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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:UBE4B-PTK2 (FusionGDB2 ID:96334)

Fusion Gene Summary for UBE4B-PTK2

check button Fusion gene summary
Fusion gene informationFusion gene name: UBE4B-PTK2
Fusion gene ID: 96334
HgeneTgene
Gene symbol

UBE4B

PTK2

Gene ID

10277

5747

Gene nameubiquitination factor E4Bprotein tyrosine kinase 2
SynonymsE4|HDNB1|UBOX3|UFD2|UFD2AFADK|FAK|FAK1|FRNK|PPP1R71|p125FAK|pp125FAK
Cytomap

1p36.22

8q24.3

Type of geneprotein-codingprotein-coding
Descriptionubiquitin conjugation factor E4 BRING-type E3 ubiquitin transferase E4 BUFD2A-III/UBE4B-III splice isoformhomologous to yeast UFD2homozygously deleted in neuroblastoma-1ubiquitin-fusion degradation protein 2ubiquitination factor E4B (UFD2 homolog, yfocal adhesion kinase 1FADK 1FAK-related non-kinase polypeptidePTK2 protein tyrosine kinase 2focal adhesion kinase isoform FAK-Del33focal adhesion kinase-related nonkinaseprotein phosphatase 1 regulatory subunit 71
Modification date2020031320200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000253251, ENST00000377157, 
ENST00000343090, ENST00000377153, 
ENST00000475795, 		ENST00000340930, 
ENST00000395218, ENST00000430260, 
ENST00000517712, ENST00000517887, 
ENST00000519419, ENST00000519465, 
ENST00000519635, ENST00000519881, 
ENST00000520151, ENST00000520892, 
ENST00000521059, ENST00000522684, 
ENST00000522950, ENST00000535192, 
ENST00000538769, 
Fusion gene scores* DoF score18 X 13 X 10=234019 X 20 X 13=4940
# samples 2329
** MAII scorelog2(23/2340*10)=-3.34680276352639
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(29/4940*10)=-4.09038623645711
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: UBE4B [Title/Abstract] AND PTK2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointUBE4B(10093094)-PTK2(141755427), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
HgeneUBE4B

GO:0008626

granzyme-mediated apoptotic signaling pathway

11802788

HgeneUBE4B

GO:0009411

response to UV

11802788

HgeneUBE4B

GO:0043161

proteasome-mediated ubiquitin-dependent protein catabolic process

23509263

TgenePTK2

GO:0007179

transforming growth factor beta receptor signaling pathway

24036928

TgenePTK2

GO:0007229

integrin-mediated signaling pathway

24036928

TgenePTK2

GO:0010763

positive regulation of fibroblast migration

26763945

TgenePTK2

GO:0018108

peptidyl-tyrosine phosphorylation

10655584|11331870

TgenePTK2

GO:0022408

negative regulation of cell-cell adhesion

21703394

TgenePTK2

GO:0030335

positive regulation of cell migration

11331870|21703394

TgenePTK2

GO:0033628

regulation of cell adhesion mediated by integrin

10655584

TgenePTK2

GO:0046777

protein autophosphorylation

10655584|11331870

TgenePTK2

GO:0048013

ephrin receptor signaling pathway

10655584

TgenePTK2

GO:0060396

growth hormone receptor signaling pathway

10925297

TgenePTK2

GO:0090303

positive regulation of wound healing

26763945


check buttonFusion gene breakpoints across UBE4B (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 PTK2 (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
ChiTaRS5.0N/ABX493754UBE4Bchr1

10093094

+PTK2chr8

141755427

-


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Fusion Gene ORF analysis for UBE4B-PTK2

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
5UTR-intronENST00000253251ENST00000340930UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000395218UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000430260UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000517712UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000517887UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000519419UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000519465UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000519635UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000519881UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000520151UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000520892UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000521059UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000522684UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000522950UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000535192UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000253251ENST00000538769UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000340930UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000395218UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000430260UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000517712UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000517887UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000519419UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000519465UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000519635UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000519881UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000520151UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000520892UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000521059UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000522684UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000522950UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000535192UBE4Bchr1

10093094

+PTK2chr8

141755427

-
5UTR-intronENST00000377157ENST00000538769UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000340930UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000395218UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000430260UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000517712UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000517887UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000519419UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000519465UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000519635UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000519881UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000520151UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000520892UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000521059UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000522684UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000522950UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000535192UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000343090ENST00000538769UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000340930UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000395218UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000430260UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000517712UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000517887UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000519419UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000519465UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000519635UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000519881UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000520151UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000520892UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000521059UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000522684UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000522950UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000535192UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000377153ENST00000538769UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000340930UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000395218UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000430260UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000517712UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000517887UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000519419UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000519465UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000519635UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000519881UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000520151UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000520892UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000521059UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000522684UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000522950UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000535192UBE4Bchr1

10093094

+PTK2chr8

141755427

-
intron-intronENST00000475795ENST00000538769UBE4Bchr1

10093094

+PTK2chr8

141755427

-

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 UBE4B-PTK2


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 UBE4B-PTK2


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/:10093094/:141755427)
- 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
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 UBE4B-PTK2


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 UBE4B-PTK2


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 UBE4B-PTK2


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 UBE4B-PTK2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource