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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-S100A10 (FusionGDB2 ID:HG378938TG6281)

Fusion Gene Summary for MALAT1-S100A10

check button Fusion gene summary
Fusion gene informationFusion gene name: MALAT1-S100A10
Fusion gene ID: hg378938tg6281
HgeneTgene
Gene symbol

MALAT1

S100A10

Gene ID

378938

6281

Gene namemetastasis associated lung adenocarcinoma transcript 1S100 calcium binding protein A10
SynonymsHCN|LINC00047|NCRNA00047|NEAT2|PRO285342C|ANX2L|ANX2LG|CAL1L|CLP11|Ca[1]|GP11|P11|p10
Cytomap('MALAT1')('S100A10')

11q13.1

1q21.3

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)protein S100-A10S100 calcium binding protein A10 (annexin II ligand, calpactin I, light polypeptide (p11))annexin II ligand, calpactin I, light polypeptideannexin II tetramer (AIIt) p11 subunitcalpactin I light chaincalpactin-1 light chaincellular l
Modification date2020032920200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000534336, 
Fusion gene scores* DoF score99 X 133 X 14=18433811 X 9 X 6=594
# samples 12912
** MAII scorelog2(129/184338*10)=-7.15883862732779
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(12/594*10)=-2.30742852519225
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: MALAT1 [Title/Abstract] AND S100A10 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMALAT1(65267975)-S100A10(151955490), # 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
TgeneS100A10

GO:0001765

membrane raft assembly

23861394

TgeneS100A10

GO:0006900

vesicle budding from membrane

23861394

TgeneS100A10

GO:0072659

protein localization to plasma membrane

12198146



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-S100A10

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-S100A10


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-S100A10


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/:65267975/:151955490)
- 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-S100A10


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-S100A10


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-S100A10


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-S100A10


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
TgeneC0011581Depressive disorder3CTD_human;PSYGENET
TgeneC0041696Unipolar Depression3CTD_human;PSYGENET
TgeneC0005586Bipolar Disorder2PSYGENET
TgeneC1269683Major Depressive Disorder2PSYGENET
TgeneC0011570Mental Depression1PSYGENET
TgeneC0011573Endogenous depression1CTD_human
TgeneC0022548Keloid1CTD_human
TgeneC0023467Leukemia, Myelocytic, Acute1CTD_human
TgeneC0023893Liver Cirrhosis, Experimental1CTD_human
TgeneC0024517Major depression, single episode1PSYGENET
TgeneC0025149Medulloblastoma1CTD_human
TgeneC0025193Melancholia1CTD_human
TgeneC0026998Acute Myeloid Leukemia, M11CTD_human
TgeneC0086133Depressive Syndrome1CTD_human
TgeneC0205833Medullomyoblastoma1CTD_human
TgeneC0278510Childhood Medulloblastoma1CTD_human
TgeneC0278876Adult Medulloblastoma1CTD_human
TgeneC0282126Depression, Neurotic1CTD_human
TgeneC0344315Depressed mood1PSYGENET
TgeneC0349217Depressive episode, unspecified1PSYGENET
TgeneC0525045Mood Disorders1PSYGENET
TgeneC0751291Desmoplastic Medulloblastoma1CTD_human
TgeneC1275668Melanotic medulloblastoma1CTD_human
TgeneC1879321Acute Myeloid Leukemia (AML-M2)1CTD_human