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Center for Computational Systems Medicine
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Fusion Gene Summary

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Fusion Gene ORF analysis

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Fusion Genomic Features

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Fusion Protein Features

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Fusion Gene Sequence

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Fusion Gene PPI analysis

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Related Drugs

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Related Diseases

Fusion gene:YAP1-USP2 (FusionGDB2 ID:99220)

Fusion Gene Summary for YAP1-USP2

check button Fusion gene summary
Fusion gene informationFusion gene name: YAP1-USP2
Fusion gene ID: 99220
HgeneTgene
Gene symbol

YAP1

USP2

Gene ID

10413

9099

Gene nameYes1 associated transcriptional regulatorubiquitin specific peptidase 2
SynonymsCOB1|YAP|YAP2|YAP65|YKIUBP41|USP9
Cytomap

11q22.1

11q23.3

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 homologubiquitin carboxyl-terminal hydrolase 241 kDa ubiquitin-specific proteasedeubiquitinating enzyme 2ubiquitin specific protease 12ubiquitin specific protease 9ubiquitin thioesterase 2ubiquitin-specific-processing protease 2
Modification date2020032920200313
UniProtAcc.

O75604

Ensembl transtripts involved in fusion geneENST00000526343, ENST00000282441, 
ENST00000537274, ENST00000345877, 
ENST00000531439, ENST00000524575, 
ENST00000528834, 		ENST00000455332, 
ENST00000260187, ENST00000525735, 
Fusion gene scores* DoF score23 X 13 X 14=41863 X 1 X 3=9
# samples 253
** MAII scorelog2(25/4186*10)=-4.06557231159362
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(3/9*10)=1.73696559416621
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: YAP1 [Title/Abstract] AND USP2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointYAP1(101985125)-USP2(119230944), # samples:2
Anticipated loss of major functional domain due to fusion event.YAP1-USP2 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
YAP1-USP2 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
YAP1-USP2 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

TgeneUSP2

GO:0016579

protein deubiquitination

17290220|19838211|19917254

TgeneUSP2

GO:0050821

protein stabilization

17290220


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.

check buttonFusion gene breakpoints across USP2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* All genome coordinats were lifted-over on hg19.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
SourceDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
ChimerDB4ESCATCGA-R6-A6XQ-01BYAP1chr11

101985125

+USP2chr11

119230944

-
ChimerDB4ESCATCGA-R6-A6XQYAP1chr11

101985125

+USP2chr11

119230944

-


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Fusion Gene ORF analysis for YAP1-USP2

check button Open reading frame (ORF) analsis of fusion genes based on Ensembl gene isoform structure.
* Click on the break point to see the gene structure around the break point region using the UCSC Genome Browser.
ORFHenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrand
Frame-shiftENST00000526343ENST00000455332YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000526343ENST00000260187YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000526343ENST00000525735YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000282441ENST00000455332YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000282441ENST00000260187YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000282441ENST00000525735YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000537274ENST00000455332YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000537274ENST00000260187YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000537274ENST00000525735YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000345877ENST00000455332YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000345877ENST00000260187YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000345877ENST00000525735YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000531439ENST00000455332YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000531439ENST00000260187YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000531439ENST00000525735YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000524575ENST00000455332YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000524575ENST00000260187YAP1chr11

101985125

+USP2chr11

119230944

-
Frame-shiftENST00000524575ENST00000525735YAP1chr11

101985125

+USP2chr11

119230944

-
intron-3CDSENST00000528834ENST00000455332YAP1chr11

101985125

+USP2chr11

119230944

-
intron-3CDSENST00000528834ENST00000260187YAP1chr11

101985125

+USP2chr11

119230944

-
intron-3CDSENST00000528834ENST00000525735YAP1chr11

101985125

+USP2chr11

119230944

-

check buttonORFfinder result based on the fusion transcript sequence of in-frame fusion genes.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)

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

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Fusion Genomic Features for YAP1-USP2


check buttonFusionAI prediction of the potential fusion gene breakpoint based on the pre-mature RNA sequence context (+/- 5kb of individual partner genes, total 20kb length sequence). FusionAI is a fusion gene breakpoint classifier based on convolutional neural network by comparing the fusion positive and negative sequence context of ~ 20K fusion gene data. From here, we can have the relative potentency of the 20K genomic sequence how individual sequnce will be likely used as the gene fusion breakpoints.
HgeneHchrHbpHstrandTgeneTchrTbpTstrand1-pp (fusion gene breakpoint)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for YAP1-USP2


