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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:PTPN1-P2RX4

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: PTPN1-P2RX4
FusionPDB ID: 70234
FusionGDB2.0 ID: 70234
HgeneTgene
Gene symbol

PTPN1

P2RX4

Gene ID

5770

5025

Gene nameprotein tyrosine phosphatase non-receptor type 1purinergic receptor P2X 4
SynonymsPTP1BP2X4|P2X4R
Cytomap

20q13.13

12q24.31

Type of geneprotein-codingprotein-coding
Descriptiontyrosine-protein phosphatase non-receptor type 1protein tyrosine phosphatase, placentalprotein-tyrosine phosphatase 1BP2X purinoceptor 4ATP receptorATP-gated cation channel proteinP2X receptor, subunit 4purinergic receptor P2X, ligand gated ion channel, 4purinergic receptor P2X4purinoceptor P2X4
Modification date2020032920200313
UniProtAcc

Q99952

.
Ensembl transtripts involved in fusion geneENST idsENST00000371621, ENST00000541713, 
ENST00000540930, ENST00000541532, 
ENST00000543171, ENST00000337233, 
ENST00000359949, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score8 X 5 X 6=2404 X 6 X 3=72
# samples 105
** MAII scorelog2(10/240*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(5/72*10)=-0.526068811667588
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: PTPN1 [Title/Abstract] AND P2RX4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)PTPN1(49127127)-P2RX4(121654937), # samples:3
Anticipated loss of major functional domain due to fusion event.PTPN1-P2RX4 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.
PTPN1-P2RX4 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.
PTPN1-P2RX4 seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
PTPN1-P2RX4 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
PTPN1-P2RX4 seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target 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
HgenePTPN1

GO:0030100

regulation of endocytosis

21135139

HgenePTPN1

GO:0030968

endoplasmic reticulum unfolded protein response

22169477

HgenePTPN1

GO:0035335

peptidyl-tyrosine dephosphorylation

21135139

HgenePTPN1

GO:0061098

positive regulation of protein tyrosine kinase activity

21216966

HgenePTPN1

GO:1903898

negative regulation of PERK-mediated unfolded protein response

21216966

TgeneP2RX4

GO:0007165

signal transduction

9016352

TgeneP2RX4

GO:0010524

positive regulation of calcium ion transport into cytosol

10969036

TgeneP2RX4

GO:0033198

response to ATP

9016352

TgeneP2RX4

GO:0034220

ion transmembrane transport

10515189

TgeneP2RX4

GO:0034405

response to fluid shear stress

10969036

TgeneP2RX4

GO:0050850

positive regulation of calcium-mediated signaling

10969036

TgeneP2RX4

GO:0051899

membrane depolarization

9016352

TgeneP2RX4

GO:0070588

calcium ion transmembrane transport

9016352

TgeneP2RX4

GO:0071318

cellular response to ATP

10515189

TgeneP2RX4

GO:0097190

apoptotic signaling pathway

17264311


check buttonFusion gene breakpoints across PTPN1 (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 P2RX4 (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
ChimerDB4HNSCTCGA-CN-5364-01APTPN1chr20

49127127

-P2RX4chr12

121654937

+
ChimerDB4HNSCTCGA-CN-5364-01APTPN1chr20

49127127

+P2RX4chr12

121654937

+
ChimerDB4HNSCTCGA-CN-5364PTPN1chr20

49127127

+P2RX4chr12

121654937

+
ChimerDB4HNSCTCGA-CN-5364PTPN1chr20

49127127

+P2RX4chr12

121659715

+
ChimerDB4HNSCTCGA-CN-5364PTPN1chr20

49127127

+P2RX4chr12

121659716

+


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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)
ENST00000371621PTPN1chr2049127127+ENST00000337233P2RX4chr12121659715+1679237781121347
ENST00000371621PTPN1chr2049127127+ENST00000359949P2RX4chr12121659715+1643237781121347
ENST00000371621PTPN1chr2049127127+ENST00000337233P2RX4chr12121659716+1679237781121347
ENST00000371621PTPN1chr2049127127+ENST00000359949P2RX4chr12121659716+1643237781121347

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
ENST00000371621ENST00000337233PTPN1chr2049127127+P2RX4chr12121659715+0.0032375790.9967624
ENST00000371621ENST00000359949PTPN1chr2049127127+P2RX4chr12121659715+0.0029084880.99709153
ENST00000371621ENST00000337233PTPN1chr2049127127+P2RX4chr12121659716+0.0032375790.9967624
ENST00000371621ENST00000359949PTPN1chr2049127127+P2RX4chr12121659716+0.0029084880.99709153

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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

>70234_70234_1_PTPN1-P2RX4_PTPN1_chr20_49127127_ENST00000371621_P2RX4_chr12_121659715_ENST00000337233_length(amino acids)=347AA_BP=52
MQRASGLRARRGLERQTAQWAEKEAQQPPWPVMEMEKEFEQIDKSGSWAAIYQEENSLFVMTNVILTMNQTQGLCPEIPDATTVCKSDAS
CTAGSAGTHSNGVSTGRCVAFNGSVKTCEVAAWCPVEDDTHVPQPAFLKAAENFTLLVKNNIWYPKFNFSKRNILPNITTTYLKSCIYDA
KTDPFCPIFRLGKIVENAGHSFQDMAVEGGIMGIQVNWDCNLDRAASLCLPRYSFRRLDTRDVEHNVSPGYNFRFAKYYRDLAGNEQRTL

