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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:BRD4-STK11 (FusionGDB2 ID:HG23476TG6794)

Fusion Gene Summary for BRD4-STK11

check button Fusion gene summary
Fusion gene informationFusion gene name: BRD4-STK11
Fusion gene ID: hg23476tg6794
HgeneTgene
Gene symbol

BRD4

STK11

Gene ID

23476

6794

Gene namebromodomain containing 4serine/threonine kinase 11
SynonymsCAP|HUNK1|HUNKI|MCAPLKB1|PJS|hLKB1
Cytomap('BRD4')('STK11')

19p13.12

19p13.3

Type of geneprotein-codingprotein-coding
Descriptionbromodomain-containing protein 4chromosome-associated proteinmitotic chromosome-associated proteinserine/threonine-protein kinase STK11liver kinase B1polarization-related protein LKB1renal carcinoma antigen NY-REN-19serine/threonine-protein kinase 11serine/threonine-protein kinase LKB1
Modification date2020032920200329
UniProtAcc

O60885

.
Ensembl transtripts involved in fusion geneENST00000360016, ENST00000263377, 
ENST00000371835, ENST00000602230, 
Fusion gene scores* DoF score20 X 15 X 13=390016 X 14 X 8=1792
# samples 2819
** MAII scorelog2(28/3900*10)=-3.79997539169201
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(19/1792*10)=-3.23749931372666
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: BRD4 [Title/Abstract] AND STK11 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointBRD4(15443101)-STK11(1218416), # 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
HgeneBRD4

GO:0032968

positive regulation of transcription elongation from RNA polymerase II promoter

19103749|23086925

HgeneBRD4

GO:0043123

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

19103749

HgeneBRD4

GO:0045944

positive regulation of transcription by RNA polymerase II

23086925|23317504|24360279

HgeneBRD4

GO:0050727

regulation of inflammatory response

19103749

HgeneBRD4

GO:1901407

regulation of phosphorylation of RNA polymerase II C-terminal domain

23086925

TgeneSTK11

GO:0006468

protein phosphorylation

12805220|25329316

TgeneSTK11

GO:0007050

cell cycle arrest

12805220|17216128

TgeneSTK11

GO:0046777

protein autophosphorylation

11430832

TgeneSTK11

GO:0071493

cellular response to UV-B

25329316

TgeneSTK11

GO:0072332

intrinsic apoptotic signaling pathway by p53 class mediator

11430832



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
ChimerDB4STADTCGA-FP-8209-01ABRD4chr19

15443101

-STK11chr19

1218416

+


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Fusion Gene ORF analysis for BRD4-STK11

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
5UTR-3UTRENST00000360016ENST00000326873BRD4chr19

15443101

-STK11chr19

1218416

+
5UTR-3UTRENST00000360016ENST00000585748BRD4chr19

15443101

-STK11chr19

1218416

+
intron-3UTRENST00000263377ENST00000326873BRD4chr19

15443101

-STK11chr19

1218416

+
intron-3UTRENST00000263377ENST00000585748BRD4chr19

15443101

-STK11chr19

1218416

+
intron-3UTRENST00000371835ENST00000326873BRD4chr19

15443101

-STK11chr19

1218416

+
intron-3UTRENST00000371835ENST00000585748BRD4chr19

15443101

-STK11chr19

1218416

+
intron-3UTRENST00000602230ENST00000326873BRD4chr19

15443101

-STK11chr19

1218416

+
intron-3UTRENST00000602230ENST00000585748BRD4chr19

15443101

-STK11chr19

1218416

+

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 BRD4-STK11


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)
BRD4chr1915443100-STK11chr191218415+2.19E-131
BRD4chr1915443100-STK11chr191218415+2.19E-131


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 BRD4-STK11


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/:15443101/:1218416)
- 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: 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}.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 BRD4-STK11


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 BRD4-STK11


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 BRD4-STK11


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 BRD4-STK11


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneBRD4C0017636Glioblastoma2CTD_human
HgeneBRD4C0334588Giant Cell Glioblastoma2CTD_human
HgeneBRD4C1621958Glioblastoma Multiforme2CTD_human
HgeneBRD4C0002170Alopecia1CTD_human
HgeneBRD4C0007102Malignant tumor of colon1CTD_human
HgeneBRD4C0009375Colonic Neoplasms1CTD_human
HgeneBRD4C0018798Congenital Heart Defects1GENOMICS_ENGLAND
HgeneBRD4C0019193Hepatitis, Toxic1CTD_human
HgeneBRD4C0020507Hyperplasia1CTD_human
HgeneBRD4C0020542Pulmonary Hypertension1CTD_human
HgeneBRD4C0025149Medulloblastoma1CTD_human
HgeneBRD4C0025958Microcephaly1GENOMICS_ENGLAND
HgeneBRD4C0029463Osteosarcoma1CTD_human
HgeneBRD4C0033578Prostatic Neoplasms1CTD_human
HgeneBRD4C0040136Thyroid Neoplasm1CTD_human
HgeneBRD4C0085413Polycystic Kidney, Autosomal Dominant1CTD_human
HgeneBRD4C0086873Pseudopelade1CTD_human
HgeneBRD4C0151468Thyroid Gland Follicular Adenoma1CTD_human
HgeneBRD4C0162311Androgenetic Alopecia1CTD_human
HgeneBRD4C0205833Medullomyoblastoma1CTD_human
HgeneBRD4C0263477Female pattern alopecia (disorder)1CTD_human
HgeneBRD4C0270972Cornelia De Lange Syndrome1CTD_human
HgeneBRD4C0278510Childhood Medulloblastoma1CTD_human
HgeneBRD4C0278876Adult Medulloblastoma1CTD_human
HgeneBRD4C0376358Malignant neoplasm of prostate1CTD_human
HgeneBRD4C0549473Thyroid carcinoma1CTD_human
HgeneBRD4C0751291Desmoplastic Medulloblastoma1CTD_human
HgeneBRD4C0860207Drug-Induced Liver Disease1CTD_human
HgeneBRD4C0887850Polycystic Kidney, Type 1 Autosomal Dominant Disease1CTD_human
HgeneBRD4C1262760Hepatitis, Drug-Induced1CTD_human
HgeneBRD4C1275668Melanotic medulloblastoma1CTD_human
HgeneBRD4C1707291NUT midline carcinoma1ORPHANET
HgeneBRD4C1802395Congenital muscular hypertrophy-cerebral syndrome1CTD_human
HgeneBRD4C1853099Cornelia de Lange Syndrome 31CTD_human
HgeneBRD4C2751306Polycystic kidney disease, type 21CTD_human
HgeneBRD4C3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneBRD4C3714756Intellectual Disability1GENOMICS_ENGLAND
HgeneBRD4C4025871Abnormality of the face1GENOMICS_ENGLAND
HgeneBRD4C4083212Alopecia, Male Pattern1CTD_human
HgeneBRD4C4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneBRD4C4279912Chemically-Induced Liver Toxicity1CTD_human
HgeneBRD4C4551851Cornelia de Lange Syndrome 11CTD_human
TgeneC0031269Peutz-Jeghers Syndrome19CLINGEN;CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneC1336708Testicular Germ Cell Tumor2CTD_human;UNIPROT
TgeneC0001418Adenocarcinoma1CTD_human
TgeneC0007137Squamous cell carcinoma1CTD_human
TgeneC0020538Hypertensive disease1CTD_human
TgeneC0024121Lung Neoplasms1CTD_human
TgeneC0030297Pancreatic Neoplasm1CGI;CTD_human
TgeneC0149721Left Ventricular Hypertrophy1CTD_human
TgeneC0152013Adenocarcinoma of lung (disorder)1CGI;CTD_human
TgeneC0205641Adenocarcinoma, Basal Cell1CTD_human
TgeneC0205642Adenocarcinoma, Oxyphilic1CTD_human
TgeneC0205643Carcinoma, Cribriform1CTD_human
TgeneC0205644Carcinoma, Granular Cell1CTD_human
TgeneC0205645Adenocarcinoma, Tubular1CTD_human
TgeneC0242379Malignant neoplasm of lung1CTD_human;UNIPROT
TgeneC0282207Cronkhite-Canada Syndrome1CTD_human
TgeneC0346647Malignant neoplasm of pancreas1CGI;CTD_human
TgeneC0887833Carcinoma, Pancreatic Ductal1CTD_human
TgeneC1257915Intestinal Polyposis1CTD_human