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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:APEX1-BRE (FusionGDB2 ID:5401)

Fusion Gene Summary for APEX1-BRE

check button Fusion gene summary
Fusion gene informationFusion gene name: APEX1-BRE
Fusion gene ID: 5401
HgeneTgene
Gene symbol

APEX1

BRE

Gene ID

328

9577

Gene nameapurinic/apyrimidinic endodeoxyribonuclease 1BRISC and BRCA1 A complex member 2
SynonymsAPE|APE1|APEN|APEX|APX|HAP1|REF1BRCC4|BRCC45|BRE
Cytomap

14q11.2

2p23.2

Type of geneprotein-codingprotein-coding
DescriptionDNA-(apurinic or apyrimidinic site) lyaseAP endonuclease class IAP lyaseAPEX nuclease (multifunctional DNA repair enzyme) 1apurinic-apyrimidinic endonuclease 1apurinic/apyrimidinic (abasic) endonucleasedeoxyribonuclease (apurinic or apyrimidinic)prBRISC and BRCA1-A complex member 2BRCA1-A complex subunit BREBRCA1/BRCA2-containing complex subunit 45BRCA1/BRCA2-containing complex, subunit 4brain and reproductive organ-expressed (TNFRSF1A modulator)brain and reproductive organ-expressed protein
Modification date2020032220200313
UniProtAcc

P27695

.
Ensembl transtripts involved in fusion geneENST00000557365, ENST00000216714, 
ENST00000398030, ENST00000555414, 
ENST00000557054, 		ENST00000342045, 
ENST00000344773, ENST00000361704, 
ENST00000379624, ENST00000379632, 
ENST00000603461, 
Fusion gene scores* DoF score3 X 4 X 2=2420 X 20 X 12=4800
# samples 430
** MAII scorelog2(4/24*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(30/4800*10)=-4
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: APEX1 [Title/Abstract] AND BRE [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAPEX1(20924929)-BRE(28340408), # 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
HgeneAPEX1

GO:0000723

telomere maintenance

24703901

HgeneAPEX1

GO:0006281

DNA repair

9560228

HgeneAPEX1

GO:0006284

base-excision repair

8932386

HgeneAPEX1

GO:0042981

regulation of apoptotic process

19934257

HgeneAPEX1

GO:0080111

DNA demethylation

21496894

HgeneAPEX1

GO:0097698

telomere maintenance via base-excision repair

24703901

TgeneBRE

GO:0043066

negative regulation of apoptotic process

15465831


check buttonFusion gene breakpoints across APEX1 (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 BRE (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
ChiTaRS5.0N/AAV694371APEX1chr14

20924929

+BREchr2

28340408

+


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Fusion Gene ORF analysis for APEX1-BRE

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
3UTR-intronENST00000557365ENST00000342045APEX1chr14

20924929

+BREchr2

28340408

+
3UTR-intronENST00000557365ENST00000344773APEX1chr14

20924929

+BREchr2

28340408

+
3UTR-intronENST00000557365ENST00000361704APEX1chr14

20924929

+BREchr2

28340408

+
3UTR-intronENST00000557365ENST00000379624APEX1chr14

20924929

+BREchr2

28340408

+
3UTR-intronENST00000557365ENST00000379632APEX1chr14

20924929

+BREchr2

28340408

+
3UTR-intronENST00000557365ENST00000603461APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000216714ENST00000342045APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000216714ENST00000344773APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000216714ENST00000361704APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000216714ENST00000379624APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000216714ENST00000379632APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000216714ENST00000603461APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000398030ENST00000342045APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000398030ENST00000344773APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000398030ENST00000361704APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000398030ENST00000379624APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000398030ENST00000379632APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000398030ENST00000603461APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000555414ENST00000342045APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000555414ENST00000344773APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000555414ENST00000361704APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000555414ENST00000379624APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000555414ENST00000379632APEX1chr14

