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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:EBF2-YAP1

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: EBF2-YAP1
FusionPDB ID: 24824
FusionGDB2.0 ID: 24824
HgeneTgene
Gene symbol

EBF2

YAP1

Gene ID

64641

10413

Gene nameEBF transcription factor 2Yes1 associated transcriptional regulator
SynonymsCOE2|EBF-2|O/E-3|OE-3COB1|YAP|YAP2|YAP65|YKI
Cytomap

8p21.2

11q22.1

Type of geneprotein-codingprotein-coding
Descriptiontranscription factor COE2Collier, Olf and EBF 2Collier, Olf and EBF transcription factor 2OLF-1/EBF-LIKE 3early B cell factor 2metencephalon-mesencephalnon-olfactory transcription factor 1transcriptional coactivator YAP165 kDa Yes-associated proteinYes associated protein 1protein yorkie homologyes-associated protein 1yes-associated protein 2yes-associated protein YAP65 homologyorkie homolog
Modification date2020031320200329
UniProtAcc

Q9HAK2

.
Ensembl transtripts involved in fusion geneENST idsENST00000408929, ENST00000520164, 
ENST00000535548, 		ENST00000528834, 
ENST00000282441, ENST00000345877, 
ENST00000524575, ENST00000526343, 
ENST00000531439, ENST00000537274, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score1 X 1 X 1=120 X 10 X 13=2600
# samples 121
** MAII scorelog2(1/1*10)=3.32192809488736log2(21/2600*10)=-3.63005039024969
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: EBF2 [Title/Abstract] AND YAP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)EBF2(25890600)-YAP1(102033186), # samples:1
Anticipated loss of major functional domain due to fusion event.EBF2-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.
EBF2-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.
EBF2-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.
EBF2-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.
EBF2-YAP1 seems lost the major protein functional domain in Hgene partner, which is a transcription factor due to the frame-shifted ORF.
EBF2-YAP1 seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
EBF2-YAP1 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
TgeneYAP1

GO:0006974

cellular response to DNA damage stimulus

18280240

TgeneYAP1

GO:0008283

cell proliferation

17974916

TgeneYAP1

GO:0032570

response to progesterone

16772533

TgeneYAP1

GO:0033148

positive regulation of intracellular estrogen receptor signaling pathway

16772533

TgeneYAP1

GO:0045893

positive regulation of transcription, DNA-templated

20368466

TgeneYAP1

GO:0045944

positive regulation of transcription by RNA polymerase II

25796446

TgeneYAP1

GO:0050767

regulation of neurogenesis

25433207

TgeneYAP1

GO:0050847

progesterone receptor signaling pathway

16772533

TgeneYAP1

GO:0060242

contact inhibition

17974916

TgeneYAP1

GO:0065003

protein-containing complex assembly

20368466

TgeneYAP1

GO:0071480

cellular response to gamma radiation

18280240

TgeneYAP1

GO:0072091

regulation of stem cell proliferation

25433207


check buttonFusion gene breakpoints across EBF2 (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 YAP1 (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 Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4Non-CancerTCGA-BH-A0BC-11AEBF2chr8

25890600

-YAP1chr11

102033186

+


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Fusion ORF Analysis


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)
ENST00000520164EBF2chr825890600-ENST00000526343YAP1chr11102033186+252210895381869443
ENST00000520164EBF2chr825890600-ENST00000282441YAP1chr11102033186+551510895382031497
ENST00000520164EBF2chr825890600-ENST00000537274YAP1chr11102033186+547910895381995485
ENST00000520164EBF2chr825890600-ENST00000345877YAP1chr11102033186+536510895381881447
ENST00000520164EBF2chr825890600-ENST00000531439YAP1chr11102033186+200710895381983481
ENST00000520164EBF2chr825890600-ENST00000524575YAP1chr11102033186+224410895382031497

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
ENST00000520164ENST00000526343EBF2chr825890600-YAP1chr11102033186+0.0040499280.9959501
ENST00000520164ENST00000282441EBF2chr825890600-YAP1chr11102033186+0.0002904040.99970955
ENST00000520164ENST00000537274EBF2chr825890600-YAP1chr11102033186+0.0002648120.9997352
ENST00000520164ENST00000345877EBF2chr825890600-YAP1chr11102033186+0.0003651760.99963486
ENST00000520164ENST00000531439EBF2chr825890600-YAP1chr11102033186+0.0110092770.98899066
ENST00000520164ENST00000524575EBF2chr825890600-YAP1chr11102033186+0.0104112570.98958874