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

>70234_70234_2_PTPN1-P2RX4_PTPN1_chr20_49127127_ENST00000371621_P2RX4_chr12_121659715_ENST00000359949_length(amino acids)=347AA_BP=52
MQRASGLRARRGLERQTAQWAEKEAQQPPWPVMEMEKEFEQIDKSGSWAAIYQEENSLFVMTNVILTMNQTQGLCPEIPDATTVCKSDAS
CTAGSAGTHSNGVSTGRCVAFNGSVKTCEVAAWCPVEDDTHVPQPAFLKAAENFTLLVKNNIWYPKFNFSKRNILPNITTTYLKSCIYDA
KTDPFCPIFRLGKIVENAGHSFQDMAVEGGIMGIQVNWDCNLDRAASLCLPRYSFRRLDTRDVEHNVSPGYNFRFAKYYRDLAGNEQRTL

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

>70234_70234_3_PTPN1-P2RX4_PTPN1_chr20_49127127_ENST00000371621_P2RX4_chr12_121659716_ENST00000337233_length(amino acids)=347AA_BP=52
MQRASGLRARRGLERQTAQWAEKEAQQPPWPVMEMEKEFEQIDKSGSWAAIYQEENSLFVMTNVILTMNQTQGLCPEIPDATTVCKSDAS
CTAGSAGTHSNGVSTGRCVAFNGSVKTCEVAAWCPVEDDTHVPQPAFLKAAENFTLLVKNNIWYPKFNFSKRNILPNITTTYLKSCIYDA
KTDPFCPIFRLGKIVENAGHSFQDMAVEGGIMGIQVNWDCNLDRAASLCLPRYSFRRLDTRDVEHNVSPGYNFRFAKYYRDLAGNEQRTL

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

>70234_70234_4_PTPN1-P2RX4_PTPN1_chr20_49127127_ENST00000371621_P2RX4_chr12_121659716_ENST00000359949_length(amino acids)=347AA_BP=52
MQRASGLRARRGLERQTAQWAEKEAQQPPWPVMEMEKEFEQIDKSGSWAAIYQEENSLFVMTNVILTMNQTQGLCPEIPDATTVCKSDAS
CTAGSAGTHSNGVSTGRCVAFNGSVKTCEVAAWCPVEDDTHVPQPAFLKAAENFTLLVKNNIWYPKFNFSKRNILPNITTTYLKSCIYDA
KTDPFCPIFRLGKIVENAGHSFQDMAVEGGIMGIQVNWDCNLDRAASLCLPRYSFRRLDTRDVEHNVSPGYNFRFAKYYRDLAGNEQRTL

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

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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/chr20:49127127/chr12:121654937)
- 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
PTPN1

Q99952

.
FUNCTION: Differentially dephosphorylate autophosphorylated tyrosine kinases which are known to be overexpressed in tumor tissues.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
TgeneP2RX4chr20:49127127chr12:121659715ENST00000337233112360_38894.0389.0Topological domainCytoplasmic
TgeneP2RX4chr20:49127127chr12:121659716ENST00000337233112360_38894.0389.0Topological domainCytoplasmic
TgeneP2RX4chr20:49127127chr12:121659715ENST00000337233112339_35994.0389.0TransmembraneHelical%3B Name%3D2
TgeneP2RX4chr20:49127127chr12:121659716ENST00000337233112339_35994.0389.0TransmembraneHelical%3B Name%3D2

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgenePTPN1chr20:49127127chr12:121659715ENST00000371621+1103_27721.0436.0DomainTyrosine-protein phosphatase
HgenePTPN1chr20:49127127chr12:121659716ENST00000371621+1103_27721.0436.0DomainTyrosine-protein phosphatase
HgenePTPN1chr20:49127127chr12:121659715ENST00000371621+110215_22121.0436.0RegionSubstrate binding
HgenePTPN1chr20:49127127chr12:121659716ENST00000371621+110215_22121.0436.0RegionSubstrate binding
TgeneP2RX4chr20:49127127chr12:121659715ENST000003372331121_3394.0389.0Topological domainCytoplasmic
TgeneP2RX4chr20:49127127chr12:121659715ENST0000033723311255_33894.0389.0Topological domainExtracellular
TgeneP2RX4chr20:49127127chr12:121659716ENST000003372331121_3394.0389.0Topological domainCytoplasmic
TgeneP2RX4chr20:49127127chr12:121659716ENST0000033723311255_33894.0389.0Topological domainExtracellular
TgeneP2RX4chr20:49127127chr12:121659715ENST0000033723311234_5494.0389.0TransmembraneHelical%3B Name%3D1
TgeneP2RX4chr20:49127127chr12:121659716ENST0000033723311234_5494.0389.0TransmembraneHelical%3B Name%3D1


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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
PTPN1
P2RX4


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


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Related Drugs to PTPN1-P2RX4


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 PTPN1-P2RX4


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