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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:NUMBL-BRD4 (FusionGDB2 ID:60942)

Fusion Gene Summary for NUMBL-BRD4

check button Fusion gene summary
Fusion gene informationFusion gene name: NUMBL-BRD4
Fusion gene ID: 60942
HgeneTgene
Gene symbol

NUMBL

BRD4

Gene ID

9253

23476

Gene nameNUMB like endocytic adaptor proteinbromodomain containing 4
SynonymsCAG3A|CTG3a|NBL|NUMB-R|NUMBLIKE|NUMBR|TNRC23CAP|HUNK1|HUNKI|MCAP
Cytomap

19q13.2

19p13.12

Type of geneprotein-codingprotein-coding
Descriptionnumb-like proteinnumb homolog-likenumb-related proteinbromodomain-containing protein 4chromosome-associated proteinmitotic chromosome-associated protein
Modification date2020031320200329
UniProtAcc.

O60885

Ensembl transtripts involved in fusion geneENST00000252891, ENST00000540131, 
ENST00000598779, ENST00000599594, 
ENST00000263377, ENST00000360016, 
ENST00000371835, ENST00000602230, 
Fusion gene scores* DoF score3 X 5 X 2=3015 X 19 X 13=3705
# samples 528
** MAII scorelog2(5/30*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(28/3705*10)=-3.72597481024823
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: NUMBL [Title/Abstract] AND BRD4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointNUMBL(41173867)-BRD4(15349699), # samples:2
NUMBL(41173866)-BRD4(15349698), # samples:2
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
HgeneNUMBL

GO:0019221

cytokine-mediated signaling pathway

18299187

HgeneNUMBL

GO:0019538

protein metabolic process

20079715

TgeneBRD4

GO:0032968

positive regulation of transcription elongation from RNA polymerase II promoter

19103749|23086925

TgeneBRD4

GO:0043123

positive regulation of I-kappaB kinase/NF-kappaB signaling

19103749

TgeneBRD4

GO:0045944

positive regulation of transcription by RNA polymerase II

23086925|23317504|24360279

TgeneBRD4

GO:0050727

regulation of inflammatory response

19103749

TgeneBRD4

GO:1901407

regulation of phosphorylation of RNA polymerase II C-terminal domain

23086925


check buttonFusion gene breakpoints across NUMBL (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 BRD4 (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
ChimerDB4LGGTCGA-DU-7007NUMBLchr19

41173866

-BRD4chr19

15349698

-
ChimerDB4LGGTCGA-E1-5311NUMBLchr19

41173867

-BRD4chr19

15349699

-
ChimerDB4LGGTCGA-P5-A780NUMBLchr19

41173867

-BRD4chr19

15349699

-
ChimerDB4LUSCTCGA-46-6025NUMBLchr19

41173866

-BRD4chr19

15349698

-


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Fusion Gene ORF analysis for NUMBL-BRD4

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
intron-3CDSENST00000252891ENST00000263377NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-3CDSENST00000252891ENST00000263377NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-3CDSENST00000540131ENST00000263377NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-3CDSENST00000540131ENST00000263377NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-3CDSENST00000598779ENST00000263377NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-3CDSENST00000598779ENST00000263377NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-3CDSENST00000599594ENST00000263377NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-3CDSENST00000599594ENST00000263377NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-intronENST00000252891ENST00000360016NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-intronENST00000252891ENST00000360016NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-intronENST00000252891ENST00000371835NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-intronENST00000252891ENST00000371835NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-intronENST00000252891ENST00000602230NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-intronENST00000252891ENST00000602230NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-intronENST00000540131ENST00000360016NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-intronENST00000540131ENST00000360016NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-intronENST00000540131ENST00000371835NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-intronENST00000540131ENST00000371835NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-intronENST00000540131ENST00000602230NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-intronENST00000540131ENST00000602230NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-intronENST00000598779ENST00000360016NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-intronENST00000598779ENST00000360016NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-intronENST00000598779ENST00000371835NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-intronENST00000598779ENST00000371835NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-intronENST00000598779ENST00000602230NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-intronENST00000598779ENST00000602230NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-intronENST00000599594ENST00000360016NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-intronENST00000599594ENST00000360016NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-intronENST00000599594ENST00000371835NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-intronENST00000599594ENST00000371835NUMBLchr19

41173867

-BRD4chr19

15349699

-
intron-intronENST00000599594ENST00000602230NUMBLchr19

41173866

-BRD4chr19

15349698

-
intron-intronENST00000599594ENST00000602230NUMBLchr19

41173867

-BRD4chr19

15349699

-

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 NUMBL-BRD4


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 NUMBL-BRD4


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/:41173867/:15349699)
- 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
.BRD4

O60885

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: Chromatin reader protein that recognizes and binds acetylated histones and plays a key role in transmission of epigenetic memory across cell divisions and transcription regulation. Remains associated with acetylated chromatin throughout the entire cell cycle and provides epigenetic memory for postmitotic G1 gene transcription by preserving acetylated chromatin status and maintaining high-order chromatin structure (PubMed:23589332, PubMed:23317504, PubMed:22334664). During interphase, plays a key role in regulating the transcription of signal-inducible genes by associating with the P-TEFb complex and recruiting it to promoters. Also recruits P-TEFb complex to distal enhancers, so called anti-pause enhancers in collaboration with JMJD6. BRD4 and JMJD6 are required to form the transcriptionally active P-TEFb complex by displacing negative regulators such as HEXIM1 and 7SKsnRNA complex from P-TEFb, thereby transforming it into an active form that can then phosphorylate the C-terminal domain (CTD) of RNA polymerase II (PubMed:23589332, PubMed:19596240, PubMed:16109377, PubMed:16109376, PubMed:24360279). Promotes phosphorylation of 'Ser-2' of the C-terminal domain (CTD) of RNA polymerase II (PubMed:23086925). According to a report, directly acts as an atypical protein kinase and mediates phosphorylation of 'Ser-2' of the C-terminal domain (CTD) of RNA polymerase II; these data however need additional evidences in vivo (PubMed:22509028). In addition to acetylated histones, also recognizes and binds acetylated RELA, leading to further recruitment of the P-TEFb complex and subsequent activation of NF-kappa-B (PubMed:19103749). Also acts as a regulator of p53/TP53-mediated transcription: following phosphorylation by CK2, recruited to p53/TP53 specific target promoters (PubMed:23317504). {ECO:0000269|PubMed:16109376, ECO:0000269|PubMed:16109377, ECO:0000269|PubMed:19103749, ECO:0000269|PubMed:19596240, ECO:0000269|PubMed:22334664, ECO:0000269|PubMed:22509028, ECO:0000269|PubMed:23086925, ECO:0000269|PubMed:23317504, ECO:0000269|PubMed:23589332, ECO:0000269|PubMed:24360279}.; FUNCTION: [Isoform B]: Acts as a chromatin insulator in the DNA damage response pathway. Inhibits DNA damage response signaling by recruiting the condensin-2 complex to acetylated histones, leading to chromatin structure remodeling, insulating the region from DNA damage response by limiting spreading of histone H2AX/H2A.x phosphorylation. {ECO:0000269|PubMed:23728299}.

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 NUMBL-BRD4


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 NUMBL-BRD4


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 NUMBL-BRD4


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 NUMBL-BRD4


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource