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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-PDPN (FusionGDB2 ID:95670)

Fusion Gene Summary for UBE4B-PDPN

check button Fusion gene summary
Fusion gene informationFusion gene name: UBE4B-PDPN
Fusion gene ID: 95670
HgeneTgene
Gene symbol

UBE4B

PDPN

Gene ID

10277

10630

Gene nameubiquitination factor E4Bpodoplanin
SynonymsE4|HDNB1|UBOX3|UFD2|UFD2AAGGRUS|GP36|GP40|Gp38|HT1A-1|OTS8|PA2.26|T1A|T1A-2|T1A2|TI1A
Cytomap

1p36.22

1p36.21

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, ypodoplaninPA2.26 antigenT1-alphaglycoprotein 36glycoprotein, 36-KDhT1alpha-1hT1alpha-2lung type I cell membrane associated glycoproteinlung type-I cell membrane-associated glycoprotein (T1A-2)
Modification date2020031320200322
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000253251, ENST00000377157, 
ENST00000343090, ENST00000377153, 
ENST00000475795, 		ENST00000294489, 
ENST00000376057, ENST00000509009, 
ENST00000376061, ENST00000513143, 
ENST00000487038, ENST00000475043, 
Fusion gene scores* DoF score18 X 13 X 10=23402 X 2 X 2=8
# samples 232
** MAII scorelog2(23/2340*10)=-3.34680276352639
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(2/8*10)=1.32192809488736
Context

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

Most frequent breakpointUBE4B(10228328)-PDPN(13933668), # samples:2
Anticipated loss of major functional domain due to fusion event.UBE4B-PDPN seems lost the major protein functional domain in Hgene 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
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

TgenePDPN

GO:0090091

positive regulation of extracellular matrix disassembly

25486435

TgenePDPN

GO:1901731

positive regulation of platelet aggregation

17222411|20110424

TgenePDPN

GO:1905863

invadopodium organization

25486435


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 PDPN (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
ChimerDB4LUSCTCGA-56-A4BW-01AUBE4Bchr1

10228328

+PDPNchr1

13933668

+
ChimerDB4LUSCTCGA-56-A4BW-01AUBE4Bchr1

10228328

-PDPNchr1

13933668

+


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Fusion Gene ORF analysis for UBE4B-PDPN

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-shiftENST00000253251ENST00000294489UBE4Bchr1

10228328

+PDPNchr1

13933668

+
Frame-shiftENST00000253251ENST00000376057UBE4Bchr1

10228328

+PDPNchr1

13933668

+
Frame-shiftENST00000253251ENST00000509009UBE4Bchr1

10228328

+PDPNchr1

13933668

+
5CDS-5UTRENST00000253251ENST00000376061UBE4Bchr1

10228328

+PDPNchr1

13933668

+
5CDS-5UTRENST00000253251ENST00000513143UBE4Bchr1

10228328

+PDPNchr1

13933668

+
5CDS-5UTRENST00000253251ENST00000487038UBE4Bchr1

10228328

+PDPNchr1

13933668

+
5CDS-5UTRENST00000253251ENST00000475043UBE4Bchr1

10228328

+PDPNchr1

13933668

+
Frame-shiftENST00000377157ENST00000294489UBE4Bchr1

10228328

+PDPNchr1

13933668

+
Frame-shiftENST00000377157ENST00000376057UBE4Bchr1

10228328

+PDPNchr1

13933668

+
Frame-shiftENST00000377157ENST00000509009UBE4Bchr1

10228328

+PDPNchr1

13933668

+
5CDS-5UTRENST00000377157ENST00000376061UBE4Bchr1

10228328

+PDPNchr1

13933668

+
5CDS-5UTRENST00000377157ENST00000513143UBE4Bchr1

10228328

+PDPNchr1

13933668

+
5CDS-5UTRENST00000377157ENST00000487038UBE4Bchr1

10228328

+PDPNchr1

13933668

+
5CDS-5UTRENST00000377157ENST00000475043UBE4Bchr1

10228328

+PDPNchr1

13933668

+
Frame-shiftENST00000343090ENST00000294489UBE4Bchr1

10228328

+PDPNchr1

13933668

+
Frame-shiftENST00000343090ENST00000376057UBE4Bchr1

10228328

+PDPNchr1

13933668

+
Frame-shiftENST00000343090ENST00000509009UBE4Bchr1

10228328

+PDPNchr1

13933668

+
5CDS-5UTRENST00000343090ENST00000376061UBE4Bchr1

10228328

+PDPNchr1

13933668

+
5CDS-5UTRENST00000343090ENST00000513143UBE4Bchr1

10228328

+PDPNchr1

13933668

+
5CDS-5UTRENST00000343090ENST00000487038UBE4Bchr1

10228328

+PDPNchr1

13933668

+
5CDS-5UTRENST00000343090ENST00000475043UBE4Bchr1

10228328

+PDPNchr1

13933668

+
intron-3CDSENST00000377153ENST00000294489UBE4Bchr1

10228328

+PDPNchr1

13933668

+
intron-3CDSENST00000377153ENST00000376057UBE4Bchr1

10228328

+PDPNchr1

13933668

+
intron-3CDSENST00000377153ENST00000509009UBE4Bchr1

10228328

+PDPNchr1

13933668

+
intron-5UTRENST00000377153ENST00000376061UBE4Bchr1

10228328

+PDPNchr1

13933668

+
intron-5UTRENST00000377153ENST00000513143UBE4Bchr1

10228328

+PDPNchr1

13933668

+
intron-5UTRENST00000377153ENST00000487038UBE4Bchr1

10228328

+PDPNchr1

13933668

+
intron-5UTRENST00000377153ENST00000475043UBE4Bchr1

10228328

+PDPNchr1

13933668

+
intron-3CDSENST00000475795ENST00000294489UBE4Bchr1

10228328

+PDPNchr1

13933668

+
intron-3CDSENST00000475795ENST00000376057UBE4Bchr1

10228328

+PDPNchr1

13933668

+
intron-3CDSENST00000475795ENST00000509009UBE4Bchr1

10228328

+PDPNchr1

13933668

+
intron-5UTRENST00000475795ENST00000376061UBE4Bchr1

10228328

+PDPNchr1

13933668

+
intron-5UTRENST00000475795ENST00000513143UBE4Bchr1

10228328

+PDPNchr1

13933668

+
intron-5UTRENST00000475795ENST00000487038UBE4Bchr1

10228328

+PDPNchr1

13933668

+
intron-5UTRENST00000475795ENST00000475043UBE4Bchr1

10228328

+PDPNchr1

13933668

+

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-PDPN


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)
UBE4Bchr110228328+PDPNchr113933667+9.05E-121
UBE4Bchr110228328+PDPNchr113933667+9.05E-121

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-PDPN


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
..
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: 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.
- 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-PDPN


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-PDPN


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-PDPN


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-PDPN


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneUBE4BC0004238Atrial Fibrillation1CTD_human
HgeneUBE4BC0043020Wallerian Degeneration1CTD_human
HgeneUBE4BC0235480Paroxysmal atrial fibrillation1CTD_human
HgeneUBE4BC0525041Neurobehavioral Manifestations1CTD_human
HgeneUBE4BC2585653Persistent atrial fibrillation1CTD_human
HgeneUBE4BC3468561familial atrial fibrillation1CTD_human
TgenePDPNC0031149Peritoneal Neoplasms1CTD_human
TgenePDPNC0345967Malignant mesothelioma1CTD_human
TgenePDPNC0346990Carcinomatosis of peritoneal cavity1CTD_human