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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:HIF1A-VRK1 (FusionGDB2 ID:36349)

Fusion Gene Summary for HIF1A-VRK1

check button Fusion gene summary
Fusion gene informationFusion gene name: HIF1A-VRK1
Fusion gene ID: 36349
HgeneTgene
Gene symbol

HIF1A

VRK1

Gene ID

3091

7443

Gene namehypoxia inducible factor 1 subunit alphaVRK serine/threonine kinase 1
SynonymsHIF-1-alpha|HIF-1A|HIF-1alpha|HIF1|HIF1-ALPHA|MOP1|PASD8|bHLHe78PCH1|PCH1A
Cytomap

14q23.2

14q32.2

Type of geneprotein-codingprotein-coding
Descriptionhypoxia-inducible factor 1-alphaARNT interacting proteinPAS domain-containing protein 8basic-helix-loop-helix-PAS protein MOP1class E basic helix-loop-helix protein 78hypoxia inducible factor 1 alpha subunithypoxia inducible factor 1, alpha subunit serine/threonine-protein kinase VRK1vaccinia related kinase 1vaccinia virus B1R-related kinase 1
Modification date2020032920200329
UniProtAcc

Q16665

.
Ensembl transtripts involved in fusion geneENST00000323441, ENST00000337138, 
ENST00000394997, ENST00000539097, 
ENST00000557206, ENST00000557538, 
ENST00000216639, ENST00000555067, 
Fusion gene scores* DoF score14 X 11 X 10=154012 X 7 X 7=588
# samples 2415
** MAII scorelog2(24/1540*10)=-2.68182403997375
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/588*10)=-1.97085365434048
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HIF1A [Title/Abstract] AND VRK1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHIF1A(62162557)-VRK1(97299804), # samples:3
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
HgeneHIF1A

GO:0001666

response to hypoxia

8756616|9887100|11782478|15261140|18419598

HgeneHIF1A

GO:0006355

regulation of transcription, DNA-templated

11782478|15261140

HgeneHIF1A

GO:0010468

regulation of gene expression

18419598

HgeneHIF1A

GO:0010573

vascular endothelial growth factor production

12958148

HgeneHIF1A

GO:0010575

positive regulation of vascular endothelial growth factor production

8756616

HgeneHIF1A

GO:0010628

positive regulation of gene expression

15459207|24244340

HgeneHIF1A

GO:0032364

oxygen homeostasis

16956324

HgeneHIF1A

GO:0043619

regulation of transcription from RNA polymerase II promoter in response to oxidative stress

8089148|8387214

HgeneHIF1A

GO:0045893

positive regulation of transcription, DNA-templated

8089148|9887100|25043030

HgeneHIF1A

GO:0045944

positive regulation of transcription by RNA polymerase II

11573933

HgeneHIF1A

GO:0046886

positive regulation of hormone biosynthetic process

1448077

HgeneHIF1A

GO:0061419

positive regulation of transcription from RNA polymerase II promoter in response to hypoxia

22735262

HgeneHIF1A

GO:0071456

cellular response to hypoxia

11573933|19528298|20889502

HgeneHIF1A

GO:1902895

positive regulation of pri-miRNA transcription by RNA polymerase II

19782034

HgeneHIF1A

GO:1903377

negative regulation of oxidative stress-induced neuron intrinsic apoptotic signaling pathway

24899725

TgeneVRK1

GO:0006468

protein phosphorylation

22194607

TgeneVRK1

GO:0043987

histone H3-S10 phosphorylation

22194607

TgeneVRK1

GO:0046777

protein autophosphorylation

21543316|22194607

TgeneVRK1

GO:0072355

histone H3-T3 phosphorylation

22194607

TgeneVRK1

GO:0090166

Golgi disassembly

19103756


check buttonFusion gene breakpoints across HIF1A (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 VRK1 (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
ChimerDB4LGGTCGA-R8-A6MK-01AHIF1Achr14

62162557

-VRK1chr14

97299804

+
ChimerDB4LGGTCGA-R8-A6MK-01AHIF1Achr14

62162557

+VRK1chr14

97299804

+
ChimerDB4LGGTCGA-R8-A6MKHIF1Achr14

62162557

+VRK1chr14

97299803

+
ChimerDB4LGGTCGA-R8-A6MKHIF1Achr14

62162557

+VRK1chr14

97299804

+


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Fusion Gene ORF analysis for HIF1A-VRK1

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-5UTRENST00000323441ENST00000216639HIF1Achr14

