLO/SMAC, MAP3K14/NIK, MAP3K5/ASK1, IKBKG/NEMO, IKBKE and MXD1/MAD1. Can also function as an E3 ubiquitin-protein ligase of the NEDD8 conjugation pathway, targeting effector caspases for neddylation and inactivation. Acts as an important regulator of innate immune signaling via regulation of Toll-like receptors (TLRs), Nodlike receptors (NLRs) and RIG-I like receptors (RLRs), collectively referred to as pattern recognition receptors (PRRs). Protects cells from spontaneous formation of the ripoptosome, a large multi-protein complex that has the capability to kill cancer cells in a caspase-dependent and caspase-independent manner. Suppresses ripoptosome formation by ubiquitinating RIPK1 and CASP8. Can stimulate the transcriptional activity of E2F1. Plays a role in the modulation of the cell cycle. {ECO:0000269|PubMed:15665297, ECO:0000269|PubMed:18082613, ECO:0000269|PubMed:21145488, ECO:0000269|PubMed:21653699, ECO:0000269|PubMed:21931591, ECO:0000269|PubMed:23453969}.
Ensembl transtripts involved in fusion geneENST idsENST00000282441, ENST00000345877, 
ENST00000524575, ENST00000526343, 
ENST00000531439, ENST00000537274, 
ENST00000528834, 		ENST00000527910, 
ENST00000227758, ENST00000530675, 
ENST00000532672, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score23 X 13 X 14=41867 X 11 X 4=308
# samples 259
** MAII scorelog2(25/4186*10)=-4.06557231159362
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/308*10)=-1.77493344436523
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Fusion gene context

PubMed: YAP1 [Title/Abstract] AND BIRC2 [Title/Abstract] AND fusion [Title/Abstract]

Fusion neoantigen context

PubMed: YAP1 [Title/Abstract] AND BIRC2 [Title/Abstract] AND neoantigen [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)BIRC2(102221674)-YAP1(102033187), # samples:1
YAP1(102080295)-BIRC2(102248226), # samples:1
YAP1(101985125)-BIRC2(102233626), # samples:1
YAP1(102080295)-BIRC2(102248227), # samples:1
YAP1(102080295)-BIRC2(102248410), # samples:1
YAP1(101985125)-BIRC2(102233627), # samples:1
YAP1(101985124)-BIRC2(102233626), # samples:1
Anticipated loss of major functional domain due to fusion event.BIRC2-YAP1 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.
BIRC2-YAP1 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.
YAP1-BIRC2 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.
YAP1-BIRC2 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.
YAP1-BIRC2 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.
YAP1-BIRC2 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.
YAP1-BIRC2 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
YAP1-BIRC2 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
YAP1-BIRC2 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
YAP1-BIRC2 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
HgeneYAP1

