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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:BGN-PTP4A2 (FusionGDB2 ID:HG633TG8073)

Fusion Gene Summary for BGN-PTP4A2

check button Fusion gene summary
Fusion gene informationFusion gene name: BGN-PTP4A2
Fusion gene ID: hg633tg8073
HgeneTgene
Gene symbol

BGN

PTP4A2

Gene ID

633

8073

Gene namebiglycanprotein tyrosine phosphatase 4A2
SynonymsDSPG1|MRLS|PG-S1|PGI|SEMDX|SLRR1AHH13|HH7-2|HU-PP-1|OV-1|PRL-2|PRL2|PTP4A|PTPCAAX2|ptp-IV1a|ptp-IV1b
Cytomap('BGN')('PTP4A2')

Xq28

1p35.2

Type of geneprotein-codingprotein-coding
Descriptionbiglycanbone/cartilage proteoglycan-Idermatan sulphate proteoglycan Ismall leucine-rich protein 1Aprotein tyrosine phosphatase type IVA 2PTP(CAAXII)phosphatase of regenerating liver 2protein tyrosine phosphatase IVAprotein tyrosine phosphatase IVA2protein tyrosine phosphatase type IVA, member 2protein-tyrosine phosphatase of regenerating liver 2
Modification date2020032020200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000331595, ENST00000480756, 
Fusion gene scores* DoF score18 X 9 X 12=194413 X 8 X 8=832
# samples 1813
** MAII scorelog2(18/1944*10)=-3.43295940727611
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(13/832*10)=-2.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BGN [Title/Abstract] AND PTP4A2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBGN(152775004)-PTP4A2(32374561), # samples:1
Anticipated loss of major functional domain due to fusion event.BGN-PTP4A2 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.
BGN-PTP4A2 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.
BGN-PTP4A2 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.
BGN-PTP4A2 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.
BGN-PTP4A2 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
BGN-PTP4A2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
BGN-PTP4A2 seems lost the major protein functional domain in Tgene partner, which is a essential gene 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

check buttonFusion gene breakpoints across BGN (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 PTP4A2 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check button Fusion gene information
* 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
ChimerDB4MESOTCGA-LK-A4NY-01ABGNchrX

152775004

-PTP4A2chr1

32374561

-


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Fusion Gene ORF analysis for BGN-PTP4A2

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
3UTR-3CDSENST00000331595ENST00000344035BGNchrX

152775004

-PTP4A2chr1

32374561

-
3UTR-3CDSENST00000331595ENST00000356536BGNchrX

152775004

-PTP4A2chr1

32374561

-
3UTR-3CDSENST00000331595ENST00000457805BGNchrX

152775004

-PTP4A2chr1

32374561

-
3UTR-3CDSENST00000331595ENST00000602725BGNchrX

152775004

-PTP4A2chr1

32374561

-
3UTR-3UTRENST00000331595ENST00000470404BGNchrX

152775004

-PTP4A2chr1

32374561

-
3UTR-intronENST00000331595ENST00000526960BGNchrX

152775004

-PTP4A2chr1

32374561

-
5CDS-3UTRENST00000480756ENST00000470404BGNchrX

152775004

-PTP4A2chr1

32374561

-
5CDS-intronENST00000480756ENST00000526960BGNchrX

152775004

-PTP4A2chr1

32374561

-
Frame-shiftENST00000480756ENST00000344035BGNchrX

152775004

-PTP4A2chr1

32374561

-
Frame-shiftENST00000480756ENST00000356536BGNchrX

152775004

-PTP4A2chr1

32374561

-
Frame-shiftENST00000480756ENST00000602725BGNchrX

152775004

-PTP4A2chr1

32374561

-
In-frameENST00000480756ENST00000457805BGNchrX

152775004

-PTP4A2chr1

32374561

-

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)
ENST00000480756BGNchrX152775004-ENST00000457805PTP4A2chr132374561-2705227813102152280

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
ENST00000480756ENST00000457805BGNchrX152775004-PTP4A2chr132374561-0.73418140.26581857

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Fusion Genomic Features for BGN-PTP4A2


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.
genomic feature

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Fusion Protein Features for BGN-PTP4A2


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/chrX:152775004/chr1:32374561)
- 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
TgenePTP4A2chrX:152775004chr1:32374561ENST0000035653624102_1076383.0RegionPhosphate binding
TgenePTP4A2chrX:152775004chr1:32374561ENST0000045780524102_107100137.0RegionPhosphate binding