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>24824_24824_1_EBF2-YAP1_EBF2_chr8_25890600_ENST00000520164_YAP1_chr11_102033186_ENST00000282441_length(amino acids)=497AA_BP=183
MFGIQDTLGRGPTLKEKSLGAEMDSVRSWVRNVGVVDANVAAQSGVALSRAHFEKQPPSNLRKSNFFHFVLALYDRQGQPVEIERTAFVD
FVENDKEQGNEKTNNGTHYKLQLLYSNGVRTEQDLYVRLIDSVTKQPIAYEGQNKNPEMCRVLLTHEVMCSRCCEKKSCGNRNETPSDPV
IIDSHIDQTTTWQDPRKAMLSQMNVTAPTSPPVQQNMMNSASGPLPDGWEQAMTQDGEIYYINHKNKTTSWLDPRLDPRFAMNQRISQSA
PVKQPPPLAPQSPQGGVMGGSNSNQQQQMRLQQLQMEKERLRLKQQELLRQAMRNINPSTANSPKCQELALRSQLPTLEQDGGTQNPVSS
PGMSQELRTMTTNSSDPFLNSGTYHSRDESTDSGLSMSSYSVPRTPDDFLNSVDEMDTGDTINQSTLPSQQNRFPDYLEAIPGTNVDLGT

--------------------------------------------------------------

>24824_24824_2_EBF2-YAP1_EBF2_chr8_25890600_ENST00000520164_YAP1_chr11_102033186_ENST00000345877_length(amino acids)=447AA_BP=183
MFGIQDTLGRGPTLKEKSLGAEMDSVRSWVRNVGVVDANVAAQSGVALSRAHFEKQPPSNLRKSNFFHFVLALYDRQGQPVEIERTAFVD
FVENDKEQGNEKTNNGTHYKLQLLYSNGVRTEQDLYVRLIDSVTKQPIAYEGQNKNPEMCRVLLTHEVMCSRCCEKKSCGNRNETPSDPV
IIDSHIDQTTTWQDPRKAMLSQMNVTAPTSPPVQQNMMNSASAMNQRISQSAPVKQPPPLAPQSPQGGVMGGSNSNQQQQMRLQQLQMEK
ERLRLKQQELLRQVRPQELALRSQLPTLEQDGGTQNPVSSPGMSQELRTMTTNSSDPFLNSGTYHSRDESTDSGLSMSSYSVPRTPDDFL

--------------------------------------------------------------

>24824_24824_3_EBF2-YAP1_EBF2_chr8_25890600_ENST00000520164_YAP1_chr11_102033186_ENST00000524575_length(amino acids)=497AA_BP=183
MFGIQDTLGRGPTLKEKSLGAEMDSVRSWVRNVGVVDANVAAQSGVALSRAHFEKQPPSNLRKSNFFHFVLALYDRQGQPVEIERTAFVD
FVENDKEQGNEKTNNGTHYKLQLLYSNGVRTEQDLYVRLIDSVTKQPIAYEGQNKNPEMCRVLLTHEVMCSRCCEKKSCGNRNETPSDPV
IIDSHIDQTTTWQDPRKAMLSQMNVTAPTSPPVQQNMMNSASGPLPDGWEQAMTQDGEIYYINHKNKTTSWLDPRLDPRFAMNQRISQSA
PVKQPPPLAPQSPQGGVMGGSNSNQQQQMRLQQLQMEKERLRLKQQELLRQAMRNINPSTANSPKCQELALRSQLPTLEQDGGTQNPVSS
PGMSQELRTMTTNSSDPFLNSGTYHSRDESTDSGLSMSSYSVPRTPDDFLNSVDEMDTGDTINQSTLPSQQNRFPDYLEAIPGTNVDLGT

--------------------------------------------------------------

>24824_24824_4_EBF2-YAP1_EBF2_chr8_25890600_ENST00000520164_YAP1_chr11_102033186_ENST00000526343_length(amino acids)=443AA_BP=183
MFGIQDTLGRGPTLKEKSLGAEMDSVRSWVRNVGVVDANVAAQSGVALSRAHFEKQPPSNLRKSNFFHFVLALYDRQGQPVEIERTAFVD
FVENDKEQGNEKTNNGTHYKLQLLYSNGVRTEQDLYVRLIDSVTKQPIAYEGQNKNPEMCRVLLTHEVMCSRCCEKKSCGNRNETPSDPV
IIDSHIDQTTTWQDPRKAMLSQMNVTAPTSPPVQQNMMNSASAMNQRISQSAPVKQPPPLAPQSPQGGVMGGSNSNQQQQMRLQQLQMEK
ERLRLKQQELLRQELALRSQLPTLEQDGGTQNPVSSPGMSQELRTMTTNSSDPFLNSGTYHSRDESTDSGLSMSSYSVPRTPDDFLNSVD