GO:0006974

cellular response to DNA damage stimulus

18280240

HgeneYAP1

GO:0008283

cell proliferation

17974916

HgeneYAP1

GO:0032570

response to progesterone

16772533

HgeneYAP1

GO:0033148

positive regulation of intracellular estrogen receptor signaling pathway

16772533

HgeneYAP1

GO:0045893

positive regulation of transcription, DNA-templated

20368466

HgeneYAP1

GO:0045944

positive regulation of transcription by RNA polymerase II

25796446

HgeneYAP1

GO:0050767

regulation of neurogenesis

25433207

HgeneYAP1

GO:0050847

progesterone receptor signaling pathway

16772533

HgeneYAP1

GO:0060242

contact inhibition

17974916

HgeneYAP1

GO:0065003

protein-containing complex assembly

20368466

HgeneYAP1

GO:0071480

cellular response to gamma radiation

18280240

HgeneYAP1

GO:0072091

regulation of stem cell proliferation

25433207

TgeneBIRC2

GO:0000209

protein polyubiquitination

11907583

TgeneBIRC2

GO:0043066

negative regulation of apoptotic process

21525013

TgeneBIRC2

GO:0043161

proteasome-mediated ubiquitin-dependent protein catabolic process

11907583

TgeneBIRC2

GO:0051726

regulation of cell cycle

15665297

TgeneBIRC2

GO:1902523

positive regulation of protein K63-linked ubiquitination

21931591

TgeneBIRC2

GO:1902524

positive regulation of protein K48-linked ubiquitination

21931591

TgeneBIRC2

GO:1902527

positive regulation of protein monoubiquitination

21931591



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/chr11:102221674/chr11:102033187)
- 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 YAP1 (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 BIRC2 (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)
ENST00000526343YAP1chr11101985125+ENST00000530675BIRC2chr11102233626+18759603881821477
ENST00000526343YAP1chr11101985125+ENST00000227758BIRC2chr11102233626+23099603881821477
ENST00000526343YAP1chr11101985125+ENST00000532672BIRC2chr11102233626+23089603881821477
ENST00000282441YAP1chr11101985125+ENST00000530675BIRC2chr11102233626+18759603881821477
ENST00000282441YAP1chr11101985125+ENST00000227758BIRC2chr11102233626+23099603881821477
ENST00000282441YAP1chr11101985125+ENST00000532672BIRC2chr11102233626+23089603881821477
ENST00000537274YAP1chr11101985125+ENST00000530675BIRC2chr11102233626+18579423701803477
ENST00000537274YAP1chr11101985125+ENST00000227758BIRC2chr11102233626+22919423701803477
ENST00000537274YAP1chr11101985125+ENST00000532672BIRC2chr11102233626+22909423701803477
ENST00000345877YAP1chr11101985125+ENST00000530675BIRC2chr11102233626+18579423701803477
ENST00000345877YAP1chr11101985125+ENST00000227758BIRC2chr11102233626+22919423701803477
ENST00000345877YAP1chr11101985125+ENST00000532672BIRC2chr11102233626+22909423701803477
ENST00000531439YAP1chr11101985125+ENST00000530675BIRC2chr11102233626+148757201433477
ENST00000531439YAP1chr11101985125+ENST00000227758BIRC2chr11102233626+192157201433477
ENST00000531439YAP1chr11101985125+ENST00000532672BIRC2chr11102233626+192057201433477
ENST00000524575YAP1chr11101985125+ENST00000530675BIRC2chr11102233626+13984832621344360
ENST00000524575YAP1chr11101985125+ENST00000227758BIRC2chr11102233626+18324832621344360
