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Center for Computational Systems Medicine
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FusionGeneSummary

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FusionProtFeature

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FusionGeneSequence

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FusionGenePPI

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RelatedDrugs

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RelatedDiseases

Fusion gene ID: 4136

FusionGeneSummary for BGN_PTP4A2

check button Fusion gene summary
Fusion gene informationFusion gene name: BGN_PTP4A2
Fusion gene ID: 4136
HgeneTgene
Gene symbol

BGN

PTP4A2

Gene ID

633

8073

Gene namebiglycanprotein tyrosine phosphatase type IVA, member 2
SynonymsDSPG1|MRLS|PG-S1|PGI|SEMDX|SLRR1AHH13|HH7-2|HU-PP-1|OV-1|PRL-2|PRL2|PTP4A|PTPCAAX2|ptp-IV1a|ptp-IV1b
Cytomap

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 4a2protein-tyrosine phosphatase of regenerating liver 2
Modification date2018052220180523
UniProtAcc

P21810

Q12974

Ensembl transtripts involved in fusion geneENST00000331595, ENST00000480756, 
ENST00000602725, ENST00000344035, 
ENST00000356536, ENST00000457805, 
ENST00000470404, ENST00000526960, 
Fusion gene scores* DoF score15 X 7 X 11=11553 X 2 X 3=18
# samples 173
** MAII scorelog2(17/1155*10)=-2.76428620016572
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

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

Functional or gene categories assigned by FusionGDB annotation
* 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 button Fusion gene information from three resources
(ChiTars (NAR, 2018), tumorfusions (NAR, 2018), Gao et al. (Cell, 2018))
* 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.
Data typeSourceCancer typeSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
TCGARVMESOTCGA-LK-A4NY-01ABGNchrX

152775004

+PTP4A2chr1

32374561

-
* LD: Li Ding group's fusion gene list
  RV: Roel Verhaak group's fusion gene list
  ChiTaRs fusion database

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-3CDSENST00000331595ENST00000602725BGNchrX

152775004

+PTP4A2chr1

32374561

-
3UTR-3CDSENST00000331595ENST00000344035BGNchrX

152775004

+PTP4A2chr1

32374561

-
3UTR-3CDSENST00000331595ENST00000356536BGNchrX

152775004

+PTP4A2chr1

32374561

-
3UTR-3CDSENST00000331595ENST00000457805BGNchrX

152775004

+PTP4A2chr1

32374561

-
3UTR-3UTRENST00000331595ENST00000470404BGNchrX

152775004

+PTP4A2chr1

32374561

-
3UTR-intronENST00000331595ENST00000526960BGNchrX

152775004

+PTP4A2chr1

32374561

-
Frame-shitENST00000480756ENST00000602725BGNchrX

152775004

+PTP4A2chr1

32374561

-
Frame-shitENST00000480756ENST00000344035BGNchrX

152775004

+PTP4A2chr1

32374561

-
Frame-shitENST00000480756ENST00000356536BGNchrX

152775004

+PTP4A2chr1

32374561

-
In-frameENST00000480756ENST00000457805BGNchrX

152775004

+PTP4A2chr1

32374561

-
5CDS-3UTRENST00000480756ENST00000470404BGNchrX

152775004

+PTP4A2chr1

32374561

-
5CDS-intronENST00000480756ENST00000526960BGNchrX

152775004

+PTP4A2chr1

32374561

-

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FusionProtFeatures for BGN_PTP4A2


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

P21810

PTP4A2

Q12974

May be involved in collagen fiber assembly.{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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FusionGeneSequence for BGN_PTP4A2


check button For in-frame fusion transcripts, we provide the fusion transcript sequences and fusion amino acid sequences.
(nt: nucleotides, aa: amino acids)

* Fusion amino acid sequences.
>In-frame_BGN_ENST00000480756_chrX_152775004_+_PTP4A2_ENST00000457805_chr1_32374561_-_795aa
SPQTAQE_VAAFGPPDTPDR_TCGRPTTPARQLVSLRLAPPLSRSIRHVAPVAPRVSAGPEPGPAL_AERLLGLHPGRWAIHDER_GSFG
R_HLGRPGPGLCHTHLQRHVDLP_HHAAGPAEQRHLRAPQG_LQGSPAPLRPRPGEQQDLQDP_EGLQPTAEAAEALHLQEPPGGDPAQP
TQLPGGAPHPRQPHPQGAQGSVQRAPEHELHRDGREPTGEQWL_TWSLRWPEAQLPAHLRGQADWHPQRPP_DPE_TPPRPQQNPGHRTG
GPASLLQAVQAGPRPQPDQDDREREPELPAHPPGAPLGQQQVGQGALRAPRPQAPPGGLSALQQHHQSGCQRLLSHGLRGEAGLLQRHQP
LQQPRALLGGAAGHFPLRH_PPGHPVWQLQKVEAAAATAGPQWGSLGNTARHPDGEAEPGS_ARAQLRPTQPPTSGP_PQLDAPSPPLPG
SQGCRWAQGPAPITCSLGLRAAPALPPQPPRGTP_SFFLVHSQTQVSKAPVLGEQSLGQQPGGGP_EWGQWALPGLPHLSRHTCSVPPPH
AFPAFQPSPTLRLPSAPLQVHGLSLPDPCSTGPSTSPPFCSLFPRPSSLSLSLSLSLSVCVCVCVCVCVCVCVLCFLRPFSLLSLVACSL
HLSEPGFACPFHSTPSGLLP_AGTAFCLSGLHPAPAHKTPGTAVSPACPAQALPPNLYCPGGGWEVEAQHPAQMTPSTARVPDTGFPRSP


* Fusion transcript sequences (only coding sequence (CDS) region).
>In-frame_BGN_ENST00000480756_chrX_152775004_+_PTP4A2_ENST00000457805_chr1_32374561_-_2387nt
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


* Fusion transcript sequences (Full-length transcript).
>In-frame_BGN_ENST00000480756_chrX_152775004_+_PTP4A2_ENST00000457805_chr1_32374561_-_2705nt
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


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FusionGenePPI 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
BGNHDL3, JPH3, TGFB1, TNF, ELN, MFAP2, APP, SGCA, APOB, HSPB2PTP4A2CNNM3, TNFAIP8, CNNM4, FNTA, FNTB, PTP4A1, USF2, RABGGTB, MYC, PON2, UNK, GNB4, SPTAN1, SPTBN1, CNNM1, EFTUD1, CNNM2, PCDHB5, FMN2, GPAA1, CYP8B1, PTP4A3, PTP4A2, FHL3, ATXN7L3B, TARBP2, PRDX4, GADD45GIP1, PRDX3, RPS19BP1, RPL22L1, RPL18A, TRIM25


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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RelatedDrugs for BGN_PTP4A2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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RelatedDiseases for BGN_PTP4A2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBGNC0003873Rheumatoid Arthritis1CTD_human
HgeneBGNC0023893Liver Cirrhosis, Experimental1CTD_human
HgeneBGNC1848097Spondyloepimetaphyseal Dysplasia, X-Linked1ORPHANET;UNIPROT