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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:HNF4A-HNF4A (FusionGDB2 ID:HG3172TG3172)

Fusion Gene Summary for HNF4A-HNF4A

check button Fusion gene summary
Fusion gene informationFusion gene name: HNF4A-HNF4A
Fusion gene ID: hg3172tg3172
HgeneTgene
Gene symbol

HNF4A

HNF4A

Gene ID

3172

3172

Gene namehepatocyte nuclear factor 4 alphahepatocyte nuclear factor 4 alpha
SynonymsFRTS4|HNF4|HNF4a7|HNF4a8|HNF4a9|HNF4alpha|MODY|MODY1|NR2A1|NR2A21|TCF|TCF14FRTS4|HNF4|HNF4a7|HNF4a8|HNF4a9|HNF4alpha|MODY|MODY1|NR2A1|NR2A21|TCF|TCF14
Cytomap('HNF4A')('HNF4A')

20q13.12

20q13.12

Type of geneprotein-codingprotein-coding
Descriptionhepatocyte nuclear factor 4-alphaHNF4alpha10/11/12TCF-14hepatic nuclear factor 4 alphanuclear receptor subfamily 2 group A member 1transcription factor 14transcription factor HNF-4hepatocyte nuclear factor 4-alphaHNF4alpha10/11/12TCF-14hepatic nuclear factor 4 alphanuclear receptor subfamily 2 group A member 1transcription factor 14transcription factor HNF-4
Modification date2020032920200329
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000316099, ENST00000316673, 
ENST00000415691, ENST00000443598, 
ENST00000457232, ENST00000609795, 
ENST00000316099, ENST00000316673, 
ENST00000415691, ENST00000443598, 
ENST00000457232, ENST00000609795, 
Fusion gene scores* DoF score6 X 5 X 3=906 X 6 X 5=180
# samples 77
** MAII scorelog2(7/90*10)=-0.362570079384708
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(7/180*10)=-1.36257007938471
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HNF4A [Title/Abstract] AND HNF4A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHNF4A(43060697)-HNF4A(43060571), # 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
HgeneHNF4A

GO:0006357

regulation of transcription by RNA polymerase II

10330009|12911579

HgeneHNF4A

GO:0007596

blood coagulation

12911579

HgeneHNF4A

GO:0019216

regulation of lipid metabolic process

10551874

HgeneHNF4A

GO:0045892

negative regulation of transcription, DNA-templated

30530698

HgeneHNF4A

GO:0045893

positive regulation of transcription, DNA-templated

16488887

HgeneHNF4A

GO:0045944

positive regulation of transcription by RNA polymerase II

7615825

TgeneHNF4A

GO:0006357

regulation of transcription by RNA polymerase II

10330009|12911579

TgeneHNF4A

GO:0007596

blood coagulation

12911579

TgeneHNF4A

GO:0019216

regulation of lipid metabolic process

10551874

TgeneHNF4A

GO:0045892

negative regulation of transcription, DNA-templated

30530698

TgeneHNF4A

GO:0045893

positive regulation of transcription, DNA-templated

16488887

TgeneHNF4A

GO:0045944

positive regulation of transcription by RNA polymerase II

7615825



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 HNF4A-HNF4A

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 HNF4A-HNF4A


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 HNF4A-HNF4A


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/:43060697/:43060571)
- 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 HNF4A-HNF4A


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 HNF4A-HNF4A


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 HNF4A-HNF4A


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 HNF4A-HNF4A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneHNF4AC1852093Maturity-Onset Diabetes of the Young, Type 18CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneHNF4AC3888631Monogenic diabetes7CLINGEN;GENOMICS_ENGLAND
HgeneHNF4AC0011860Diabetes Mellitus, Non-Insulin-Dependent5CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneHNF4AC4014962FANCONI RENOTUBULAR SYNDROME 4 WITH MATURITY-ONSET DIABETES OF THE YOUNG5CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneHNF4AC0342276Maturity onset diabetes mellitus in young2GENOMICS_ENGLAND;ORPHANET
HgeneHNF4AC4274078Hyperinsulinism due to HNF4A deficiency2ORPHANET
HgeneHNF4AC0009324Ulcerative Colitis1CTD_human
HgeneHNF4AC0431693Renal cysts and diabetes syndrome1ORPHANET
TgeneC1852093Maturity-Onset Diabetes of the Young, Type 18CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC3888631Monogenic diabetes7CLINGEN;GENOMICS_ENGLAND
TgeneC0011860Diabetes Mellitus, Non-Insulin-Dependent5CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC4014962FANCONI RENOTUBULAR SYNDROME 4 WITH MATURITY-ONSET DIABETES OF THE YOUNG5CTD_human;GENOMICS_ENGLAND;UNIPROT
TgeneC0342276Maturity onset diabetes mellitus in young2GENOMICS_ENGLAND;ORPHANET
TgeneC4274078Hyperinsulinism due to HNF4A deficiency2ORPHANET
TgeneC0009324Ulcerative Colitis1CTD_human
TgeneC0431693Renal cysts and diabetes syndrome1ORPHANET