Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:CCNE1-PSMA4 (FusionGDB2 ID:HG898TG5685)

Fusion Gene Summary for CCNE1-PSMA4

check button Fusion gene summary
Fusion gene informationFusion gene name: CCNE1-PSMA4
Fusion gene ID: hg898tg5685
HgeneTgene
Gene symbol

CCNE1

PSMA4

Gene ID

898

5685

Gene namecyclin E1proteasome 20S subunit alpha 4
SynonymsCCNE|pCCNE1HC9|HsT17706|PSC9
Cytomap('CCNE1')('PSMA4')

19q12

15q25.1

Type of geneprotein-codingprotein-coding
DescriptionG1/S-specific cyclin-E1proteasome subunit alpha type-4macropain subunit C9multicatalytic endopeptidase complex subunit C9proteasome (prosome, macropain) subunit, alpha type, 4proteasome component C9proteasome subunit HC9proteasome subunit Lproteasome subunit alpha 4prot
Modification date2020032920200327
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000262643, ENST00000444983, 
ENST00000357943, 
Fusion gene scores* DoF score3 X 3 X 2=1811 X 11 X 5=605
# samples 311
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(11/605*10)=-2.4594316186373
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: CCNE1 [Title/Abstract] AND PSMA4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointCCNE1(30311755)-PSMA4(78834824), # 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


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
ChimerDB4OVTCGA-61-1917CCNE1chr19

30311755

+PSMA4chr15

78834824

+


Top

Fusion Gene ORF analysis for CCNE1-PSMA4

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-3UTRENST00000262643ENST00000557929CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-3UTRENST00000262643ENST00000558281CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-3UTRENST00000262643ENST00000558341CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-3UTRENST00000444983ENST00000557929CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-3UTRENST00000444983ENST00000558281CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-3UTRENST00000444983ENST00000558341CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-intronENST00000262643ENST00000044462CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-intronENST00000262643ENST00000413382CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-intronENST00000262643ENST00000558094CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-intronENST00000262643ENST00000559082CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-intronENST00000262643ENST00000560217CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-intronENST00000444983ENST00000044462CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-intronENST00000444983ENST00000413382CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-intronENST00000444983ENST00000558094CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-intronENST00000444983ENST00000559082CCNE1chr19

30311755

+PSMA4chr15

78834824

+
5CDS-intronENST00000444983ENST00000560217CCNE1chr19

30311755

+PSMA4chr15

78834824

+
intron-3UTRENST00000357943ENST00000557929CCNE1chr19

30311755

+PSMA4chr15

78834824

+
intron-3UTRENST00000357943ENST00000558281CCNE1chr19

30311755

+PSMA4chr15

78834824

+
intron-3UTRENST00000357943ENST00000558341CCNE1chr19

30311755

+PSMA4chr15

78834824

+
intron-intronENST00000357943ENST00000044462CCNE1chr19

30311755

+PSMA4chr15

78834824

+
intron-intronENST00000357943ENST00000413382CCNE1chr19

30311755

+PSMA4chr15

78834824

+
intron-intronENST00000357943ENST00000558094CCNE1chr19

30311755

+PSMA4chr15

78834824

+
intron-intronENST00000357943ENST00000559082CCNE1chr19

30311755

+PSMA4chr15

78834824

+
intron-intronENST00000357943ENST00000560217CCNE1chr19

30311755

+PSMA4chr15

78834824

+

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

Top

Fusion Genomic Features for CCNE1-PSMA4


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)
CCNE1chr1930311755+PSMA4chr1578834824+4.06E-060.99999595
CCNE1chr1930311755+PSMA4chr1578834824+4.06E-060.99999595


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%

Top

Fusion Protein Features for CCNE1-PSMA4


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/:30311755/:78834824)
- 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


Top

Fusion Gene Sequence for CCNE1-PSMA4


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.

Top

Fusion Gene PPI Analysis for CCNE1-PSMA4


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


Top

Related Drugs for CCNE1-PSMA4


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

Top

Related Diseases for CCNE1-PSMA4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCCNE1C0005684Malignant neoplasm of urinary bladder2CTD_human
HgeneCCNE1C0005695Bladder Neoplasm2CTD_human
HgeneCCNE1C0006142Malignant neoplasm of breast2CTD_human
HgeneCCNE1C0678222Breast Carcinoma2CTD_human
HgeneCCNE1C1257931Mammary Neoplasms, Human2CTD_human
HgeneCCNE1C1458155Mammary Neoplasms2CTD_human
HgeneCCNE1C2239176Liver carcinoma2CTD_human
HgeneCCNE1C4704874Mammary Carcinoma, Human2CTD_human
HgeneCCNE1C0025149Medulloblastoma1CTD_human
HgeneCCNE1C0205833Medullomyoblastoma1CTD_human
HgeneCCNE1C0235874Disease Exacerbation1CTD_human
HgeneCCNE1C0278510Childhood Medulloblastoma1CTD_human
HgeneCCNE1C0278876Adult Medulloblastoma1CTD_human
HgeneCCNE1C0751291Desmoplastic Medulloblastoma1CTD_human
HgeneCCNE1C0919267ovarian neoplasm1CGI;CTD_human
HgeneCCNE1C1140680Malignant neoplasm of ovary1CGI;CTD_human
HgeneCCNE1C1168401Squamous cell carcinoma of the head and neck1CTD_human
HgeneCCNE1C1275668Melanotic medulloblastoma1CTD_human
TgeneC0007097Carcinoma1CTD_human
TgeneC0019693HIV Infections1CTD_human
TgeneC0023903Liver neoplasms1CTD_human
TgeneC0024667Animal Mammary Neoplasms1CTD_human
TgeneC0024668Mammary Neoplasms, Experimental1CTD_human
TgeneC0035222Respiratory Distress Syndrome, Adult1CTD_human
TgeneC0205696Anaplastic carcinoma1CTD_human
TgeneC0205697Carcinoma, Spindle-Cell1CTD_human
TgeneC0205698Undifferentiated carcinoma1CTD_human
TgeneC0205699Carcinomatosis1CTD_human
TgeneC0345904Malignant neoplasm of liver1CTD_human
TgeneC1257925Mammary Carcinoma, Animal1CTD_human
TgeneC4505456HIV Coinfection1CTD_human