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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:APAF1-FMN1 (FusionGDB2 ID:5323)

Fusion Gene Summary for APAF1-FMN1

check button Fusion gene summary
Fusion gene informationFusion gene name: APAF1-FMN1
Fusion gene ID: 5323
HgeneTgene
Gene symbol

APAF1

FMN1

Gene ID

317

342184

Gene nameapoptotic peptidase activating factor 1formin 1
SynonymsAPAF-1|CED4FMN|LD
Cytomap

12q23.1

15q13.3

Type of geneprotein-codingprotein-coding
Descriptionapoptotic protease-activating factor 1formin-1formin (limb deformity)limb deformity protein homolog
Modification date2020031520200313
UniProtAcc

O14727

Q68DA7

Ensembl transtripts involved in fusion geneENST00000339433, ENST00000357310, 
ENST00000359972, ENST00000547045, 
ENST00000549007, ENST00000550527, 
ENST00000551964, ENST00000333991, 
ENST00000547666, ENST00000547743, 
ENST00000552268, 		ENST00000320930, 
ENST00000558197, ENST00000559150, 
ENST00000334528, ENST00000559047, 
ENST00000561249, 
Fusion gene scores* DoF score5 X 5 X 4=1009 X 8 X 4=288
# samples 59
** MAII scorelog2(5/100*10)=-1
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(9/288*10)=-1.67807190511264
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: APAF1 [Title/Abstract] AND FMN1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAPAF1(99065497)-FMN1(33261678), # samples:1
Anticipated loss of major functional domain due to fusion event.APAF1-FMN1 seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
APAF1-FMN1 seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
* 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
HgeneAPAF1

GO:0006919

activation of cysteine-type endopeptidase activity involved in apoptotic process

21827945

HgeneAPAF1

GO:0008635

activation of cysteine-type endopeptidase activity involved in apoptotic process by cytochrome c

9267021


check buttonFusion gene breakpoints across APAF1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check buttonFusion gene breakpoints across FMN1 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

check button Fusion gene information from two resources (ChiTars 5.0 and ChimerDB 4.0)
* 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
ChimerDB4STADTCGA-KB-A93JAPAF1chr12

99065497

+FMN1chr15

33261678

-


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Fusion Gene ORF analysis for APAF1-FMN1

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-intronENST00000339433ENST00000320930APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000339433ENST00000558197APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000339433ENST00000559150APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000357310ENST00000320930APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000357310ENST00000558197APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000357310ENST00000559150APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000359972ENST00000320930APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000359972ENST00000558197APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000359972ENST00000559150APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000547045ENST00000320930APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000547045ENST00000558197APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000547045ENST00000559150APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000549007ENST00000320930APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000549007ENST00000558197APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000549007ENST00000559150APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000550527ENST00000320930APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000550527ENST00000558197APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000550527ENST00000559150APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000551964ENST00000320930APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000551964ENST00000558197APAF1chr12

99065497

+FMN1chr15

33261678

-
5CDS-intronENST00000551964ENST00000559150APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000339433ENST00000334528APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000339433ENST00000559047APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000339433ENST00000561249APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000357310ENST00000334528APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000357310ENST00000559047APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000357310ENST00000561249APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000359972ENST00000334528APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000359972ENST00000559047APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000359972ENST00000561249APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000547045ENST00000334528APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000547045ENST00000559047APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000547045ENST00000561249APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000549007ENST00000334528APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000549007ENST00000559047APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000549007ENST00000561249APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000550527ENST00000334528APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000550527ENST00000559047APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000550527ENST00000561249APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000551964ENST00000334528APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000551964ENST00000559047APAF1chr12

99065497

+FMN1chr15

33261678

-
Frame-shiftENST00000551964ENST00000561249APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-3CDSENST00000333991ENST00000334528APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-3CDSENST00000333991ENST00000559047APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-3CDSENST00000333991ENST00000561249APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-3CDSENST00000547666ENST00000334528APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-3CDSENST00000547666ENST00000559047APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-3CDSENST00000547666ENST00000561249APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-3CDSENST00000547743ENST00000334528APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-3CDSENST00000547743ENST00000559047APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-3CDSENST00000547743ENST00000561249APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-3CDSENST00000552268ENST00000334528APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-3CDSENST00000552268ENST00000559047APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-3CDSENST00000552268ENST00000561249APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-intronENST00000333991ENST00000320930APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-intronENST00000333991ENST00000558197APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-intronENST00000333991ENST00000559150APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-intronENST00000547666ENST00000320930APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-intronENST00000547666ENST00000558197APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-intronENST00000547666ENST00000559150APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-intronENST00000547743ENST00000320930APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-intronENST00000547743ENST00000558197APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-intronENST00000547743ENST00000559150APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-intronENST00000552268ENST00000320930APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-intronENST00000552268ENST00000558197APAF1chr12

99065497

+FMN1chr15

33261678

-
intron-intronENST00000552268ENST00000559150APAF1chr12

99065497

+FMN1chr15

33261678

-

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 APAF1-FMN1


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)

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions. We integrated a total of 44 different types of human genomic feature loci information across five big categories including virus integration sites, repeats, structural variants, chromatin states, and gene expression regulation. More details are in help page.

check buttonDistribution of 44 human genomic features loci across 20kb length fusion breakpoint regions that are ovelapped with the top 1% feature importance score regions. More details are in help page.

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Fusion Protein Features for APAF1-FMN1


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/:99065497/:33261678)
- 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
APAF1

O14727

FMN1

Q68DA7

FUNCTION: Oligomeric Apaf-1 mediates the cytochrome c-dependent autocatalytic activation of pro-caspase-9 (Apaf-3), leading to the activation of caspase-3 and apoptosis. This activation requires ATP. Isoform 6 is less effective in inducing apoptosis. {ECO:0000269|PubMed:10393175, ECO:0000269|PubMed:12804598}.FUNCTION: Plays a role in the formation of adherens junction and the polymerization of linear actin cables. {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 APAF1-FMN1


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 APAF1-FMN1


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 APAF1-FMN1


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 APAF1-FMN1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource