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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:PTPN4-PCDP1 (FusionGDB2 ID:70286)

Fusion Gene Summary for PTPN4-PCDP1

check button Fusion gene summary
Fusion gene informationFusion gene name: PTPN4-PCDP1
Fusion gene ID: 70286
HgeneTgene
Gene symbol

PTPN4

PCDP1

Gene ID

5775

200373

Gene nameprotein tyrosine phosphatase non-receptor type 4cilia and flagella associated protein 221
SynonymsMEG|PTPMEG|PTPMEG1FAP221|PCDP1
Cytomap

2q14.2

2q14.2

Type of geneprotein-codingprotein-coding
Descriptiontyrosine-protein phosphatase non-receptor type 4PTPase-MEG1megakaryocyte phosphatasemegakaryocyte protein-tyrosine phosphataseprotein tyrosine phosphatase MEG1protein tyrosine phosphatase, non-receptor type 4 (megakaryocyte)cilia- and flagella-associated protein 221flagellar associated protein 221 homologprimary ciliary dyskinesia 1 homologprimary ciliary dyskinesia protein 1
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000263708, ENST00000460162, 
ENST00000544261, 		ENST00000413369, 
ENST00000598644, ENST00000602047, 
ENST00000597189, 
Fusion gene scores* DoF score5 X 4 X 5=1002 X 4 X 3=24
# samples 64
** MAII scorelog2(6/100*10)=-0.736965594166206
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: PTPN4 [Title/Abstract] AND PCDP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPTPN4(120658382)-PCDP1(120306660), # samples:2
Anticipated loss of major functional domain due to fusion event.PTPN4-PCDP1 seems lost the major protein functional domain in Hgene 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 PTPN4 (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 PCDP1 (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
ChimerDB4ESCATCGA-L5-A4OQPTPN4chr2

120658382

+PCDP1chr2

120306660

+
ChimerDB4UCECTCGA-EO-A1Y7-01APTPN4chr2

120567567

+PCDP1chr2

120409550

+


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Fusion Gene ORF analysis for PTPN4-PCDP1

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
5CDS-5UTRENST00000263708ENST00000413369PTPN4chr2

120658382

+PCDP1chr2

120306660

+
5CDS-5UTRENST00000263708ENST00000598644PTPN4chr2

120658382

+PCDP1chr2

120306660

+
5CDS-5UTRENST00000263708ENST00000602047PTPN4chr2

120658382

+PCDP1chr2

120306660

+
5CDS-intronENST00000263708ENST00000597189PTPN4chr2

120658382

+PCDP1chr2

120306660

+
5CDS-intronENST00000263708ENST00000597189PTPN4chr2

120567567

+PCDP1chr2

120409550

+
5CDS-intronENST00000263708ENST00000598644PTPN4chr2

120567567

+PCDP1chr2

120409550

+
Frame-shiftENST00000263708ENST00000413369PTPN4chr2

120567567

+PCDP1chr2

120409550

+
Frame-shiftENST00000263708ENST00000602047PTPN4chr2

120567567

+PCDP1chr2

120409550

+
intron-3CDSENST00000460162ENST00000413369PTPN4chr2

120567567

+PCDP1chr2

120409550

+
intron-3CDSENST00000460162ENST00000602047PTPN4chr2

120567567

+PCDP1chr2

120409550

+
intron-3CDSENST00000544261ENST00000413369PTPN4chr2

120567567

+PCDP1chr2

120409550

+
intron-3CDSENST00000544261ENST00000602047PTPN4chr2

120567567

+PCDP1chr2

120409550

+
intron-5UTRENST00000460162ENST00000413369PTPN4chr2

120658382

+PCDP1chr2

120306660

+
intron-5UTRENST00000460162ENST00000598644PTPN4chr2

120658382

+PCDP1chr2

120306660

+
intron-5UTRENST00000460162ENST00000602047PTPN4chr2

120658382

+PCDP1chr2

120306660

+
intron-5UTRENST00000544261ENST00000413369PTPN4chr2

120658382

+PCDP1chr2

120306660

+
intron-5UTRENST00000544261ENST00000598644PTPN4chr2

120658382

+PCDP1chr2

120306660

+
intron-5UTRENST00000544261ENST00000602047PTPN4chr2

120658382

+PCDP1chr2

120306660

+
intron-intronENST00000460162ENST00000597189PTPN4chr2

120658382

+PCDP1chr2

120306660

+
intron-intronENST00000460162ENST00000597189PTPN4chr2

120567567

+PCDP1chr2

120409550

+
intron-intronENST00000460162ENST00000598644PTPN4chr2

120567567

+PCDP1chr2

120409550

+
intron-intronENST00000544261ENST00000597189PTPN4chr2

120658382

+PCDP1chr2

120306660

+
intron-intronENST00000544261ENST00000597189PTPN4chr2

120567567

+PCDP1chr2

120409550

+
intron-intronENST00000544261ENST00000598644PTPN4chr2

120567567

+PCDP1chr2

120409550

+

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 PTPN4-PCDP1


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)
PTPN4chr2120658382+PCDP1chr2120306660+0.0047429310.9952571
PTPN4chr2120567567+PCDP1chr2120409549+8.87E-060.9999912
PTPN4chr2120658382+PCDP1chr2120306660+0.0047429310.9952571
PTPN4chr2120567567+PCDP1chr2120409549+8.87E-060.9999912

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.
genomic feature of top 1%

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Fusion Protein Features for PTPN4-PCDP1


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/:120658382/:120306660)
- 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 PTPN4-PCDP1


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 PTPN4-PCDP1


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 PTPN4-PCDP1


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 PTPN4-PCDP1


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