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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: 19598

FusionGeneSummary for LDOC1L_PTPRM

check button Fusion gene summary
Fusion gene informationFusion gene name: LDOC1L_PTPRM
Fusion gene ID: 19598
HgeneTgene
Gene symbol

LDOC1L

PTPRM

Gene ID

5797

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

18p11.23

Type of geneprotein-coding
Descriptionreceptor-type tyrosine-protein phosphatase muprotein tyrosine phosphatase muprotein tyrosine phosphatase, receptor type, mu polypeptide
Modification date20180522
UniProtAcc

P28827

Ensembl transtripts involved in fusion geneENST00000341255, ENST00000580170, 
ENST00000332175, ENST00000400060, 
ENST00000400053, ENST00000444013, 
ENST00000578571, 
Fusion gene scores* DoF score1 X 1 X 1=16 X 8 X 4=192
# samples 18
** MAII scorelog2(1/1*10)=3.32192809488736log2(8/192*10)=-1.26303440583379
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: LDOC1L [Title/Abstract] AND PTPRM [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
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 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
ChiTaRS3.1BF848439LDOC1Lchr22

44890440

-PTPRMchr18

7745715

-
* 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
intron-intronENST00000341255ENST00000580170LDOC1Lchr22

44890440

-PTPRMchr18

7745715

-
intron-intronENST00000341255ENST00000332175LDOC1Lchr22

44890440

-PTPRMchr18

7745715

-
intron-intronENST00000341255ENST00000400060LDOC1Lchr22

44890440

-PTPRMchr18

7745715

-
intron-intronENST00000341255ENST00000400053LDOC1Lchr22

44890440

-PTPRMchr18

7745715

-
intron-intronENST00000341255ENST00000444013LDOC1Lchr22

44890440

-PTPRMchr18

7745715

-
intron-intronENST00000341255ENST00000578571LDOC1Lchr22

44890440

-PTPRMchr18

7745715

-

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FusionProtFeatures for LDOC1L_PTPRM


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
LDOC1L

PTPRM

P28827

Lectin that binds to various sugars: galactose > mannose= fucose > N-acetylglucosamine > N-acetylgalactosamine(PubMed:10224141). Acts as a chemoattractant, probably involved inthe regulation of cell migration (PubMed:28301481).{ECO:0000269|PubMed:10224141, ECO:0000269|PubMed:28301481}. Involved in cell-cell adhesion through homophilicinteractions. May play a key role in signal transduction andgrowth control. {ECO:0000269|PubMed:16456543}.

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 LDOC1L_PTPRM


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 LDOC1L_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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RelatedDrugs for LDOC1L_PTPRM


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 LDOC1L_PTPRM


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