ENST00000524575YAP1chr11101985125+ENST00000532672BIRC2chr11102233626+18314832621344360
ENST00000526343YAP1chr11101985125+ENST00000530675BIRC2chr11102233627+18759603881821477
ENST00000526343YAP1chr11101985125+ENST00000227758BIRC2chr11102233627+23099603881821477
ENST00000526343YAP1chr11101985125+ENST00000532672BIRC2chr11102233627+23089603881821477
ENST00000282441YAP1chr11101985125+ENST00000530675BIRC2chr11102233627+18759603881821477
ENST00000282441YAP1chr11101985125+ENST00000227758BIRC2chr11102233627+23099603881821477
ENST00000282441YAP1chr11101985125+ENST00000532672BIRC2chr11102233627+23089603881821477
ENST00000537274YAP1chr11101985125+ENST00000530675BIRC2chr11102233627+18579423701803477
ENST00000537274YAP1chr11101985125+ENST00000227758BIRC2chr11102233627+22919423701803477
ENST00000537274YAP1chr11101985125+ENST00000532672BIRC2chr11102233627+22909423701803477
ENST00000345877YAP1chr11101985125+ENST00000530675BIRC2chr11102233627+18579423701803477
ENST00000345877YAP1chr11101985125+ENST00000227758BIRC2chr11102233627+22919423701803477
ENST00000345877YAP1chr11101985125+ENST00000532672BIRC2chr11102233627+22909423701803477
ENST00000531439YAP1chr11101985125+ENST00000530675BIRC2chr11102233627+148757201433477
ENST00000531439YAP1chr11101985125+ENST00000227758BIRC2chr11102233627+192157201433477
ENST00000531439YAP1chr11101985125+ENST00000532672BIRC2chr11102233627+192057201433477
ENST00000524575YAP1chr11101985125+ENST00000530675BIRC2chr11102233627+13984832621344360
ENST00000524575YAP1chr11101985125+ENST00000227758BIRC2chr11102233627+18324832621344360
ENST00000524575YAP1chr11101985125+ENST00000532672BIRC2chr11102233627+18314832621344360
ENST00000526343YAP1chr11101985124+ENST00000530675BIRC2chr11102233626+18759603881821477
ENST00000526343YAP1chr11101985124+ENST00000227758BIRC2chr11102233626+23099603881821477
ENST00000526343YAP1chr11101985124+ENST00000532672BIRC2chr11102233626+23089603881821477
ENST00000282441YAP1chr11101985124+ENST00000530675BIRC2chr11102233626+18759603881821477
ENST00000282441YAP1chr11101985124+ENST00000227758BIRC2chr11102233626+23099603881821477
ENST00000282441YAP1chr11101985124+ENST00000532672BIRC2chr11102233626+23089603881821477
ENST00000537274YAP1chr11101985124+ENST00000530675BIRC2chr11102233626+18579423701803477
ENST00000537274YAP1chr11101985124+ENST00000227758BIRC2chr11102233626+22919423701803477
ENST00000537274YAP1chr11101985124+ENST00000532672BIRC2chr11102233626+22909423701803477
ENST00000345877YAP1chr11101985124+ENST00000530675BIRC2chr11102233626+18579423701803477
ENST00000345877YAP1chr11101985124+ENST00000227758BIRC2chr11102233626+22919423701803477
ENST00000345877YAP1chr11101985124+ENST00000532672BIRC2chr11102233626+22909423701803477
ENST00000531439YAP1chr11101985124+ENST00000530675BIRC2chr11102233626+148757201433477
ENST00000531439YAP1chr11101985124+ENST00000227758BIRC2chr11102233626+192157201433477
ENST00000531439YAP1chr11101985124+ENST00000532672BIRC2chr11102233626+192057201433477
ENST00000524575YAP1chr11101985124+ENST00000530675BIRC2chr11102233626+13984832621344360
ENST00000524575YAP1chr11101985124+ENST00000227758BIRC2chr11102233626+18324832621344360
ENST00000524575YAP1chr11101985124+ENST00000532672BIRC2chr11102233626+18314832621344360

