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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:PTPN2-PTPRD (FusionGDB2 ID:69812)

Fusion Gene Summary for PTPN2-PTPRD

check button Fusion gene summary
Fusion gene informationFusion gene name: PTPN2-PTPRD
Fusion gene ID: 69812
HgeneTgene
Gene symbol

PTPN2

PTPRD

Gene ID

5771

5789

Gene nameprotein tyrosine phosphatase non-receptor type 2protein tyrosine phosphatase receptor type D
SynonymsPTN2|PTPT|TC-PTP|TCELLPTP|TCPTPHPTP|HPTPD|HPTPDELTA|PTPD|R-PTP-delta|RPTPDELTA
Cytomap

18p11.21

9p24.1-p23

Type of geneprotein-codingprotein-coding
Descriptiontyrosine-protein phosphatase non-receptor type 2T-cell protein tyrosine phosphatasereceptor-type tyrosine-protein phosphatase deltaprotein tyrosine phosphatase, receptor type, delta polypeptiderceptor-type tyrosine-protein phosphatase delta
Modification date2020032920200320
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000327283, ENST00000591115, 
ENST00000353319, ENST00000309660, 
ENST00000589086, ENST00000591497, 
ENST00000381196, ENST00000360074, 
ENST00000537002, ENST00000397617, 
ENST00000358503, ENST00000397611, 
ENST00000355233, ENST00000356435, 
ENST00000540109, ENST00000486161, 
ENST00000397606, ENST00000463477, 
ENST00000471274, 
Fusion gene scores* DoF score14 X 10 X 8=112027 X 25 X 10=6750
# samples 1528
** MAII scorelog2(15/1120*10)=-2.90046432644909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(28/6750*10)=-4.59138876988059
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PTPN2 [Title/Abstract] AND PTPRD [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPTPN2(12859163)-PTPRD(8341978), # samples:1
Anticipated loss of major functional domain due to fusion event.PTPN2-PTPRD seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
PTPN2-PTPRD seems lost the major protein functional domain in Tgene partner, which is a CGC due to the frame-shifted ORF.
PTPN2-PTPRD seems lost the major protein functional domain in Tgene partner, which is a tumor suppressor due to the frame-shifted ORF.
PTPN2-PTPRD 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
TgenePTPRD

GO:0099545

trans-synaptic signaling by trans-synaptic complex

21926414

TgenePTPRD

GO:0099560

synaptic membrane adhesion

23345436

TgenePTPRD

GO:1905606

regulation of presynapse assembly

21926414


check buttonFusion gene breakpoints across PTPN2 (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 PTPRD (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
ChimerDB4OVTCGA-31-1959-01APTPN2chr18

12859163

-PTPRDchr9

8341978

-


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Fusion Gene ORF analysis for PTPN2-PTPRD

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-shiftENST00000327283ENST00000381196PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000327283ENST00000360074PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000327283ENST00000537002PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000327283ENST00000397617PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000327283ENST00000358503PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000327283ENST00000397611PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000327283ENST00000355233PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000327283ENST00000356435PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000327283ENST00000540109PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000327283ENST00000486161PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000327283ENST00000397606PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5CDS-intronENST00000327283ENST00000463477PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5CDS-intronENST00000327283ENST00000471274PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000591115ENST00000381196PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000591115ENST00000360074PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000591115ENST00000537002PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000591115ENST00000397617PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000591115ENST00000358503PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000591115ENST00000397611PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000591115ENST00000355233PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000591115ENST00000356435PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000591115ENST00000540109PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000591115ENST00000486161PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000591115ENST00000397606PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5CDS-intronENST00000591115ENST00000463477PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5CDS-intronENST00000591115ENST00000471274PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000353319ENST00000381196PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000353319ENST00000360074PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000353319ENST00000537002PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000353319ENST00000397617PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000353319ENST00000358503PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000353319ENST00000397611PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000353319ENST00000355233PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000353319ENST00000356435PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000353319ENST00000540109PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000353319ENST00000486161PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000353319ENST00000397606PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5CDS-intronENST00000353319ENST00000463477PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5CDS-intronENST00000353319ENST00000471274PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000309660ENST00000381196PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000309660ENST00000360074PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000309660ENST00000537002PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000309660ENST00000397617PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000309660ENST00000358503PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000309660ENST00000397611PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000309660ENST00000355233PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000309660ENST00000356435PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000309660ENST00000540109PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000309660ENST00000486161PTPN2chr18