--------------------------------------------------------------

>24824_24824_5_EBF2-YAP1_EBF2_chr8_25890600_ENST00000520164_YAP1_chr11_102033186_ENST00000531439_length(amino acids)=481AA_BP=183
MFGIQDTLGRGPTLKEKSLGAEMDSVRSWVRNVGVVDANVAAQSGVALSRAHFEKQPPSNLRKSNFFHFVLALYDRQGQPVEIERTAFVD
FVENDKEQGNEKTNNGTHYKLQLLYSNGVRTEQDLYVRLIDSVTKQPIAYEGQNKNPEMCRVLLTHEVMCSRCCEKKSCGNRNETPSDPV
IIDSHIDQTTTWQDPRKAMLSQMNVTAPTSPPVQQNMMNSASGPLPDGWEQAMTQDGEIYYINHKNKTTSWLDPRLDPRFAMNQRISQSA
PVKQPPPLAPQSPQGGVMGGSNSNQQQQMRLQQLQMEKERLRLKQQELLRQELALRSQLPTLEQDGGTQNPVSSPGMSQELRTMTTNSSD
PFLNSGTYHSRDESTDSGLSMSSYSVPRTPDDFLNSVDEMDTGDTINQSTLPSQQNRFPDYLEAIPGTNVDLGTLEGDGMNIEGEELMPS

--------------------------------------------------------------

>24824_24824_6_EBF2-YAP1_EBF2_chr8_25890600_ENST00000520164_YAP1_chr11_102033186_ENST00000537274_length(amino acids)=485AA_BP=183
MFGIQDTLGRGPTLKEKSLGAEMDSVRSWVRNVGVVDANVAAQSGVALSRAHFEKQPPSNLRKSNFFHFVLALYDRQGQPVEIERTAFVD
FVENDKEQGNEKTNNGTHYKLQLLYSNGVRTEQDLYVRLIDSVTKQPIAYEGQNKNPEMCRVLLTHEVMCSRCCEKKSCGNRNETPSDPV
IIDSHIDQTTTWQDPRKAMLSQMNVTAPTSPPVQQNMMNSASGPLPDGWEQAMTQDGEIYYINHKNKTTSWLDPRLDPRFAMNQRISQSA
PVKQPPPLAPQSPQGGVMGGSNSNQQQQMRLQQLQMEKERLRLKQQELLRQVRPQELALRSQLPTLEQDGGTQNPVSSPGMSQELRTMTT
NSSDPFLNSGTYHSRDESTDSGLSMSSYSVPRTPDDFLNSVDEMDTGDTINQSTLPSQQNRFPDYLEAIPGTNVDLGTLEGDGMNIEGEE

--------------------------------------------------------------

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Fusion Protein Functional Features


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/chr8:25890600/chr11:102033186)
- 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 buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
EBF2

Q9HAK2

.
FUNCTION: Transcription factor that, in osteoblasts, activates the decoy receptor for RANKL, TNFRSF11B, which in turn regulates osteoclast differentiation. Acts in synergy with the Wnt-responsive LEF1/CTNNB1 pathway. Recognizes variations of the palindromic sequence 5'-ATTCCCNNGGGAATT-3' (By similarity). {ECO:0000250}.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.

