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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:APOA2-TYK2 (FusionGDB2 ID:5523)

Fusion Gene Summary for APOA2-TYK2

check button Fusion gene summary
Fusion gene informationFusion gene name: APOA2-TYK2
Fusion gene ID: 5523
HgeneTgene
Gene symbol

APOA2

TYK2

Gene ID

336

7297

Gene nameapolipoprotein A2tyrosine kinase 2
SynonymsApo-AII|ApoA-II|apoAIIIMD35|JTK1
Cytomap

1q23.3

19p13.2

Type of geneprotein-codingprotein-coding
Descriptionapolipoprotein A-IInon-receptor tyrosine-protein kinase TYK2
Modification date2020032720200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000367990, ENST00000463812, 
ENST00000468465, ENST00000470459, 
ENST00000464492, ENST00000491350, 
ENST00000264818, ENST00000524462, 
ENST00000525621, ENST00000529370, 
ENST00000529422, 
Fusion gene scores* DoF score28 X 4 X 2=22452 X 14 X 18=13104
# samples 2954
** MAII scorelog2(29/224*10)=0.37255416795733
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(54/13104*10)=-4.60090404459018
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: APOA2 [Title/Abstract] AND TYK2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAPOA2(161192082)-TYK2(10491352), # 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
HgeneAPOA2

GO:0002740

negative regulation of cytokine secretion involved in immune response

12458630

HgeneAPOA2

GO:0006656

phosphatidylcholine biosynthetic process

14967812

HgeneAPOA2

GO:0009395

phospholipid catabolic process

14967812

HgeneAPOA2

GO:0009749

response to glucose

14988251

HgeneAPOA2

GO:0010873

positive regulation of cholesterol esterification

14967812

HgeneAPOA2

GO:0010903

negative regulation of very-low-density lipoprotein particle remodeling

14967812

HgeneAPOA2

GO:0018158

protein oxidation

12576517

HgeneAPOA2

GO:0018206

peptidyl-methionine modification

12576517

HgeneAPOA2

GO:0031647

regulation of protein stability

14967812

HgeneAPOA2

GO:0033344

cholesterol efflux

11162594

HgeneAPOA2

GO:0033700

phospholipid efflux

11162594

HgeneAPOA2

GO:0034370

triglyceride-rich lipoprotein particle remodeling

14967812

HgeneAPOA2

GO:0034374

low-density lipoprotein particle remodeling

8106353

HgeneAPOA2

GO:0034375

high-density lipoprotein particle remodeling

8106353|14967812

HgeneAPOA2

GO:0034380

high-density lipoprotein particle assembly

218942

HgeneAPOA2

GO:0034384

high-density lipoprotein particle clearance

10764676

HgeneAPOA2

GO:0042632

cholesterol homeostasis

14967812

HgeneAPOA2

GO:0043691

reverse cholesterol transport

14967812

HgeneAPOA2

GO:0045416

positive regulation of interleukin-8 biosynthetic process

11591715

HgeneAPOA2

GO:0046340

diacylglycerol catabolic process

14967812

HgeneAPOA2

GO:0050766

positive regulation of phagocytosis

20495215

HgeneAPOA2

GO:0050821

protein stabilization

20495215

HgeneAPOA2

GO:0050995

negative regulation of lipid catabolic process

14967812

HgeneAPOA2

GO:0050996

positive regulation of lipid catabolic process

8640403

HgeneAPOA2

GO:0060192

negative regulation of lipase activity

14967812

HgeneAPOA2

GO:0060621

negative regulation of cholesterol import

10764676

HgeneAPOA2

GO:0060695

negative regulation of cholesterol transporter activity

8106353


check buttonFusion gene breakpoints across APOA2 (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 TYK2 (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
ChimerDB4LIHCTCGA-G3-A3CH-01AAPOA2chr1

161192082

-TYK2chr19

10491352

-


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Fusion Gene ORF analysis for APOA2-TYK2

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-intronENST00000367990ENST00000264818APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000367990ENST00000524462APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000367990ENST00000525621APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000367990ENST00000529370APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000367990ENST00000529422APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000463812ENST00000264818APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000463812ENST00000524462APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000463812ENST00000525621APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000463812ENST00000529370APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000463812ENST00000529422APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000468465ENST00000264818APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000468465ENST00000524462APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000468465ENST00000525621APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000468465ENST00000529370APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000468465ENST00000529422APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000470459ENST00000264818APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000470459ENST00000524462APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000470459ENST00000525621APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000470459ENST00000529370APOA2chr1

161192082

-TYK2chr19

10491352

-
5CDS-intronENST00000470459ENST00000529422APOA2chr1

161192082

-TYK2chr19

10491352

-
intron-intronENST00000464492ENST00000264818APOA2chr1

161192082

-TYK2chr19

10491352

-
intron-intronENST00000464492ENST00000524462APOA2chr1

161192082

-TYK2chr19

10491352

-
intron-intronENST00000464492ENST00000525621APOA2chr1

161192082

-TYK2chr19

10491352

-
intron-intronENST00000464492ENST00000529370APOA2chr1

161192082

-TYK2chr19

10491352

-
intron-intronENST00000464492ENST00000529422APOA2chr1

161192082

-TYK2chr19

10491352

-
intron-intronENST00000491350ENST00000264818APOA2chr1

161192082

-TYK2chr19

10491352

-
intron-intronENST00000491350ENST00000524462APOA2chr1

161192082

-TYK2chr19

10491352

-
intron-intronENST00000491350ENST00000525621APOA2chr1

161192082

-TYK2chr19

10491352

-
intron-intronENST00000491350ENST00000529370APOA2chr1

161192082

-TYK2chr19

10491352

-
intron-intronENST00000491350ENST00000529422APOA2chr1

161192082

-TYK2chr19

10491352

-

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 APOA2-TYK2


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 APOA2-TYK2


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/:161192082/:10491352)
- 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 APOA2-TYK2


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 APOA2-TYK2


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 APOA2-TYK2


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 APOA2-TYK2


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