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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:DDX11-DERA (FusionGDB2 ID:HG1663TG51071)

Fusion Gene Summary for DDX11-DERA

check button Fusion gene summary
Fusion gene informationFusion gene name: DDX11-DERA
Fusion gene ID: hg1663tg51071
HgeneTgene
Gene symbol

DDX11

DERA

Gene ID

1663

51071

Gene nameDEAD/H-box helicase 11deoxyribose-phosphate aldolase
SynonymsCHL1|CHLR1|KRG2|WABSCGI-26|DEOC
Cytomap('DDX11')('DERA')

12p11.21

12p12.3

Type of geneprotein-codingprotein-coding
DescriptionATP-dependent DNA helicase DDX11CHL1-like helicase homologCHL1-related helicase gene-1CHL1-related protein 1DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (CHL1-like helicase homolog, S. cerevisiae)DEAD/Hdeoxyribose-phosphate aldolase2-deoxy-D-ribose 5-phosphate aldolase2-deoxyribose-5-phosphate aldolase homologdeoxyriboaldolasedeoxyribose-phosphate aldolase (putative)phosphodeoxyriboaldolaseputative deoxyribose-phosphate aldolase
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000251758, ENST00000539673, 
ENST00000228264, ENST00000350437, 
ENST00000407793, ENST00000542838, 
ENST00000545668, 
Fusion gene scores* DoF score3 X 3 X 2=1810 X 7 X 6=420
# samples 39
** MAII scorelog2(3/18*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(9/420*10)=-2.22239242133645
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: DDX11 [Title/Abstract] AND DERA [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointDDX11(31250931)-DERA(16109870), # samples:1
Anticipated loss of major functional domain due to fusion event.DDX11-DERA seems lost the major protein functional domain in Hgene partner, which is a essential gene 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
HgeneDDX11

GO:0007062

sister chromatid cohesion

17105772

HgeneDDX11

GO:0032079

positive regulation of endodeoxyribonuclease activity

18499658

HgeneDDX11

GO:0032508

DNA duplex unwinding

10648783|18499658|26503245

HgeneDDX11

GO:0035563

positive regulation of chromatin binding

26089203

HgeneDDX11

GO:0044806

G-quadruplex DNA unwinding

26503245

TgeneDERA

GO:0046121

deoxyribonucleoside catabolic process

9226884



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
ChimerDB4BRCATCGA-E2-A1LL-01ADDX11chr12

31250931

+DERAchr12

16109870

+


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Fusion Gene ORF analysis for DDX11-DERA

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-3CDSENST00000251758ENST00000428559DDX11chr12

31250931

+DERAchr12

16109870

+
3UTR-3CDSENST00000251758ENST00000532964DDX11chr12

31250931

+DERAchr12

16109870

+
3UTR-3CDSENST00000539673ENST00000428559DDX11chr12

31250931

+DERAchr12

16109870

+
3UTR-3CDSENST00000539673ENST00000532964DDX11chr12

31250931

+DERAchr12

16109870

+
3UTR-5UTRENST00000251758ENST00000526530DDX11chr12

31250931

+DERAchr12

16109870

+
3UTR-5UTRENST00000539673ENST00000526530DDX11chr12

31250931

+DERAchr12

16109870

+
3UTR-intronENST00000251758ENST00000532573DDX11chr12

31250931

+DERAchr12

16109870

+
3UTR-intronENST00000539673ENST00000532573DDX11chr12

31250931

+DERAchr12

16109870

+
5CDS-5UTRENST00000228264ENST00000526530DDX11chr12

31250931

+DERAchr12

16109870

+
5CDS-5UTRENST00000350437ENST00000526530DDX11chr12

31250931

+DERAchr12

16109870

+
5CDS-5UTRENST00000407793ENST00000526530DDX11chr12

31250931

+DERAchr12

16109870

+
5CDS-5UTRENST00000542838ENST00000526530DDX11chr12

31250931

+DERAchr12

16109870

+
5CDS-5UTRENST00000545668ENST00000526530DDX11chr12

31250931

+DERAchr12

16109870

+
5CDS-intronENST00000228264ENST00000532573DDX11chr12

31250931

+DERAchr12

16109870

+
5CDS-intronENST00000350437ENST00000532573DDX11chr12

31250931

+DERAchr12

16109870

+
5CDS-intronENST00000407793ENST00000532573DDX11chr12

31250931

+DERAchr12

16109870

+
5CDS-intronENST00000542838ENST00000532573DDX11chr12

31250931

+DERAchr12

16109870

+
5CDS-intronENST00000545668ENST00000532573DDX11chr12

31250931

+DERAchr12

16109870

+
Frame-shiftENST00000228264ENST00000428559DDX11chr12

31250931

+DERAchr12

16109870

+
Frame-shiftENST00000228264ENST00000532964DDX11chr12

31250931

+DERAchr12

16109870

+
Frame-shiftENST00000350437ENST00000428559DDX11chr12

31250931

+DERAchr12

16109870

+
Frame-shiftENST00000350437ENST00000532964DDX11chr12

31250931

+DERAchr12

16109870

+
Frame-shiftENST00000407793ENST00000428559DDX11chr12

31250931

+DERAchr12

16109870

+
Frame-shiftENST00000407793ENST00000532964DDX11chr12

31250931

+DERAchr12

16109870

+
Frame-shiftENST00000542838ENST00000428559DDX11chr12

31250931

+DERAchr12

16109870

+
Frame-shiftENST00000542838ENST00000532964DDX11chr12

31250931

+DERAchr12

16109870

+
Frame-shiftENST00000545668ENST00000428559DDX11chr12

31250931

+DERAchr12

16109870

+
Frame-shiftENST00000545668ENST00000532964DDX11chr12

31250931

+DERAchr12

16109870

+

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 DDX11-DERA


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)
DDX11chr1231250931+DERAchr1216109869+0.0003965380.99960345
DDX11chr1231250931+DERAchr1216109869+0.0003965380.99960345


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 DDX11-DERA


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/:31250931/:16109870)
- 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 DDX11-DERA


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 DDX11-DERA


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 DDX11-DERA


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 DDX11-DERA


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneDDX11C3150658WARSAW BREAKAGE SYNDROME4CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneDDX11C0333704Chromosome Breaks1CTD_human
HgeneDDX11C0376628Chromosome Breakage1CTD_human