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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:SMAD2-RPS4Y1 (FusionGDB2 ID:HG4087TG6192)

Fusion Gene Summary for SMAD2-RPS4Y1

check button Fusion gene summary
Fusion gene informationFusion gene name: SMAD2-RPS4Y1
Fusion gene ID: hg4087tg6192
HgeneTgene
Gene symbol

SMAD2

RPS4Y1

Gene ID

4087

6192

Gene nameSMAD family member 2ribosomal protein S4 Y-linked 1
SynonymsJV18|JV18-1|MADH2|MADR2|hMAD-2|hSMAD2RPS4Y|S4
Cytomap('SMAD2')('RPS4Y1')

18q21.1

Yp11.2

Type of geneprotein-codingprotein-coding
Descriptionmothers against decapentaplegic homolog 2MAD homolog 2SMAD, mothers against DPP homolog 2Sma- and Mad-related protein 2mother against DPP homolog 240S ribosomal protein S4, Y isoform 140S ribosomal protein S4, Yribosomal protein S4, Y-linkedribosomal protein S4Ysmall ribosomal subunit protein eS4
Modification date2020032220200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000262160, ENST00000356825, 
ENST00000402690, ENST00000586040, 
ENST00000587353, ENST00000591214, 
Fusion gene scores* DoF score21 X 18 X 8=302412 X 13 X 3=468
# samples 2313
** MAII scorelog2(23/3024*10)=-3.7167523732767
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(13/468*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: SMAD2 [Title/Abstract] AND RPS4Y1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointSMAD2(45363929)-RPS4Y1(2734988), # 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
HgeneSMAD2

GO:0007179

transforming growth factor beta receptor signaling pathway

8752209|9389648|9732876|18548003

HgeneSMAD2

GO:0007182

common-partner SMAD protein phosphorylation

16806156

HgeneSMAD2

GO:0007183

SMAD protein complex assembly

9111321

HgeneSMAD2

GO:0045893

positive regulation of transcription, DNA-templated

9311995|9389648|9732876

HgeneSMAD2

GO:0045944

positive regulation of transcription by RNA polymerase II

9389648

HgeneSMAD2

GO:0070723

response to cholesterol

17878231



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 SMAD2-RPS4Y1

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 SMAD2-RPS4Y1


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 SMAD2-RPS4Y1


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/:45363929/:2734988)
- 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 SMAD2-RPS4Y1


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 SMAD2-RPS4Y1


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 SMAD2-RPS4Y1


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 SMAD2-RPS4Y1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneSMAD2C4707243Familial thoracic aortic aneurysm and aortic dissection6CLINGEN;GENOMICS_ENGLAND
HgeneSMAD2C0376634Craniofacial Abnormalities2CTD_human
HgeneSMAD2C0019189Hepatitis, Chronic1CTD_human
HgeneSMAD2C0023893Liver Cirrhosis, Experimental1CTD_human
HgeneSMAD2C0149519Chronic Persistent Hepatitis1CTD_human
HgeneSMAD2C0152021Congenital heart disease1GENOMICS_ENGLAND
HgeneSMAD2C0265287Acromicric Dysplasia1CTD_human
HgeneSMAD2C0520463Chronic active hepatitis1CTD_human
HgeneSMAD2C0524611Cryptogenic Chronic Hepatitis1CTD_human
HgeneSMAD2C0600519Ventricular Remodeling1CTD_human
HgeneSMAD2C0600520Left Ventricle Remodeling1CTD_human
HgeneSMAD2C1876165Copper-Overload Cirrhosis1CTD_human
HgeneSMAD2C2697932Loeys-Dietz Syndrome1GENOMICS_ENGLAND
HgeneSMAD2C3489726Geleophysic dysplasia1CTD_human