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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:HLA-A-EPAS1 (FusionGDB2 ID:HG3105TG2034)

Fusion Gene Summary for HLA-A-EPAS1

check button Fusion gene summary
Fusion gene informationFusion gene name: HLA-A-EPAS1
Fusion gene ID: hg3105tg2034
HgeneTgene
Gene symbol

HLA-A

EPAS1

Gene ID

3105

2034

Gene namemajor histocompatibility complex, class I, Aendothelial PAS domain protein 1
SynonymsHLAAECYT4|HIF2A|HLF|MOP2|PASD2|bHLHe73
Cytomap('HLA-A')('EPAS1')

6p22.1

2p21

Type of geneprotein-codingprotein-coding
DescriptionHLA class I histocompatibility antigen, A alpha chainHLA class I histocompatibility antigen, A-1 alpha chainMHC class I antigen HLA-A heavy chainleukocyte antigen class I-Aendothelial PAS domain-containing protein 1EPAS-1HIF-1-alpha-like factorHIF-1alpha-like factorHIF-2-alphaHIF2-alphaPAS domain-containing protein 2basic-helix-loop-helix-PAS protein MOP2class E basic helix-loop-helix protein 73hypoxia-inducible fa
Modification date2020032820200313
UniProtAcc.

Q99814

Ensembl transtripts involved in fusion geneENST00000376802, ENST00000376806, 
ENST00000376809, ENST00000396634, 
ENST00000376822, ENST00000383605, 
ENST00000383619, ENST00000414592, 
ENST00000416096, ENST00000417978, 
ENST00000431930, ENST00000438861, 
ENST00000442939, ENST00000443552, 
ENST00000444289, ENST00000450342, 
ENST00000453975, ENST00000454091, 
ENST00000456012, ENST00000457879, 
ENST00000488889, ENST00000547112, 
ENST00000547271, ENST00000547522, 
ENST00000549224, ENST00000549869, 
ENST00000550728, ENST00000551120, 
ENST00000551578, ENST00000552193, 
ENST00000552493, ENST00000552498, 
Fusion gene scores* DoF score11 X 11 X 3=36311 X 10 X 5=550
# samples 1111
** MAII scorelog2(11/363*10)=-1.72246602447109
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(11/550*10)=-2.32192809488736
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HLA-A [Title/Abstract] AND EPAS1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHLA-A(29913464)-EPAS1(46602976), # 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
HgeneHLA-A

GO:0001913

T cell mediated cytotoxicity

7504010

HgeneHLA-A

GO:0002419

T cell mediated cytotoxicity directed against tumor cell target

1402688|17189421|20364150

HgeneHLA-A

GO:0002726

positive regulation of T cell cytokine production

24643698

HgeneHLA-A

GO:0019885

antigen processing and presentation of endogenous peptide antigen via MHC class I

1402688|20364150|24643698

HgeneHLA-A

GO:0036037

CD8-positive, alpha-beta T cell activation

1402688|2784196|7504010|8630735|12138174|17189421|20364150

HgeneHLA-A

GO:0042590

antigen processing and presentation of exogenous peptide antigen via MHC class I

7504010|12138174

HgeneHLA-A

GO:0050852

T cell receptor signaling pathway

10435578

HgeneHLA-A

GO:2001187

positive regulation of CD8-positive, alpha-beta T cell activation

24643698

TgeneEPAS1

GO:0001666

response to hypoxia

11782478

TgeneEPAS1

GO:0045944

positive regulation of transcription by RNA polymerase II

11573933

TgeneEPAS1

GO:0071456

cellular response to hypoxia

11573933



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


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Fusion Gene ORF analysis for HLA-A-EPAS1

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

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 HLA-A-EPAS1


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 HLA-A-EPAS1


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/:29913464/:46602976)
- 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
.EPAS1

Q99814

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: Transcription factor involved in the induction of oxygen regulated genes. Heterodimerizes with ARNT; heterodimer binds to core DNA sequence 5'-TACGTG-3' within the hypoxia response element (HRE) of target gene promoters (By similarity). Regulates the vascular endothelial growth factor (VEGF) expression and seems to be implicated in the development of blood vessels and the tubular system of lung. May also play a role in the formation of the endothelium that gives rise to the blood brain barrier. Potent activator of the Tie-2 tyrosine kinase expression. Activation requires recruitment of transcriptional coactivators such as CREBBP and probably EP300. Interaction with redox regulatory protein APEX1 seems to activate CTAD (By similarity). {ECO:0000250, ECO:0000250|UniProtKB:P97481}.

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 HLA-A-EPAS1


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 HLA-A-EPAS1


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 HLA-A-EPAS1


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 HLA-A-EPAS1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneHLA-AC0036341Schizophrenia4PSYGENET
HgeneHLA-AC0019193Hepatitis, Toxic2CTD_human
HgeneHLA-AC0860207Drug-Induced Liver Disease2CTD_human
HgeneHLA-AC1262760Hepatitis, Drug-Induced2CTD_human
HgeneHLA-AC3658290Drug-Induced Acute Liver Injury2CTD_human
HgeneHLA-AC4277682Chemical and Drug Induced Liver Injury2CTD_human
HgeneHLA-AC4279912Chemically-Induced Liver Toxicity2CTD_human
HgeneHLA-AC0004352Autistic Disorder1CTD_human
HgeneHLA-AC0014799Erythroderma, Maculopapular1CTD_human
HgeneHLA-AC0017638Glioma1CTD_human
HgeneHLA-AC0026764Multiple Myeloma1CTD_human
HgeneHLA-AC0030437Parakeratosis Variegata1CTD_human
HgeneHLA-AC0030491Parapsoriasis1CTD_human
HgeneHLA-AC0036349Paranoid Schizophrenia1PSYGENET
HgeneHLA-AC0040034Thrombocytopenia1CTD_human
HgeneHLA-AC0162442Parapsoriasis en Plaques1CTD_human
HgeneHLA-AC0259783mixed gliomas1CTD_human
HgeneHLA-AC0555198Malignant Glioma1CTD_human
HgeneHLA-AC1456784Paranoia1PSYGENET
HgeneHLA-AC1853959Birdshot chorioretinopathy1ORPHANET
TgeneC2673187Erythrocytosis, Familial, 44CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC1708353Hereditary Paraganglioma-Pheochromocytoma Syndrome3CLINGEN
TgeneC0004403Autosome Abnormalities1CTD_human
TgeneC0007134Renal Cell Carcinoma1CTD_human
TgeneC0007621Neoplastic Cell Transformation1CTD_human
TgeneC0008625Chromosome Aberrations1CTD_human
TgeneC0030421Paraganglioma1GENOMICS_ENGLAND
TgeneC0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
TgeneC1266042Chromophobe Renal Cell Carcinoma1CTD_human
TgeneC1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
TgeneC1266044Collecting Duct Carcinoma of the Kidney1CTD_human
TgeneC1306837Papillary Renal Cell Carcinoma1CTD_human
TgeneC2973725Pulmonary arterial hypertension1GENOMICS_ENGLAND
TgeneC3203102Idiopathic pulmonary arterial hypertension1GENOMICS_ENGLAND