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneBGNchrX:152775004chr1:32374561ENST00000331595-1863_760369.0Compositional biasNote=Cys-rich
HgeneBGNchrX:152775004chr1:32374561ENST00000331595-18103_1260369.0RepeatNote=LRR 2
HgeneBGNchrX:152775004chr1:32374561ENST00000331595-18127_1500369.0RepeatNote=LRR 3
HgeneBGNchrX:152775004chr1:32374561ENST00000331595-18151_1710369.0RepeatNote=LRR 4
HgeneBGNchrX:152775004chr1:32374561ENST00000331595-18172_1950369.0RepeatNote=LRR 5
HgeneBGNchrX:152775004chr1:32374561ENST00000331595-18196_2200369.0RepeatNote=LRR 6
HgeneBGNchrX:152775004chr1:32374561ENST00000331595-18221_2410369.0RepeatNote=LRR 7
HgeneBGNchrX:152775004chr1:32374561ENST00000331595-18242_2650369.0RepeatNote=LRR 8
HgeneBGNchrX:152775004chr1:32374561ENST00000331595-18266_2890369.0RepeatNote=LRR 9
HgeneBGNchrX:152775004chr1:32374561ENST00000331595-18290_3120369.0RepeatNote=LRR 10
HgeneBGNchrX:152775004chr1:32374561ENST00000331595-18313_3420369.0RepeatNote=LRR 11
HgeneBGNchrX:152775004chr1:32374561ENST00000331595-18343_3680369.0RepeatNote=LRR 12
HgeneBGNchrX:152775004chr1:32374561ENST00000331595-1882_1020369.0RepeatNote=LRR 1
TgenePTP4A2chrX:152775004chr1:32374561ENST00000344035465_158131168.0DomainTyrosine-protein phosphatase
TgenePTP4A2chrX:152775004chr1:32374561ENST00000356536245_1586383.0DomainTyrosine-protein phosphatase
TgenePTP4A2chrX:152775004chr1:32374561ENST00000457805245_158100137.0DomainTyrosine-protein phosphatase
TgenePTP4A2chrX:152775004chr1:32374561ENST00000602725355_158131168.0DomainTyrosine-protein phosphatase
TgenePTP4A2chrX:152775004chr1:32374561ENST0000034403546102_107131168.0RegionPhosphate binding
TgenePTP4A2chrX:152775004chr1:32374561ENST0000060272535102_107131168.0RegionPhosphate binding


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Fusion Gene Sequence for BGN-PTP4A2