12859163

-PTPRDchr9

8341978

-
Frame-shiftENST00000309660ENST00000397606PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5CDS-intronENST00000309660ENST00000463477PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5CDS-intronENST00000309660ENST00000471274PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5UTR-3CDSENST00000589086ENST00000381196PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5UTR-3CDSENST00000589086ENST00000360074PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5UTR-3CDSENST00000589086ENST00000537002PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5UTR-3CDSENST00000589086ENST00000397617PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5UTR-3CDSENST00000589086ENST00000358503PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5UTR-3CDSENST00000589086ENST00000397611PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5UTR-3CDSENST00000589086ENST00000355233PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5UTR-3CDSENST00000589086ENST00000356435PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5UTR-3CDSENST00000589086ENST00000540109PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5UTR-3CDSENST00000589086ENST00000486161PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5UTR-3CDSENST00000589086ENST00000397606PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5UTR-intronENST00000589086ENST00000463477PTPN2chr18

12859163

-PTPRDchr9

8341978

-
5UTR-intronENST00000589086ENST00000471274PTPN2chr18

12859163

-PTPRDchr9

8341978

-
intron-3CDSENST00000591497ENST00000381196PTPN2chr18

12859163

-PTPRDchr9

8341978

-
intron-3CDSENST00000591497ENST00000360074PTPN2chr18

12859163

-PTPRDchr9

8341978

-
intron-3CDSENST00000591497ENST00000537002PTPN2chr18

12859163

-PTPRDchr9

8341978

-
intron-3CDSENST00000591497ENST00000397617PTPN2chr18

12859163

-PTPRDchr9

8341978

-
intron-3CDSENST00000591497ENST00000358503PTPN2chr18

12859163

-PTPRDchr9

8341978

-
intron-3CDSENST00000591497ENST00000397611PTPN2chr18

12859163

-PTPRDchr9

8341978

-
intron-3CDSENST00000591497ENST00000355233PTPN2chr18

12859163

-PTPRDchr9

8341978

-
intron-3CDSENST00000591497ENST00000356435PTPN2chr18

12859163

-PTPRDchr9

8341978

-
intron-3CDSENST00000591497ENST00000540109PTPN2chr18

12859163

-PTPRDchr9

8341978

-
intron-3CDSENST00000591497ENST00000486161PTPN2chr18

12859163

-PTPRDchr9

8341978

-
intron-3CDSENST00000591497ENST00000397606PTPN2chr18

12859163

-PTPRDchr9

8341978

-
intron-intronENST00000591497ENST00000463477PTPN2chr18

12859163

-PTPRDchr9

8341978

-
intron-intronENST00000591497ENST00000471274PTPN2chr18

12859163

-PTPRDchr9

8341978

-

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 PTPN2-PTPRD


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.

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 PTPN2-PTPRD


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 PTPN2-PTPRD


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 PTPN2-PTPRD


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 PTPN2-PTPRD


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 PTPN2-PTPRD


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgenePTPN2C0003873Rheumatoid Arthritis1CTD_human
HgenePTPN2C0009324Ulcerative Colitis1CTD_human;GENOMICS_ENGLAND
HgenePTPN2C0010346Crohn Disease1CTD_human
HgenePTPN2C0023492Leukemia, T-Cell1CTD_human
HgenePTPN2C0156147Crohn's disease of large bowel1CTD_human
HgenePTPN2C0267380Crohn's disease of the ileum1CTD_human
HgenePTPN2C0678202Regional enteritis1CTD_human
HgenePTPN2C0949272IIeocolitis1CTD_human
HgenePTPN2C1961099Precursor T-Cell Lymphoblastic Leukemia-Lymphoma1CTD_human
HgenePTPN2C2931171Juvenile pauciarticular chronic arthritis1ORPHANET
TgenePTPRDC0009402Colorectal Carcinoma2CTD_human;UNIPROT
TgenePTPRDC0009404Colorectal Neoplasms2CTD_human
TgenePTPRDC0006142Malignant neoplasm of breast1CTD_human
TgenePTPRDC0023893Liver Cirrhosis, Experimental1CTD_human
TgenePTPRDC0035258Restless Legs Syndrome1CTD_human
TgenePTPRDC0041671Attention Deficit Disorder1CTD_human
TgenePTPRDC0678222Breast Carcinoma1CTD_human
TgenePTPRDC1257931Mammary Neoplasms, Human1CTD_human
TgenePTPRDC1263846Attention deficit hyperactivity disorder1CTD_human
TgenePTPRDC1321905Minimal Brain Dysfunction1CTD_human
TgenePTPRDC1458155Mammary Neoplasms1CTD_human
TgenePTPRDC4704874Mammary Carcinoma, Human1CTD_human