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
ENST00000526343ENST00000530675YAP1chr11101985125+BIRC2chr11102233626+0.0018696010.9981304
ENST00000526343ENST00000227758YAP1chr11101985125+BIRC2chr11102233626+0.0005486790.99945134
ENST00000526343ENST00000532672YAP1chr11101985125+BIRC2chr11102233626+0.0005448550.99945515
ENST00000282441ENST00000530675YAP1chr11101985125+BIRC2chr11102233626+0.0018696010.9981304
ENST00000282441ENST00000227758YAP1chr11101985125+BIRC2chr11102233626+0.0005486790.99945134
ENST00000282441ENST00000532672YAP1chr11101985125+BIRC2chr11102233626+0.0005448550.99945515
ENST00000537274ENST00000530675YAP1chr11101985125+BIRC2chr11102233626+0.0018309720.99816906
ENST00000537274ENST00000227758YAP1chr11101985125+BIRC2chr11102233626+0.0005445690.9994554
ENST00000537274ENST00000532672YAP1chr11101985125+BIRC2chr11102233626+0.0005411390.99945885
ENST00000345877ENST00000530675YAP1chr11101985125+BIRC2chr11102233626+0.0018309720.99816906
ENST00000345877ENST00000227758YAP1chr11101985125+BIRC2chr11102233626+0.0005445690.9994554
ENST00000345877ENST00000532672YAP1chr11101985125+BIRC2chr11102233626+0.0005411390.99945885
ENST00000531439ENST00000530675YAP1chr11101985125+BIRC2chr11102233626+0.0010380660.9989619
ENST00000531439ENST00000227758YAP1chr11101985125+BIRC2chr11102233626+0.0003331330.9996669
ENST00000531439ENST00000532672YAP1chr11101985125+BIRC2chr11102233626+0.0003331850.9996668
ENST00000524575ENST00000530675YAP1chr11101985125+BIRC2chr11102233626+0.0009965380.99900347
ENST00000524575ENST00000227758YAP1chr11101985125+BIRC2chr11102233626+0.0005705260.9994294
ENST00000524575ENST00000532672YAP1chr11101985125+BIRC2chr11102233626+0.0005699950.99943
ENST00000526343ENST00000530675YAP1chr11101985125+BIRC2chr11102233627+0.0018696010.9981304
ENST00000526343ENST00000227758YAP1chr11101985125+BIRC2chr11102233627+0.0005486790.99945134
ENST00000526343ENST00000532672YAP1chr11101985125+BIRC2chr11102233627+0.0005448550.99945515
ENST00000282441ENST00000530675YAP1chr11101985125+BIRC2chr11102233627+0.0018696010.9981304
ENST00000282441ENST00000227758YAP1chr11101985125+BIRC2chr11102233627+0.0005486790.99945134
ENST00000282441ENST00000532672YAP1chr11101985125+BIRC2chr11102233627+0.0005448550.99945515
ENST00000537274ENST00000530675YAP1chr11101985125+BIRC2chr11102233627+0.0018309720.99816906
ENST00000537274ENST00000227758YAP1chr11101985125+BIRC2chr11102233627+0.0005445690.9994554
ENST00000537274ENST00000532672YAP1chr11101985125+BIRC2chr11102233627+0.0005411390.99945885
ENST00000345877ENST00000530675YAP1chr11101985125+BIRC2chr11102233627+0.0018309720.99816906
ENST00000345877ENST00000227758YAP1chr11101985125+BIRC2chr11102233627+0.0005445690.9994554
ENST00000345877ENST00000532672YAP1chr11101985125+BIRC2chr11102233627+0.0005411390.99945885
ENST00000531439ENST00000530675YAP1chr11101985125+BIRC2chr11102233627+0.0010380660.9989619
ENST00000531439ENST00000227758YAP1chr11101985125+BIRC2chr11102233627+0.0003331330.9996669
ENST00000531439ENST00000532672YAP1chr11101985125+BIRC2chr11102233627+0.0003331850.9996668
ENST00000524575ENST00000530675YAP1chr11101985125+BIRC2chr11102233627+0.0009965380.99900347
ENST00000524575ENST00000227758YAP1chr11101985125+BIRC2chr11102233627+0.0005705260.9994294
ENST00000524575ENST00000532672YAP1chr11101985125+BIRC2chr11102233627+0.0005699950.99943
ENST00000526343ENST00000530675YAP1chr11101985124+BIRC2chr11102233626+0.0018696010.9981304
ENST00000526343ENST00000227758YAP1chr11101985124+BIRC2chr11102233626+0.0005486790.99945134
ENST00000526343ENST00000532672YAP1chr11101985124+BIRC2chr11102233626+0.0005448550.99945515
ENST00000282441ENST00000530675YAP1chr11101985124+BIRC2chr11102233626+0.0018696010.9981304
ENST00000282441ENST00000227758YAP1chr11101985124+BIRC2chr11102233626+0.0005486790.99945134
ENST00000282441ENST00000532672YAP1chr11101985124+BIRC2chr11102233626+0.0005448550.99945515
ENST00000537274ENST00000530675YAP1chr11101985124+BIRC2chr11102233626+0.0018309720.99816906
ENST00000537274ENST00000227758YAP1chr11101985124+BIRC2chr11102233626+0.0005445690.9994554
ENST00000537274ENST00000532672YAP1chr11101985124+BIRC2chr11102233626+0.0005411390.99945885
ENST00000345877ENST00000530675YAP1chr11101985124+BIRC2chr11102233626+0.0018309720.99816906
ENST00000345877ENST00000227758YAP1chr11101985124+BIRC2chr11102233626+0.0005445690.9994554
ENST00000345877ENST00000532672YAP1chr11101985124+BIRC2chr11102233626+0.0005411390.99945885
ENST00000531439ENST00000530675YAP1chr11101985124+BIRC2chr11102233626+0.0010380660.9989619
ENST00000531439ENST00000227758YAP1chr11101985124+BIRC2chr11102233626+0.0003331330.9996669
ENST00000531439ENST00000532672YAP1chr11101985124+BIRC2chr11102233626+0.0003331850.9996668
ENST00000524575ENST00000530675YAP1chr11101985124+BIRC2chr11102233626+0.0009965380.99900347
ENST00000524575ENST00000227758YAP1chr11101985124+BIRC2chr11102233626+0.0005705260.9994294
ENST00000524575ENST00000532672YAP1chr11101985124+BIRC2chr11102233626+0.0005699950.99943

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 YAP1-BIRC2

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 YAP1-BIRC2 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 YAP1-BIRC2 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 YAP1-BIRC2

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 YAP1-BIRC2

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 YAP1-BIRC2

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 YAP1-BIRC2

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 YAP1-BIRC2

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 YAP1-BIRC2

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

Top

Related Diseases to YAP1-BIRC2

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