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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:PTPRM-PTPRM (FusionGDB2 ID:70040)

Fusion Gene Summary for PTPRM-PTPRM

check button Fusion gene summary
Fusion gene informationFusion gene name: PTPRM-PTPRM
Fusion gene ID: 70040
HgeneTgene
Gene symbol

PTPRM

PTPRM

Gene ID

5797

5797

Gene nameprotein tyrosine phosphatase receptor type Mprotein tyrosine phosphatase receptor type M
SynonymsPTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPuPTPRL1|R-PTP-MU|RPTPM|RPTPU|hR-PTPu
Cytomap

18p11.23

18p11.23

Type of geneprotein-codingprotein-coding
Descriptionreceptor-type tyrosine-protein phosphatase muprotein tyrosine phosphatase muprotein tyrosine phosphatase, receptor type, mu polypeptidereceptor-type tyrosine-protein phosphatase muprotein tyrosine phosphatase muprotein tyrosine phosphatase, receptor type, mu polypeptide
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000580170, ENST00000332175, 
ENST00000400060, ENST00000400053, 
ENST00000444013, ENST00000578571, 
ENST00000580170, ENST00000332175, 
ENST00000400060, ENST00000400053, 
ENST00000444013, ENST00000578571, 
Fusion gene scores* DoF score11 X 10 X 6=66020 X 18 X 6=2160
# samples 1121
** MAII scorelog2(11/660*10)=-2.58496250072116
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(21/2160*10)=-3.36257007938471
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: PTPRM [Title/Abstract] AND PTPRM [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointPTPRM(8406477)-PTPRM(8370944), # samples:1
Anticipated loss of major functional domain due to fusion event.
* 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
HgenePTPRM

GO:0006470

protein dephosphorylation

8393854|10809770

HgenePTPRM

GO:0007156

homophilic cell adhesion via plasma membrane adhesion molecules

8393854

HgenePTPRM

GO:0007165

signal transduction

15080886

HgenePTPRM

GO:0031175

neuron projection development

16380380

HgenePTPRM

GO:0031290

retinal ganglion cell axon guidance

15080886

HgenePTPRM

GO:0042493

response to drug

18566238

TgenePTPRM

GO:0006470

protein dephosphorylation

8393854|10809770

TgenePTPRM

GO:0007156

homophilic cell adhesion via plasma membrane adhesion molecules

8393854

TgenePTPRM

GO:0007165

signal transduction

15080886

TgenePTPRM

GO:0031175

neuron projection development

16380380

TgenePTPRM

GO:0031290

retinal ganglion cell axon guidance

15080886

TgenePTPRM

GO:0042493

response to drug

18566238


check buttonFusion gene breakpoints across PTPRM (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 PTPRM (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
ChiTaRS5.0N/AW27760PTPRMchr18

8406477

-PTPRMchr18

8370944

+


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Fusion Gene ORF analysis for PTPRM-PTPRM

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-3CDSENST00000580170ENST00000580170PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000580170ENST00000332175PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000580170ENST00000400060PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000580170ENST00000400053PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000580170ENST00000444013PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-intronENST00000580170ENST00000578571PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000332175ENST00000580170PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000332175ENST00000332175PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000332175ENST00000400060PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000332175ENST00000400053PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000332175ENST00000444013PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-intronENST00000332175ENST00000578571PTPRMchr18

8406477

-PTPRMchr18

8370944

+
intron-3CDSENST00000400060ENST00000580170PTPRMchr18

8406477

-PTPRMchr18

8370944

+
intron-3CDSENST00000400060ENST00000332175PTPRMchr18

8406477

-PTPRMchr18

8370944

+
intron-3CDSENST00000400060ENST00000400060PTPRMchr18

8406477

-PTPRMchr18

8370944

+
intron-3CDSENST00000400060ENST00000400053PTPRMchr18

8406477

-PTPRMchr18

8370944

+
intron-3CDSENST00000400060ENST00000444013PTPRMchr18

8406477

-PTPRMchr18

8370944

+
intron-intronENST00000400060ENST00000578571PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000400053ENST00000580170PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000400053ENST00000332175PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000400053ENST00000400060PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000400053ENST00000400053PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000400053ENST00000444013PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-intronENST00000400053ENST00000578571PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000444013ENST00000580170PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000444013ENST00000332175PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000444013ENST00000400060PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000444013ENST00000400053PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-3CDSENST00000444013ENST00000444013PTPRMchr18

8406477

-PTPRMchr18

8370944

+
3UTR-intronENST00000444013ENST00000578571PTPRMchr18

8406477

-PTPRMchr18

8370944

+
intron-3CDSENST00000578571ENST00000580170PTPRMchr18

8406477

-PTPRMchr18

8370944

+
intron-3CDSENST00000578571ENST00000332175PTPRMchr18

8406477

-PTPRMchr18

8370944

+
intron-3CDSENST00000578571ENST00000400060PTPRMchr18

8406477

-PTPRMchr18

8370944

+
intron-3CDSENST00000578571ENST00000400053PTPRMchr18

8406477

-PTPRMchr18

8370944

+
intron-3CDSENST00000578571ENST00000444013PTPRMchr18

8406477

-PTPRMchr18

8370944

+
intron-intronENST00000578571ENST00000578571PTPRMchr18

8406477

-PTPRMchr18

8370944

+

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 PTPRM-PTPRM


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 PTPRM-PTPRM


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 PTPRM-PTPRM


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 PTPRM-PTPRM


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 PTPRM-PTPRM


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 PTPRM-PTPRM


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