20924929

+BREchr2

28340408

+
5CDS-intronENST00000555414ENST00000603461APEX1chr14

20924929

+BREchr2

28340408

+
intron-intronENST00000557054ENST00000342045APEX1chr14

20924929

+BREchr2

28340408

+
intron-intronENST00000557054ENST00000344773APEX1chr14

20924929

+BREchr2

28340408

+
intron-intronENST00000557054ENST00000361704APEX1chr14

20924929

+BREchr2

28340408

+
intron-intronENST00000557054ENST00000379624APEX1chr14

20924929

+BREchr2

28340408

+
intron-intronENST00000557054ENST00000379632APEX1chr14

20924929

+BREchr2

28340408

+
intron-intronENST00000557054ENST00000603461APEX1chr14

20924929

+BREchr2

28340408

+

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 APEX1-BRE


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 APEX1-BRE


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/:20924929/:28340408)
- 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
APEX1

P27695

.
FUNCTION: Multifunctional protein that plays a central role in the cellular response to oxidative stress. The two major activities of APEX1 are DNA repair and redox regulation of transcriptional factors. Functions as a apurinic/apyrimidinic (AP) endodeoxyribonuclease in the DNA base excision repair (BER) pathway of DNA lesions induced by oxidative and alkylating agents. Initiates repair of AP sites in DNA by catalyzing hydrolytic incision of the phosphodiester backbone immediately adjacent to the damage, generating a single-strand break with 5'-deoxyribose phosphate and 3'-hydroxyl ends. Does also incise at AP sites in the DNA strand of DNA/RNA hybrids, single-stranded DNA regions of R-loop structures, and single-stranded RNA molecules. Has a 3'-5' exoribonuclease activity on mismatched deoxyribonucleotides at the 3' termini of nicked or gapped DNA molecules during short-patch BER. Possesses a DNA 3' phosphodiesterase activity capable of removing lesions (such as phosphoglycolate) blocking the 3' side of DNA strand breaks. May also play a role in the epigenetic regulation of gene expression by participating in DNA demethylation. Acts as a loading factor for POLB onto non-incised AP sites in DNA and stimulates the 5'-terminal deoxyribose 5'-phosphate (dRp) excision activity of POLB. Plays a role in the protection from granzymes-mediated cellular repair leading to cell death. Also involved in the DNA cleavage step of class switch recombination (CSR). On the other hand, APEX1 also exerts reversible nuclear redox activity to regulate DNA binding affinity and transcriptional activity of transcriptional factors by controlling the redox status of their DNA-binding domain, such as the FOS/JUN AP-1 complex after exposure to IR. Involved in calcium-dependent down-regulation of parathyroid hormone (PTH) expression by binding to negative calcium response elements (nCaREs). Together with HNRNPL or the dimer XRCC5/XRCC6, associates with nCaRE, acting as an activator of transcriptional repression. Stimulates the YBX1-mediated MDR1 promoter activity, when acetylated at Lys-6 and Lys-7, leading to drug resistance. Acts also as an endoribonuclease involved in the control of single-stranded RNA metabolism. Plays a role in regulating MYC mRNA turnover by preferentially cleaving in between UA and CA dinucleotides of the MYC coding region determinant (CRD). In association with NMD1, plays a role in the rRNA quality control process during cell cycle progression. Associates, together with YBX1, on the MDR1 promoter. Together with NPM1, associates with rRNA. Binds DNA and RNA. {ECO:0000269|PubMed:10023679, ECO:0000269|PubMed:11118054, ECO:0000269|PubMed:11452037, ECO:0000269|PubMed:11809897, ECO:0000269|PubMed:11832948, ECO:0000269|PubMed:12524539, ECO:0000269|PubMed:16617147, ECO:0000269|PubMed:1719477, ECO:0000269|PubMed:18179823, ECO:0000269|PubMed:18439621, ECO:0000269|PubMed:18579163, ECO:0000269|PubMed:18809583, ECO:0000269|PubMed:19188445, ECO:0000269|PubMed:19401441, ECO:0000269|PubMed:19934257, ECO:0000269|PubMed:20699270, ECO:0000269|PubMed:21496894, ECO:0000269|PubMed:21762700, ECO:0000269|PubMed:8355688, ECO:0000269|PubMed:8621488, ECO:0000269|PubMed:8932375, ECO:0000269|PubMed:9108029, ECO:0000269|PubMed:9207062, ECO:0000269|PubMed:9560228, ECO:0000269|PubMed:9804799}.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 APEX1-BRE


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 APEX1-BRE


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 APEX1-BRE


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 APEX1-BRE


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