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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: 20631

FusionGeneSummary for MALAT1_LIFR

check button Fusion gene summary
Fusion gene informationFusion gene name: MALAT1_LIFR
Fusion gene ID: 20631
HgeneTgene
Gene symbol

MALAT1

LIFR

Gene ID

378938

3977

Gene namemetastasis associated lung adenocarcinoma transcript 1LIF receptor alpha
SynonymsHCN|LINC00047|NCRNA00047|NEAT2|PRO2853CD118|LIF-R|SJS2|STWS|SWS
Cytomap

11q13.1

5p13.1

Type of genencRNAprotein-coding
Descriptionhepcarcinlong intergenic non-protein coding RNA 47metastasis associated lung adenocarcinoma transcript 1 (non-protein coding)nuclear enriched abundant transcript 2nuclear paraspeckle assembly transcript 2 (non-protein coding)leukemia inhibitory factor receptorCD118 antigenLIF receptorleukemia inhibitory factor receptor alpha
Modification date2018052720180523
UniProtAcc

P42702

Ensembl transtripts involved in fusion geneENST00000534336, ENST00000263409, 
ENST00000453190, ENST00000503088, 
Fusion gene scores* DoF score83 X 128 X 5=531202 X 2 X 2=8
# samples 1412
** MAII scorelog2(141/53120*10)=-5.23548807894813
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(2/8*10)=1.32192809488736
Context

PubMed: MALAT1 [Title/Abstract] AND LIFR [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
TgeneLIFR

GO:0008284

positive regulation of cell proliferation

7957045|8999038

TgeneLIFR

GO:0019221

cytokine-mediated signaling pathway

7957045

TgeneLIFR

GO:0034097

response to cytokine

8999038

TgeneLIFR

GO:0048861

leukemia inhibitory factor signaling pathway

8999038|12643274

TgeneLIFR

GO:0070120

ciliary neurotrophic factor-mediated signaling pathway

12643274


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
ChiTaRS3.1BG434574MALAT1chr11

65272307

+LIFRchr5

38530212

-
* 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
3UTR-intronENST00000534336ENST00000263409MALAT1chr11

65272307

+LIFRchr5

38530212

-
3UTR-intronENST00000534336ENST00000453190MALAT1chr11

65272307

+LIFRchr5

38530212

-
3UTR-intronENST00000534336ENST00000503088MALAT1chr11

65272307

+LIFRchr5

38530212

-

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FusionProtFeatures for MALAT1_LIFR


check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
MALAT1

LIFR

P42702

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}. Signal-transducing molecule. May have a common pathwaywith IL6ST. The soluble form inhibits the biological activity ofLIF by blocking its binding to receptors on target cells.

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 MALAT1_LIFR


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 MALAT1_LIFR


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 MALAT1_LIFR


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 MALAT1_LIFR


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMALAT1C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneMALAT1C0023903Liver neoplasms1CTD_human
HgeneMALAT1C0027626Neoplasm Invasiveness1CTD_human
HgeneMALAT1C0027627Neoplasm Metastasis1CTD_human
HgeneMALAT1C0032460Polycystic Ovary Syndrome1CTD_human
HgeneMALAT1C0236663Alcohol withdrawal syndrome1PSYGENET
HgeneMALAT1C0279626Squamous cell carcinoma of esophagus1CTD_human
TgeneLIFRC0796176STUVE-WIEDEMANN SYNDROME2CTD_human;ORPHANET;UNIPROT
TgeneLIFRC0032460Polycystic Ovary Syndrome1CTD_human
TgeneLIFRC0033578Prostatic Neoplasms1CTD_human
TgeneLIFRC0036341Schizophrenia1PSYGENET
TgeneLIFRC0349398Paranoid delusion1PSYGENET