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
.USP2

O75604

FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Hydrolase that deubiquitinates polyubiquitinated target proteins such as MDM2, MDM4 and CCND1 (PubMed:17290220, PubMed:19917254, PubMed:19838211). Isoform 1 and isoform 4 possess both ubiquitin-specific peptidase and isopeptidase activities (By similarity). Deubiquitinates MDM2 without reversing MDM2-mediated p53/TP53 ubiquitination and thus indirectly promotes p53/TP53 degradation and limits p53 activity (PubMed:17290220, PubMed:19838211). Has no deubiquitinase activity against p53/TP53 (PubMed:17290220). Prevents MDM2-mediated degradation of MDM4 (PubMed:17290220). Plays a role in the G1/S cell-cycle progression in normal and cancer cells (PubMed:19917254). Regulates the circadian clock by modulating its intrinsic circadian rhythm and its capacity to respond to external cues (By similarity). Associates with clock proteins and deubiquitinates core clock component PER1 but does not affect its overall stability (By similarity). Regulates the nucleocytoplasmic shuttling and nuclear retention of PER1 and its repressive role on the clock transcription factors CLOCK and ARNTL/BMAL1 (By similarity). Plays a role in the regulation of myogenic differentiation of embryonic muscle cells (By similarity). {ECO:0000250|UniProtKB:O88623, ECO:0000250|UniProtKB:Q5U349, ECO:0000269|PubMed:17290220, ECO:0000269|PubMed:19838211, ECO:0000269|PubMed:19917254}.; FUNCTION: [Isoform 4]: Circadian clock output effector that regulates Ca(2+) absorption in the small intestine. Probably functions by regulating protein levels of the membrane scaffold protein NHERF4 in a rhythmic manner, and is therefore likely to control Ca(2+) membrane permeability mediated by the Ca(2+) channel TRPV6 in the intestine. {ECO:0000250|UniProtKB:O88623}.

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, because of limited space for viewing, we only show the protein feature retention information belong to the 13 regional features. All retention annotation result can be downloaded at

download page


* Minus value of BPloci means that the break pointn is located before the CDS.
- In-frame and retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note


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Fusion Gene Sequence for YAP1-USP2


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences. To have fusion amino acid sequence, we ran ORFfinder and chose the longest ORF among the all predicted ones.

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Fusion Gene PPI Analysis for YAP1-USP2


check button Go to ChiPPI (Chimeric Protein-Protein interactions) to see the chimeric PPI interaction in

ChiPPI page.


check button Protein-protein interactors with each fusion partner protein in wild-type (BIOGRID-3.4.160)
HgeneHgene's interactorsTgeneTgene's interactors


check button - Retained PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost PPIs in in-frame fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


check button - Retained PPIs, but lost function due to frame-shift fusion.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs for YAP1-USP2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases for YAP1-USP2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneYAP1C3805432COLOBOMA, OCULAR, WITH OR WITHOUT HEARING IMPAIRMENT, CLEFT LIP/PALATE, AND/OR MENTAL RETARDATION3CTD_human;GENOMICS_ENGLAND
HgeneYAP1C0006118Brain Neoplasms1CTD_human
HgeneYAP1C0006142Malignant neoplasm of breast1CTD_human
HgeneYAP1C0009402Colorectal Carcinoma1CTD_human
HgeneYAP1C0009404Colorectal Neoplasms1CTD_human
HgeneYAP1C0018916Hemangioma1CTD_human
HgeneYAP1C0027627Neoplasm Metastasis1CTD_human
HgeneYAP1C0027819Neuroblastoma1CTD_human
HgeneYAP1C0153633Malignant neoplasm of brain1CTD_human
HgeneYAP1C0205788Histiocytoid hemangioma1CTD_human
HgeneYAP1C0205789Hemangioma, Intramuscular1CTD_human
HgeneYAP1C0206656Embryonal Rhabdomyosarcoma1CTD_human
HgeneYAP1C0206732Epithelioid hemangioendothelioma1ORPHANET
HgeneYAP1C0235874Disease Exacerbation1CTD_human
HgeneYAP1C0496899Benign neoplasm of brain, unspecified1CTD_human
HgeneYAP1C0677608Chorioangioma1CTD_human
HgeneYAP1C0678222Breast Carcinoma1CTD_human
HgeneYAP1C0750974Brain Tumor, Primary1CTD_human
HgeneYAP1C0750977Recurrent Brain Neoplasm1CTD_human
HgeneYAP1C0750979Primary malignant neoplasm of brain1CTD_human
HgeneYAP1C0795902Coloboma, cleft lip-palate and mental retardation syndrome1ORPHANET
HgeneYAP1C0919267ovarian neoplasm1CTD_human
HgeneYAP1C1140680Malignant neoplasm of ovary1CTD_human
HgeneYAP1C1168401Squamous cell carcinoma of the head and neck1CTD_human
HgeneYAP1C1257931Mammary Neoplasms, Human1CTD_human
HgeneYAP1C1458155Mammary Neoplasms1CTD_human
HgeneYAP1C1527390Neoplasms, Intracranial1CTD_human
HgeneYAP1C1959588Angioma1CTD_human
HgeneYAP1C2239176Liver carcinoma1CTD_human
HgeneYAP1C3539878Triple Negative Breast Neoplasms1CTD_human
HgeneYAP1C4704874Mammary Carcinoma, Human1CTD_human
TgeneUSP2C2239176Liver carcinoma1CTD_human