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.
>9648_9648_1_BGN-PTP4A2_BGN_chrX_152775004_ENST00000480756_PTP4A2_chr1_32374561_ENST00000457805_length(transcript)=2705nt_BP=2278nt
TCTCCACAAACTGCCCAGGAGTGAGTAGCTGCTTTCGGTCCGCCGGACACACCGGACAGATAGACGTGCGGACGGCCCACCACCCCAGCC
CGCCAACTAGTCAGCCTGCGCCTGGCGCCTCCCCTCTCCAGGTCCATCCGCCATGTGGCCCCTGTGGCGCCTCGTGTCTCTGCTGGCCCT
GAGCCAGGCCCTGCCCTTTGAGCAGAGAGGCTTCTGGGACTTCACCCTGGACGATGGGCCATTCATGATGAACGATGAGGAAGCTTCGGG
CGCTGACACCTCGGGCGTCCTGGACCCGGACTCTGTCACACCCACCTACAGCGCCATGTAGATCTCCCCTGACACCACGCTGCTGGACCT
GCAGAACAACGACATCTCCGAGCTCCGCAAGGATGACTTCAAGGGTCTCCAGCACCTCTACGCCCTCGTCCTGGTGAACAACAAGATCTC
CAAGATCCATGAGAAGGCCTTCAGCCCACTGCGGAAGCTGCAGAAGCTCTACATCTCCAAGAACCACCTGGTGGAGATCCCGCCCAACCT
ACCCAGCTCCCTGGTGGAGCTCCGCATCCACGACAACCGCATCCGCAAGGTGCCCAAGGGAGTGTTCAGCGGGCTCCGGAACATGAACTG
CATCGAGATGGGCGGGAACCCACTGGAGAACAGTGGCTTTGAACCTGGAGCCTTCGATGGCCTGAAGCTCAACTACCTGCGCATCTCAGA
GGCCAAGCTGACTGGCATCCCCAAAGACCTCCCTGAGACCCTGAATGAACTCCACCTAGACCACAACAAAATCCAGGCCATCGAACTGGA
GGACCTGCTTCGCTACTCCAAGCTGTACAGGCTGGGCCTAGGCCACAACCAGATCAGGATGATCGAGAACGGGAGCCTGAGCTTCCTGCC
CACCCTCCGGGAGCTCCACTTGGACAACAACAAGTTGGCCAGGGTGCCCTCAGGGCTCCCAGACCTCAAGCTCCTCCAGGTGGTCTATCT
GCACTCCAACAACATCACCAAAGTGGGTGTCAACGACTTCTGTCCCATGGGCTTCGGGGTGAAGCGGGCCTACTACAACGGCATCAGCCT
CTTCAACAACCCCGTGCCCTACTGGGAGGTGCAGCCGGCCACTTTCCGCTGCGTCACTGACCGCCTGGCCATCCAGTTTGGCAACTACAA
AAAGTAGAGGCAGCTGCAGCCACCGCGGGGCCTCAGTGGGGGTCTCTGGGGAACACAGCCAGACATCCTGATGGGGAGGCAGAGCCAGGA
AGCTAAGCCAGGGCCCAGCTGCGTCCAACCCAGCCCCCCACCTCGGGTCCCTGACCCCAGCTCGATGCCCCATCACCGCCTCTCCCTGGC
TCCCAAGGGTGCAGGTGGGCGCAAGGCCCGGCCCCCATCACATGTTCCCTTGGCCTCAGAGCTGCCCCTGCTCTCCCACCACAGCCACCC
AGAGGCACCCCATGAAGCTTTTTTCTCGTTCACTCCCAAACCCAAGTGTCCAAGGCTCCAGTCCTAGGAGAACAGTCCCTGGGTCAGCAG
CCAGGAGGCGGTCCATAAGAATGGGGACAGTGGGCTCTGCCAGGGCTGCCGCACCTGTCCAGACACACATGTTCTGTTCCTCCTCCTCAT
GCATTTCCAGCCTTTCAACCCTCCCCGACTCTGCGGCTCCCCTCAGCCCCCTTGCAAGTTCATGGCCTGTCCCTCCCAGACCCCTGCTCC
ACTGGCCCTTCGACCAGTCCTCCCTTCTGTTCTCTCTTTCCCCGTCCTTCCTCTCTCTCTCTCTCTCTCTCTCTCTCTCTTTCTGTGTGT
GTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTGTCTTGTGCTTCCTCAGACCTTTCTCGCTTCTGAGCTTGGTGGCCTGTTCCCTC
CATCTCTCCGAACCTGGCTTCGCCTGTCCCTTTCACTCCACACCCTCTGGCCTTCTGCCTTGAGCTGGGACTGCTTTCTGTCTGTCCGGC
CTGCACCCAGCCCCTGCCCACAAAACCCCAGGGACAGCAGTCTCCCCAGCCTGCCCTGCTCAGGCCTTGCCCCCAAACCTGTACTGTCCC
GGAGGAGGTTGGGAGGTGGAGGCCCAGCATCCCGCGCAGATGACACCATCAACCGCCAGAGTCCCAGACACCGGTTTTCCTAGAAGCCCC
TCACCCCCACTGGCCCACTGGTGGCTAGGTCTCCCCTTATCCTTCTGGTCCAGCGCAAGGAGGGGCTGCTTCTGAGGTCGGTGGCTGTCT
TTCCATTAAAGAAACACCGTGCAACGTGAAAAAGAAGGGGAGCGTTCAATTCCAAACAGCTGCTTTATTTGGAGAAATACCGACCTAAGA
TGCGATTACGCTTCAGAGATACCAATGGGCATTGCTGTGTTCAGTAGAAGGAAATGTAAACGAAGGCTGACTTGATTGTGCCATTTAGAG
GGAACTCTTGGTACCTGGAAATGTGAATCTGGAATATTACCTGTGTCATCAAAGTAGTGATGGATTCAGTACTCCTCAACCACTCTCCTA
ATGATTGGAACAAAAGCAAACAAAAAAGAAATCTCTCTATAAAATGAATAAAATGTTTAAGAAAAGAGAAAGAGAAAAGGAATTAATTCA
GTGAAGGATGATTTTGCTCCTAGTTTTGGAGTTTGAATTTCTGCCAGGATTGAATTATTTTGAAATCTCCTGTCTTTTTAAACTTTTTCA

>9648_9648_1_BGN-PTP4A2_BGN_chrX_152775004_ENST00000480756_PTP4A2_chr1_32374561_ENST00000457805_length(amino acids)=280AA_BP=
MTPARCPITASPWLPRVQVGARPGPHHMFPWPQSCPCSPTTATQRHPMKLFSRSLPNPSVQGSSPRRTVPGSAARRRSIRMGTVGSARAA
APVQTHMFCSSSSCISSLSTLPDSAAPLSPLASSWPVPPRPLLHWPFDQSSLLFSLSPSFLSLSLSLSLSFCVCVCVCVCVCVCVCLVLP
QTFLASELGGLFPPSLRTWLRLSLSLHTLWPSALSWDCFLSVRPAPSPCPQNPRDSSLPSLPCSGLAPKPVLSRRRLGGGGPASRADDTI

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Fusion Gene PPI Analysis for BGN-PTP4A2


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 BGN-PTP4A2


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 BGN-PTP4A2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBGNC1848097Spondyloepimetaphyseal Dysplasia, X-Linked2CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneBGNC4707243Familial thoracic aortic aneurysm and aortic dissection2CLINGEN;GENOMICS_ENGLAND
HgeneBGNC0003873Rheumatoid Arthritis1CTD_human
HgeneBGNC0023893Liver Cirrhosis, Experimental1CTD_human
HgeneBGNC4310811MEESTER-LOEYS SYNDROME1CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC1135196Heart Failure, Diastolic1CTD_human