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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:MALAT1-CDH2 (FusionGDB2 ID:HG378938TG1000)

Fusion Gene Summary for MALAT1-CDH2

check button Fusion gene summary
Fusion gene informationFusion gene name: MALAT1-CDH2
Fusion gene ID: hg378938tg1000
HgeneTgene
Gene symbol

MALAT1

CDH2

Gene ID

378938

1000

Gene namemetastasis associated lung adenocarcinoma transcript 1cadherin 2
SynonymsHCN|LINC00047|NCRNA00047|NEAT2|PRO2853CD325|CDHN|CDw325|NCAD
Cytomap('MALAT1')('CDH2')

11q13.1

18q12.1

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)cadherin-2N-cadherin 1cadherin 2, type 1, N-cadherin (neuronal)calcium-dependent adhesion protein, neuronalneural cadherin
Modification date2020032920200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000534336, 
Fusion gene scores* DoF score99 X 133 X 14=1843389 X 10 X 3=270
# samples 12912
** MAII scorelog2(129/184338*10)=-7.15883862732779
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(12/270*10)=-1.16992500144231
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MALAT1 [Title/Abstract] AND CDH2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMALAT1(65266676)-CDH2(25591338), # 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


check button Fusion gene information
* 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


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Fusion Gene ORF analysis for MALAT1-CDH2

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

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 MALAT1-CDH2


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)


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Fusion Protein Features for MALAT1-CDH2


check button Four levels of functional features of fusion genes
Go to FGviewer search page for the most frequent breakpoint (https://ccsmweb.uth.edu/FGviewer/:65266676/:25591338)
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
- How to search
1. Put your fusion gene symbol.
2. Press the tab key until there will be shown the breakpoint information filled.
4. Go down and press 'Search' tab twice.
4. Go down to have the hyperlink of the search result.
5. Click the hyperlink.
6. See the FGviewer result for your fusion gene.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.FUNCTION: Transcriptional activator which is required for calcium-dependent dendritic growth and branching in cortical neurons. Recruits CREB-binding protein (CREBBP) to nuclear bodies. Component of the CREST-BRG1 complex, a multiprotein complex that regulates promoter activation by orchestrating a calcium-dependent release of a repressor complex and a recruitment of an activator complex. In resting neurons, transcription of the c-FOS promoter is inhibited by BRG1-dependent recruitment of a phospho-RB1-HDAC1 repressor complex. Upon calcium influx, RB1 is dephosphorylated by calcineurin, which leads to release of the repressor complex. At the same time, there is increased recruitment of CREBBP to the promoter by a CREST-dependent mechanism, which leads to transcriptional activation. The CREST-BRG1 complex also binds to the NR2B promoter, and activity-dependent induction of NR2B expression involves a release of HDAC1 and recruitment of CREBBP (By similarity). {ECO:0000250}.

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 MALAT1-CDH2


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 MALAT1-CDH2


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 MALAT1-CDH2


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 MALAT1-CDH2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneMALAT1C0006142Malignant neoplasm of breast2CTD_human
HgeneMALAT1C0027627Neoplasm Metastasis2CTD_human
HgeneMALAT1C0678222Breast Carcinoma2CTD_human
HgeneMALAT1C1257931Mammary Neoplasms, Human2CTD_human
HgeneMALAT1C1458155Mammary Neoplasms2CTD_human
HgeneMALAT1C4704874Mammary Carcinoma, Human2CTD_human
HgeneMALAT1C0019193Hepatitis, Toxic1CTD_human
HgeneMALAT1C0023467Leukemia, Myelocytic, Acute1CTD_human
HgeneMALAT1C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneMALAT1C0023903Liver neoplasms1CTD_human
HgeneMALAT1C0026998Acute Myeloid Leukemia, M11CTD_human
HgeneMALAT1C0027626Neoplasm Invasiveness1CTD_human
HgeneMALAT1C0032460Polycystic Ovary Syndrome1CTD_human
HgeneMALAT1C0236663Alcohol withdrawal syndrome1PSYGENET
HgeneMALAT1C0279626Squamous cell carcinoma of esophagus1CTD_human
HgeneMALAT1C0345904Malignant neoplasm of liver1CTD_human
HgeneMALAT1C0860207Drug-Induced Liver Disease1CTD_human
HgeneMALAT1C1136382Sclerocystic Ovaries1CTD_human
HgeneMALAT1C1262760Hepatitis, Drug-Induced1CTD_human
HgeneMALAT1C1879321Acute Myeloid Leukemia (AML-M2)1CTD_human
HgeneMALAT1C3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneMALAT1C4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneMALAT1C4279912Chemically-Induced Liver Toxicity1CTD_human
TgeneC0006142Malignant neoplasm of breast1CTD_human
TgeneC0013261Duane Retraction Syndrome1GENOMICS_ENGLAND
TgeneC0024623Malignant neoplasm of stomach1CTD_human
TgeneC0027626Neoplasm Invasiveness1CTD_human
TgeneC0027627Neoplasm Metastasis1CTD_human
TgeneC0027746Nerve Degeneration1CTD_human
TgeneC0038220Status Epilepticus1CTD_human
TgeneC0038356Stomach Neoplasms1CTD_human
TgeneC0151744Myocardial Ischemia1CTD_human
TgeneC0235874Disease Exacerbation1CTD_human
TgeneC0270823Petit mal status1CTD_human
TgeneC0311335Grand Mal Status Epilepticus1CTD_human
TgeneC0393734Complex Partial Status Epilepticus1CTD_human
TgeneC0454455Mirror movements disorder1GENOMICS_ENGLAND
TgeneC0557874Global developmental delay1GENOMICS_ENGLAND
TgeneC0678222Breast Carcinoma1CTD_human
TgeneC0744356Abnormality of the genital system1GENOMICS_ENGLAND
TgeneC0751522Status Epilepticus, Subclinical1CTD_human
TgeneC0751523Non-Convulsive Status Epilepticus1CTD_human
TgeneC0751524Simple Partial Status Epilepticus1CTD_human
TgeneC1257931Mammary Neoplasms, Human1CTD_human
TgeneC1458155Mammary Neoplasms1CTD_human
TgeneC1708349Hereditary Diffuse Gastric Cancer1CTD_human
TgeneC1837249Malformations of Cortical Development, Group II1GENOMICS_ENGLAND
TgeneC1842581Abnormal corpus callosum morphology1GENOMICS_ENGLAND
TgeneC3714756Intellectual Disability1GENOMICS_ENGLAND
TgeneC4316870Abnormality of the eye1GENOMICS_ENGLAND
TgeneC4704874Mammary Carcinoma, Human1CTD_human