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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:37013)

Fusion Gene Summary for HNF4A-HNF4A

check button Fusion gene summary
Fusion gene informationFusion gene name: HNF4A-HNF4A
Fusion gene ID: 37013
HgeneTgene
Gene symbol

HNF4A

HNF4A

Gene ID

6927

6927

Gene nameHNF1 homeobox AHNF1 homeobox A
SynonymsHNF-1A|HNF1|HNF4A|IDDM20|LFB1|MODY3|TCF-1|TCF1HNF-1A|HNF1|HNF4A|IDDM20|LFB1|MODY3|TCF-1|TCF1
Cytomap

12q24.31

12q24.31

Type of geneprotein-codingprotein-coding
Descriptionhepatocyte nuclear factor 1-alphaHNF-1-alphaalbumin proximal factorhepatic nuclear factor 1interferon production regulator factorliver-specific transcription factor LF-B1transcription factor 1, hepatictruncated hepatocyte nuclear factor 1 alphahepatocyte nuclear factor 1-alphaHNF-1-alphaalbumin proximal factorhepatic nuclear factor 1interferon production regulator factorliver-specific transcription factor LF-B1transcription factor 1, hepatictruncated hepatocyte nuclear factor 1 alpha
Modification date2020031320200313
UniProtAcc

P41235

P41235

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:0001779

natural killer cell differentiation

11301190

HgeneHNF4A

GO:0006357

regulation of transcription by RNA polymerase II

10330009

HgeneHNF4A

GO:0045893

positive regulation of transcription, DNA-templated

1989880|11980910|12453420

TgeneHNF4A

GO:0001779

natural killer cell differentiation

11301190

TgeneHNF4A

GO:0006357

regulation of transcription by RNA polymerase II

10330009

TgeneHNF4A

GO:0045893

positive regulation of transcription, DNA-templated

1989880|11980910|12453420


check buttonFusion gene breakpoints across HNF4A (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 HNF4A (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/AAW006913HNF4Achr20

43060697

-HNF4Achr20

43060571

+


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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
3UTR-3UTRENST00000316099ENST00000316099HNF4Achr20

43060697

-HNF4Achr20

43060571

+
3UTR-intronENST00000316099ENST00000316673HNF4Achr20

43060697

-HNF4Achr20

43060571

+
3UTR-intronENST00000316099ENST00000415691HNF4Achr20

43060697

-HNF4Achr20

43060571

+
3UTR-intronENST00000316099ENST00000443598HNF4Achr20

43060697

-HNF4Achr20

43060571

+
3UTR-intronENST00000316099ENST00000457232HNF4Achr20

43060697

-HNF4Achr20

43060571

+
3UTR-intronENST00000316099ENST00000609795HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-3UTRENST00000316673ENST00000316099HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-3UTRENST00000415691ENST00000316099HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-3UTRENST00000443598ENST00000316099HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-3UTRENST00000457232ENST00000316099HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-3UTRENST00000609795ENST00000316099HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000316673ENST00000316673HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000316673ENST00000415691HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000316673ENST00000443598HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000316673ENST00000457232HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000316673ENST00000609795HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000415691ENST00000316673HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000415691ENST00000415691HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000415691ENST00000443598HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000415691ENST00000457232HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000415691ENST00000609795HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000443598ENST00000316673HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000443598ENST00000415691HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000443598ENST00000443598HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000443598ENST00000457232HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000443598ENST00000609795HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000457232ENST00000316673HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000457232ENST00000415691HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000457232ENST00000443598HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000457232ENST00000457232HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000457232ENST00000609795HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000609795ENST00000316673HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000609795ENST00000415691HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000609795ENST00000443598HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000609795ENST00000457232HNF4Achr20

43060697

-HNF4Achr20

43060571

+
intron-intronENST00000609795ENST00000609795HNF4Achr20

43060697

-HNF4Achr20

43060571

+

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)

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 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
HNF4A

P41235

HNF4A

P41235

FUNCTION: Transcriptional regulator which controls the expression of hepatic genes during the transition of endodermal cells to hepatic progenitor cells, facilitating the recruitment of RNA pol II to the promoters of target genes (PubMed:30597922). Activates the transcription of CYP2C38 (By similarity). Represses the CLOCK-ARNTL/BMAL1 transcriptional activity and is essential for circadian rhythm maintenance and period regulation in the liver and colon cells (PubMed:30530698). {ECO:0000250|UniProtKB:P49698, ECO:0000269|PubMed:30530698, ECO:0000269|PubMed:30597922}.FUNCTION: Transcriptional regulator which controls the expression of hepatic genes during the transition of endodermal cells to hepatic progenitor cells, facilitating the recruitment of RNA pol II to the promoters of target genes (PubMed:30597922). Activates the transcription of CYP2C38 (By similarity). Represses the CLOCK-ARNTL/BMAL1 transcriptional activity and is essential for circadian rhythm maintenance and period regulation in the liver and colon cells (PubMed:30530698). {ECO:0000250|UniProtKB:P49698, ECO:0000269|PubMed:30530698, ECO:0000269|PubMed:30597922}.

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