62162557

+VRK1chr14

97299804

+
5CDS-5UTRENST00000323441ENST00000216639HIF1Achr14

62162557

+VRK1chr14

97299803

+
5CDS-5UTRENST00000337138ENST00000216639HIF1Achr14

62162557

+VRK1chr14

97299804

+
5CDS-5UTRENST00000337138ENST00000216639HIF1Achr14

62162557

+VRK1chr14

97299803

+
5CDS-5UTRENST00000394997ENST00000216639HIF1Achr14

62162557

+VRK1chr14

97299804

+
5CDS-5UTRENST00000394997ENST00000216639HIF1Achr14

62162557

+VRK1chr14

97299803

+
5CDS-intronENST00000323441ENST00000555067HIF1Achr14

62162557

+VRK1chr14

97299804

+
5CDS-intronENST00000323441ENST00000555067HIF1Achr14

62162557

+VRK1chr14

97299803

+
5CDS-intronENST00000337138ENST00000555067HIF1Achr14

62162557

+VRK1chr14

97299804

+
5CDS-intronENST00000337138ENST00000555067HIF1Achr14

62162557

+VRK1chr14

97299803

+
5CDS-intronENST00000394997ENST00000555067HIF1Achr14

62162557

+VRK1chr14

97299804

+
5CDS-intronENST00000394997ENST00000555067HIF1Achr14

62162557

+VRK1chr14

97299803

+
intron-5UTRENST00000539097ENST00000216639HIF1Achr14

62162557

+VRK1chr14

97299804

+
intron-5UTRENST00000539097ENST00000216639HIF1Achr14

62162557

+VRK1chr14

97299803

+
intron-5UTRENST00000557206ENST00000216639HIF1Achr14

62162557

+VRK1chr14

97299804

+
intron-5UTRENST00000557206ENST00000216639HIF1Achr14

62162557

+VRK1chr14

97299803

+
intron-5UTRENST00000557538ENST00000216639HIF1Achr14

62162557

+VRK1chr14

97299804

+
intron-5UTRENST00000557538ENST00000216639HIF1Achr14

62162557

+VRK1chr14

97299803

+
intron-intronENST00000539097ENST00000555067HIF1Achr14

62162557

+VRK1chr14

97299804

+
intron-intronENST00000539097ENST00000555067HIF1Achr14

62162557

+VRK1chr14

97299803

+
intron-intronENST00000557206ENST00000555067HIF1Achr14

62162557

+VRK1chr14

97299804

+
intron-intronENST00000557206ENST00000555067HIF1Achr14

62162557

+VRK1chr14

97299803

+
intron-intronENST00000557538ENST00000555067HIF1Achr14

62162557

+VRK1chr14

97299804

+
intron-intronENST00000557538ENST00000555067HIF1Achr14

62162557

+VRK1chr14

97299803

+

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 HIF1A-VRK1


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)
HIF1Achr1462162557+VRK1chr1497299803+0.0004408870.9995591
HIF1Achr1462162557+VRK1chr1497299803+0.0004408870.9995591
HIF1Achr1462162557+VRK1chr1497299803+0.0004408870.9995591
HIF1Achr1462162557+VRK1chr1497299803+0.0004408870.9995591

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.
genomic feature of top 1%

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Fusion Protein Features for HIF1A-VRK1


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/:62162557/:97299804)
- 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
HIF1A

Q16665

.
FUNCTION: Functions as a master transcriptional regulator of the adaptive response to hypoxia. Under hypoxic conditions, activates the transcription of over 40 genes, including erythropoietin, glucose transporters, glycolytic enzymes, vascular endothelial growth factor, HILPDA, and other genes whose protein products increase oxygen delivery or facilitate metabolic adaptation to hypoxia. Plays an essential role in embryonic vascularization, tumor angiogenesis and pathophysiology of ischemic disease. Heterodimerizes with ARNT; heterodimer binds to core DNA sequence 5'-TACGTG-3' within the hypoxia response element (HRE) of target gene promoters (By similarity). Activation requires recruitment of transcriptional coactivators such as CREBBP and EP300. Activity is enhanced by interaction with both, NCOA1 or NCOA2. Interaction with redox regulatory protein APEX1 seems to activate CTAD and potentiates activation by NCOA1 and CREBBP. Involved in the axonal distribution and transport of mitochondria in neurons during hypoxia. {ECO:0000250|UniProtKB:Q61221, ECO:0000269|PubMed:11292861, ECO:0000269|PubMed:11566883, ECO:0000269|PubMed:15465032, ECO:0000269|PubMed:16543236, ECO:0000269|PubMed:16973622, ECO:0000269|PubMed:17610843, ECO:0000269|PubMed:19528298, ECO:0000269|PubMed:20624928, ECO:0000269|PubMed:22009797, ECO:0000269|PubMed:9887100}.; FUNCTION: (Microbial infection) Upon infection by human coronavirus SARS-CoV-2, is required for induction of glycolysis in monocytes and the consequent proinflammatory state (PubMed:32697943). In monocytes, induces expression of ACE2 and cytokines such as IL1B, TNF, IL6, and interferons (PubMed:32697943). Promotes human coronavirus SARS-CoV-2 replication and monocyte inflammatory response (PubMed:32697943). {ECO:0000269|PubMed:32697943}.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 HIF1A-VRK1


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 HIF1A-VRK1


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 HIF1A-VRK1


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 HIF1A-VRK1


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