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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:HEPH-KDM2A (FusionGDB2 ID:HG9843TG22992)

Fusion Gene Summary for HEPH-KDM2A

check button Fusion gene summary
Fusion gene informationFusion gene name: HEPH-KDM2A
Fusion gene ID: hg9843tg22992
HgeneTgene
Gene symbol

HEPH

KDM2A

Gene ID

9843

22992

Gene namehephaestinlysine demethylase 2A
SynonymsCPLCXXC8|FBL11|FBL7|FBXL11|JHDM1A|LILINA
Cytomap('HEPH')('KDM2A')

Xq12

11q13.2

Type of geneprotein-codingprotein-coding
Descriptionhephaestinlysine-specific demethylase 2ACXXC-type zinc finger protein 8F-box and leucine-rich repeat protein 11F-box/LRR-repeat protein 11[Histone-H3]-lysine-36 demethylase 1AjmjC domain-containing histone demethylation protein 1Ajumonji C domain-containing h
Modification date2020031320200320
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000519389, ENST00000374727, 
ENST00000336279, ENST00000343002, 
ENST00000419594, ENST00000441993, 
Fusion gene scores* DoF score5 X 3 X 3=4528 X 27 X 8=6048
# samples 532
** MAII scorelog2(5/45*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(32/6048*10)=-4.24031432933371
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HEPH [Title/Abstract] AND KDM2A [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHEPH(65382718)-KDM2A(66982810), # samples:1
Anticipated loss of major functional domain due to fusion event.HEPH-KDM2A seems lost the major protein functional domain in Tgene partner, which is a epigenetic factor due to the frame-shifted ORF.
HEPH-KDM2A seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
HEPH-KDM2A seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
HEPH-KDM2A seems lost the major protein functional domain in Tgene partner, which is a transcription factor due to the frame-shifted ORF.
* 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


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
ChimerDB4Non-CancerTCGA-IC-A6RE-11AHEPHchrX

65382718

+KDM2Achr11

66982810

+


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Fusion Gene ORF analysis for HEPH-KDM2A

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-3UTRENST00000519389ENST00000526258HEPHchrX

65382718

+KDM2Achr11

66982810

+
5CDS-intronENST00000519389ENST00000308783HEPHchrX

65382718

+KDM2Achr11

66982810

+
5CDS-intronENST00000519389ENST00000530342HEPHchrX

65382718

+KDM2Achr11

66982810

+
5UTR-3CDSENST00000374727ENST00000398645HEPHchrX

65382718

+KDM2Achr11

66982810

+
5UTR-3CDSENST00000374727ENST00000529006HEPHchrX

65382718

+KDM2Achr11

66982810

+
5UTR-3UTRENST00000374727ENST00000526258HEPHchrX

65382718

+KDM2Achr11

66982810

+
5UTR-intronENST00000374727ENST00000308783HEPHchrX

65382718

+KDM2Achr11

66982810

+
5UTR-intronENST00000374727ENST00000530342HEPHchrX

65382718

+KDM2Achr11

66982810

+
Frame-shiftENST00000519389ENST00000398645HEPHchrX

65382718

+KDM2Achr11

66982810

+
Frame-shiftENST00000519389ENST00000529006HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-3CDSENST00000336279ENST00000398645HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-3CDSENST00000336279ENST00000529006HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-3CDSENST00000343002ENST00000398645HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-3CDSENST00000343002ENST00000529006HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-3CDSENST00000419594ENST00000398645HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-3CDSENST00000419594ENST00000529006HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-3CDSENST00000441993ENST00000398645HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-3CDSENST00000441993ENST00000529006HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-3UTRENST00000336279ENST00000526258HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-3UTRENST00000343002ENST00000526258HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-3UTRENST00000419594ENST00000526258HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-3UTRENST00000441993ENST00000526258HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-intronENST00000336279ENST00000308783HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-intronENST00000336279ENST00000530342HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-intronENST00000343002ENST00000308783HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-intronENST00000343002ENST00000530342HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-intronENST00000419594ENST00000308783HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-intronENST00000419594ENST00000530342HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-intronENST00000441993ENST00000308783HEPHchrX

65382718

+KDM2Achr11

66982810

+
intron-intronENST00000441993ENST00000530342HEPHchrX

65382718

+KDM2Achr11

66982810

+

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 HEPH-KDM2A


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)
HEPHchrX65382718+KDM2Achr1166982810+2.85E-050.9999715
HEPHchrX65382718+KDM2Achr1166982810+2.85E-050.9999715


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 HEPH-KDM2A


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/:65382718/:66982810)
- 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 HEPH-KDM2A


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 HEPH-KDM2A


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 HEPH-KDM2A


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 HEPH-KDM2A


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneHEPHC0345967Malignant mesothelioma1CTD_human
TgeneC0009402Colorectal Carcinoma1CTD_human
TgeneC0009404Colorectal Neoplasms1CTD_human
TgeneC2931456Prostate cancer, familial1CTD_human
TgeneC4722327PROSTATE CANCER, HEREDITARY, 11CTD_human