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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: 29470

FusionGeneSummary for PTPN9_CSPG4

check button Fusion gene summary
Fusion gene informationFusion gene name: PTPN9_CSPG4
Fusion gene ID: 29470
HgeneTgene
Gene symbol

PTPN9

CSPG4

Gene ID

5780

1464

Gene nameprotein tyrosine phosphatase, non-receptor type 9chondroitin sulfate proteoglycan 4
SynonymsMEG2|PTPMEG2HMW-MAA|MCSP|MCSPG|MEL-CSPG|MSK16|NG2
Cytomap

15q24.2

15q24.2

Type of geneprotein-codingprotein-coding
Descriptiontyrosine-protein phosphatase non-receptor type 9PTPase-MEG2protein-tyrosine phosphatase MEG2chondroitin sulfate proteoglycan 4chondroitin sulfate proteoglycan 4 (melanoma-associated)chondroitin sulfate proteoglycan NG2melanoma chondroitin sulfate proteoglycanmelanoma-associated chondroitin sulfate proteoglycan
Modification date2018052020180522
UniProtAcc

P43378

Q6UVK1

Ensembl transtripts involved in fusion geneENST00000306726, ENST00000564970, 
ENST00000308508, 
Fusion gene scores* DoF score8 X 6 X 7=3362 X 2 X 2=8
# samples 132
** MAII scorelog2(13/336*10)=-1.36994960975031
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context

PubMed: PTPN9 [Title/Abstract] AND CSPG4 [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
HgenePTPN9

GO:0010977

negative regulation of neuron projection development

27655914

HgenePTPN9

GO:0035335

peptidyl-tyrosine dephosphorylation

27655914

HgenePTPN9

GO:1903078

positive regulation of protein localization to plasma membrane

27655914

TgeneCSPG4

GO:0035556

intracellular signal transduction

10587647

TgeneCSPG4

GO:0050731

positive regulation of peptidyl-tyrosine phosphorylation

10587647


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
TCGALDLGGTCGA-TM-A7CF-01APTPN9chr15

75815462

-CSPG4chr15

75975382

-
* 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
Frame-shitENST00000306726ENST00000308508PTPN9chr15

75815462

-CSPG4chr15

75975382

-
intron-3CDSENST00000564970ENST00000308508PTPN9chr15

75815462

-CSPG4chr15

75975382

-

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FusionProtFeatures for PTPN9_CSPG4


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PTPN9

P43378

CSPG4

Q6UVK1

Protein-tyrosine phosphatase that could participate inthe transfer of hydrophobic ligands or in functions of the Golgiapparatus. {ECO:0000269|PubMed:19167335}. Proteoglycan playing a role in cell proliferation andmigration which stimulates endothelial cells motility duringmicrovascular morphogenesis. May also inhibit neurite outgrowthand growth cone collapse during axon regeneration. Cell surfacereceptor for collagen alpha 2(VI) which may confer cells abilityto migrate on that substrate. Binds through its extracellular N-terminus growth factors, extracellular matrix proteases modulatingtheir activity. May regulate MPP16-dependent degradation andinvasion of type I collagen participating in melanoma cellsinvasion properties. May modulate the plasminogen system byenhancing plasminogen activation and inhibiting angiostatin.Functions also as a signal transducing protein by binding throughits cytoplasmic C-terminus scaffolding and signaling proteins. Maypromote retraction fiber formation and cell polarization throughRho GTPase activation. May stimulate alpha-4, beta-1 integrin-mediated adhesion and spreading by recruiting and activating asignaling cascade through CDC42, ACK1 and BCAR1. May activate FAKand ERK1/ERK2 signaling cascades. {ECO:0000269|PubMed:10587647,ECO:0000269|PubMed:11278606, ECO:0000269|PubMed:15210734}.

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 PTPN9_CSPG4


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.

* Fusion transcript sequences (only coding sequence (CDS) region).

* Fusion transcript sequences (Full-length transcript).

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FusionGenePPI for PTPN9_CSPG4


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
PTPN9RTN3, GHR, MYC, TP53BP1, VCP, AGTRAP, REEP6, MAL2, CMTM5, ENO1, MOV10, NXF1, NTRK1, CREB3, LZTR1, PC, EYA1, RAD51C, FAM26D, VSIG8, C5AR2, MDK, PDCD1, PTPN9, GEMIN8, FSIP1, SMN1, DDX20, GEMIN4, PMPCA, SLC39A7, STRAP, TUBA3C, AAR2, SMN2, TUBA3D, LMNACSPG4GRIP2, CDC42, GRIP1, CAPNS1, LGALS3, LGALS8, LGALS9, PCBP4, SORT1, ZNF644


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 PTPN9_CSPG4


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 PTPN9_CSPG4


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