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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:CASP9-FBXO42 (FusionGDB2 ID:HG842TG54455)

Fusion Gene Summary for CASP9-FBXO42

check button Fusion gene summary
Fusion gene informationFusion gene name: CASP9-FBXO42
Fusion gene ID: hg842tg54455
HgeneTgene
Gene symbol

CASP9

FBXO42

Gene ID

842

54455

Gene namecaspase 9F-box protein 42
SynonymsAPAF-3|APAF3|ICE-LAP6|MCH6|PPP1R56Fbx42|JFK
Cytomap('CASP9')('FBXO42')

1p36.21

1p36.13

Type of geneprotein-codingprotein-coding
Descriptioncaspase-9ICE-like apoptotic protease 6apoptotic protease MCH-6apoptotic protease activating factor 3caspase 9, apoptosis-related cysteine peptidaseprotein phosphatase 1, regulatory subunit 56F-box only protein 42just one F-box and Kelch domain-containing protein
Modification date2020032220200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000333868, ENST00000348549, 
ENST00000375890, ENST00000546424, 
ENST00000469637, 
Fusion gene scores* DoF score1 X 1 X 1=110 X 11 X 6=660
# samples 114
** MAII scorelog2(1/1*10)=3.32192809488736log2(14/660*10)=-2.23703919730085
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CASP9 [Title/Abstract] AND FBXO42 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCASP9(15844604)-FBXO42(16641930), # 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
HgeneCASP9

GO:0006974

cellular response to DNA damage stimulus

15657060

HgeneCASP9

GO:0034644

cellular response to UV

15657060

HgeneCASP9

GO:0042770

signal transduction in response to DNA damage

15657060



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
ChimerDB4ESCATCGA-IG-A3YACASP9chr1

15844604

-FBXO42chr1

16641930

-


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Fusion Gene ORF analysis for CASP9-FBXO42

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
5CDS-5UTRENST00000333868ENST00000375592CASP9chr1

15844604

-FBXO42chr1

16641930

-
5CDS-5UTRENST00000348549ENST00000375592CASP9chr1

15844604

-FBXO42chr1

16641930

-
5CDS-5UTRENST00000375890ENST00000375592CASP9chr1

15844604

-FBXO42chr1

16641930

-
5CDS-5UTRENST00000546424ENST00000375592CASP9chr1

15844604

-FBXO42chr1

16641930

-
5CDS-intronENST00000333868ENST00000478089CASP9chr1

15844604

-FBXO42chr1

16641930

-
5CDS-intronENST00000348549ENST00000478089CASP9chr1

15844604

-FBXO42chr1

16641930

-
5CDS-intronENST00000375890ENST00000478089CASP9chr1

15844604

-FBXO42chr1

16641930

-
5CDS-intronENST00000546424ENST00000478089CASP9chr1

15844604

-FBXO42chr1

16641930

-
intron-5UTRENST00000469637ENST00000375592CASP9chr1

15844604

-FBXO42chr1

16641930

-
intron-intronENST00000469637ENST00000478089CASP9chr1

15844604

-FBXO42chr1

16641930

-

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 CASP9-FBXO42


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 CASP9-FBXO42


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/:15844604/:16641930)
- 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 CASP9-FBXO42


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 CASP9-FBXO42


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 CASP9-FBXO42


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 CASP9-FBXO42


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCASP9C0007786Brain Ischemia1CTD_human
HgeneCASP9C0007787Transient Ischemic Attack1CTD_human
HgeneCASP9C0013604Edema1CTD_human
HgeneCASP9C0027055Myocardial Reperfusion Injury1CTD_human
HgeneCASP9C0027765nervous system disorder1CTD_human
HgeneCASP9C0033578Prostatic Neoplasms1CTD_human
HgeneCASP9C0035305Retinal Detachment1CTD_human
HgeneCASP9C0151603Anasarca1CTD_human
HgeneCASP9C0339546Retinal Pigment Epithelial Detachment1CTD_human
HgeneCASP9C0376358Malignant neoplasm of prostate1CTD_human
HgeneCASP9C0472381Posterior Circulation Transient Ischemic Attack1CTD_human
HgeneCASP9C0751019Carotid Circulation Transient Ischemic Attack1CTD_human
HgeneCASP9C0751020Transient Ischemic Attack, Vertebrobasilar Circulation1CTD_human
HgeneCASP9C0751021Crescendo Transient Ischemic Attacks1CTD_human
HgeneCASP9C0751022Brain Stem Ischemia, Transient1CTD_human
HgeneCASP9C0917798Cerebral Ischemia1CTD_human
HgeneCASP9C0917805Transient Cerebral Ischemia1CTD_human
HgeneCASP9C1527335Transient Ischemic Attack, Anterior Circulation1CTD_human
HgeneCASP9C4721453Peripheral Nervous System Diseases1CTD_human