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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: 29460

FusionGeneSummary for PTPN4_LCT

check button Fusion gene summary
Fusion gene informationFusion gene name: PTPN4_LCT
Fusion gene ID: 29460
HgeneTgene
Gene symbol

PTPN4

LCT

Gene ID

5775

3938

Gene nameprotein tyrosine phosphatase, non-receptor type 4lactase
SynonymsMEG|PTPMEG|PTPMEG1LAC|LPH|LPH1
Cytomap

2q14.2

2q21.3

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)lactase-phlorizin hydrolaselactase-glycosylceramidaselactase-phlorizin hydrolase-1
Modification date2018051920180523
UniProtAcc

P29074

P09848

Ensembl transtripts involved in fusion geneENST00000263708, ENST00000544261, 
ENST00000460162, 
ENST00000264162, 
Fusion gene scores* DoF score4 X 3 X 3=363 X 3 X 3=27
# samples 43
** MAII scorelog2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: PTPN4 [Title/Abstract] AND LCT [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

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
TCGARVBLCATCGA-ZF-AA4T-01APTPN4chr2

120567567

+LCTchr2

136590760

-
* 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-shiftENST00000263708ENST00000264162PTPN4chr2

120567567

+LCTchr2

136590760

-
intron-3CDSENST00000544261ENST00000264162PTPN4chr2

120567567

+LCTchr2

136590760

-
intron-3CDSENST00000460162ENST00000264162PTPN4chr2

120567567

+LCTchr2

136590760

-

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FusionProtFeatures for PTPN4_LCT


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
PTPN4

P29074

LCT

P09848

May act at junctions between the membrane and thecytoskeleton. LPH splits lactose in the small intestine.

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 PTPN4_LCT


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 PTPN4_LCT


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
PTPN4ZZEF1, ATRX, LPL, KAT5, EEF1A1, EEF1G, GRID2, GRIN2A, MGMT, TK1, CRK, KCTD17, ADH5, CADM1, GOLIM4, LTBP1, MPP7, PAK4, PEX19, SHKBP1, SNRPD1, YWHAG, YWHAH, YWHAQ, YWHAZ, PTPN4, CRKL, C18orf25, UNC13B, CSNK2A1, CSNK2A2, SIRT1, YWHABLCTCANX, HSPA5


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 PTPN4_LCT


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.0 2018-04-02)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgenePTPN4P29074DB00630Alendronic acidTyrosine-protein phosphatase non-receptor type 4small moleculeapproved
TgeneLCTP09848DB00126Vitamin CLactase-phlorizin hydrolasesmall moleculeapproved|nutraceutical

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RelatedDiseases for PTPN4_LCT


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneLCTC0035222Respiratory Distress Syndrome, Adult1CTD_human
TgeneLCTC0268179Lactase Deficiency, Congenital1CTD_human;ORPHANET;UNIPROT