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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneEBF2chr8:25890600chr11:102033186ENST00000520164-616150_169183.66666666666666576.0Zinc fingerC5-type
TgeneYAP1chr8:25890600chr11:102033186ENST0000028244119298_359190.66666666666666505.0Coiled coilOntology_term=ECO:0000255
TgeneYAP1chr8:25890600chr11:102033186ENST0000034587717298_359190.66666666666666455.0Coiled coilOntology_term=ECO:0000255
TgeneYAP1chr8:25890600chr11:102033186ENST0000052457519298_35912.666666666666666327.0Coiled coilOntology_term=ECO:0000255
TgeneYAP1chr8:25890600chr11:102033186ENST000005245751986_10012.666666666666666327.0Coiled coilOntology_term=ECO:0000269
TgeneYAP1chr8:25890600chr11:102033186ENST0000052634317298_359190.66666666666666451.0Coiled coilOntology_term=ECO:0000255
TgeneYAP1chr8:25890600chr11:102033186ENST0000053143918298_359190.66666666666666489.0Coiled coilOntology_term=ECO:0000255
TgeneYAP1chr8:25890600chr11:102033186ENST0000053727418298_359190.66666666666666493.0Coiled coilOntology_term=ECO:0000255
TgeneYAP1chr8:25890600chr11:102033186ENST0000028244119230_263190.66666666666666505.0DomainWW 2
TgeneYAP1chr8:25890600chr11:102033186ENST0000034587717230_263190.66666666666666455.0DomainWW 2
TgeneYAP1chr8:25890600chr11:102033186ENST0000052457519171_20412.666666666666666327.0DomainWW 1
TgeneYAP1chr8:25890600chr11:102033186ENST0000052457519230_26312.666666666666666327.0DomainWW 2
TgeneYAP1chr8:25890600chr11:102033186ENST0000052634317230_263190.66666666666666451.0DomainWW 2
TgeneYAP1chr8:25890600chr11:102033186ENST0000053143918230_263190.66666666666666489.0DomainWW 2
TgeneYAP1chr8:25890600chr11:102033186ENST0000053727418230_263190.66666666666666493.0DomainWW 2
TgeneYAP1chr8:25890600chr11:102033186ENST0000028244119291_504190.66666666666666505.0RegionNote=Transactivation domain
TgeneYAP1chr8:25890600chr11:102033186ENST0000034587717291_504190.66666666666666455.0RegionNote=Transactivation domain
TgeneYAP1chr8:25890600chr11:102033186ENST0000052457519291_50412.666666666666666327.0RegionNote=Transactivation domain
TgeneYAP1chr8:25890600chr11:102033186ENST0000052634317291_504190.66666666666666451.0RegionNote=Transactivation domain
TgeneYAP1chr8:25890600chr11:102033186ENST0000053143918291_504190.66666666666666489.0RegionNote=Transactivation domain
TgeneYAP1chr8:25890600chr11:102033186ENST0000053727418291_504190.66666666666666493.0RegionNote=Transactivation domain

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneEBF2chr8:25890600chr11:102033186ENST00000520164-616453_534183.66666666666666576.0Compositional biasNote=Pro/Ser/Thr-rich
HgeneEBF2chr8:25890600chr11:102033186ENST00000520164-616253_336183.66666666666666576.0DomainNote=IPT/TIG
TgeneYAP1chr8:25890600chr11:102033186ENST000002824411986_100190.66666666666666505.0Coiled coilOntology_term=ECO:0000269
TgeneYAP1chr8:25890600chr11:102033186ENST000003458771786_100190.66666666666666455.0Coiled coilOntology_term=ECO:0000269
TgeneYAP1chr8:25890600chr11:102033186ENST000005263431786_100190.66666666666666451.0Coiled coilOntology_term=ECO:0000269
TgeneYAP1chr8:25890600chr11:102033186ENST000005314391886_100190.66666666666666489.0Coiled coilOntology_term=ECO:0000269
TgeneYAP1chr8:25890600chr11:102033186ENST000005372741886_100190.66666666666666493.0Coiled coilOntology_term=ECO:0000269
TgeneYAP1chr8:25890600chr11:102033186ENST00000282441193_49190.66666666666666505.0Compositional biasNote=Pro-rich
TgeneYAP1chr8:25890600chr11:102033186ENST00000345877173_49190.66666666666666455.0Compositional biasNote=Pro-rich
TgeneYAP1chr8:25890600chr11:102033186ENST00000524575193_4912.666666666666666327.0Compositional biasNote=Pro-rich
TgeneYAP1chr8:25890600chr11:102033186ENST00000526343173_49190.66666666666666451.0Compositional biasNote=Pro-rich
TgeneYAP1chr8:25890600chr11:102033186ENST00000531439183_49190.66666666666666489.0Compositional biasNote=Pro-rich
TgeneYAP1chr8:25890600chr11:102033186ENST00000537274183_49190.66666666666666493.0Compositional biasNote=Pro-rich
TgeneYAP1chr8:25890600chr11:102033186ENST0000028244119171_204190.66666666666666505.0DomainWW 1
TgeneYAP1chr8:25890600chr11:102033186ENST0000034587717171_204190.66666666666666455.0DomainWW 1
TgeneYAP1chr8:25890600chr11:102033186ENST0000052634317171_204190.66666666666666451.0DomainWW 1
TgeneYAP1chr8:25890600chr11:102033186ENST0000053143918171_204190.66666666666666489.0DomainWW 1
TgeneYAP1chr8:25890600chr11:102033186ENST0000053727418171_204190.66666666666666493.0DomainWW 1


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
EBF2
YAP1


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with
HgeneEBF2chr8:25890600chr11:102033186ENST00000520164-616196_203183.66666666666666576.0DNA
HgeneEBF2chr8:25890600chr11:102033186ENST00000520164-616235_238183.66666666666666576.0DNA


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Related Drugs to EBF2-YAP1


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 EBF2-YAP1


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