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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:TBL1XR1-LINC00578 (FusionGDB2 ID:HG79718TG100505566)

Fusion Gene Summary for TBL1XR1-LINC00578

check button Fusion gene summary
Fusion gene informationFusion gene name: TBL1XR1-LINC00578
Fusion gene ID: hg79718tg100505566
HgeneTgene
Gene symbol

TBL1XR1

LINC00578

Gene ID

79718

100505566

Gene nameTBL1X receptor 1long intergenic non-protein coding RNA 578
SynonymsC21|DC42|IRA1|MRD41|TBLR1-
Cytomap('TBL1XR1')('LINC00578')

3q26.32

3q26.32

Type of geneprotein-codingncRNA
DescriptionF-box-like/WD repeat-containing protein TBL1XR1TBL1-related protein 1nuclear receptor co-repressor/HDAC3 complex subunitnuclear receptor corepressor/HDAC3 complex subunit TBLR1transducin beta like 1 X-linked receptor 1-
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000457928, ENST00000430069, 
Fusion gene scores* DoF score51 X 31 X 15=237156 X 9 X 6=324
# samples 669
** MAII scorelog2(66/23715*10)=-5.16719003372107
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/324*10)=-1.84799690655495
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TBL1XR1 [Title/Abstract] AND LINC00578 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTBL1XR1(176914908)-LINC00578(177257182), # samples:1
TBL1XR1(176914908)-LINC00578(177347204), # samples:1
TBL1XR1(176914908)-LINC00578(177469698), # samples:1
TBL1XR1(176914909)-LINC00578(177347205), # samples:1
TBL1XR1(176914909)-LINC00578(177257183), # samples:1
TBL1XR1(176816253)-LINC00578(177454946), # 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
HgeneTBL1XR1

GO:0000122

negative regulation of transcription by RNA polymerase II

12628926

HgeneTBL1XR1

GO:0045893

positive regulation of transcription, DNA-templated

18193033

HgeneTBL1XR1

GO:0045944

positive regulation of transcription by RNA polymerase II

18193033



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
ChimerDB4BLCATCGA-DK-A3X2-01ATBL1XR1chr3

176914909

-LINC00578chr3

177257183

+
ChimerDB4BLCATCGA-DK-A3X2-01ATBL1XR1chr3

176914909

-LINC00578chr3

177347205

+
ChimerDB4BLCATCGA-DK-A3X2TBL1XR1chr3

176914908

-LINC00578chr3

177257182

+
ChimerDB4BLCATCGA-DK-A3X2TBL1XR1chr3

176914908

-LINC00578chr3

177347204

+
ChimerDB4BRCATCGA-C8-A12P-01ATBL1XR1chr3

176816253

-LINC00578chr3

177454946

-
ChimerDB4LUSCTCGA-56-7730TBL1XR1chr3

176914908

-LINC00578chr3

177469698

+


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Fusion Gene ORF analysis for TBL1XR1-LINC00578

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-3UTRENST00000457928ENST00000442937TBL1XR1chr3

176914909

-LINC00578chr3

177257183

+
5UTR-3UTRENST00000457928ENST00000442937TBL1XR1chr3

176914909

-LINC00578chr3

177347205

+
5UTR-3UTRENST00000457928ENST00000442937TBL1XR1chr3

176914908

-LINC00578chr3

177257182

+
5UTR-3UTRENST00000457928ENST00000442937TBL1XR1chr3

176914908

-LINC00578chr3

177347204

+
5UTR-3UTRENST00000457928ENST00000442937TBL1XR1chr3

176914908

-LINC00578chr3

177469698

+
5UTR-intronENST00000430069ENST00000442937TBL1XR1chr3

176816253

-LINC00578chr3

177454946

-
5UTR-intronENST00000457928ENST00000442937TBL1XR1chr3

176816253

-LINC00578chr3

177454946

-
intron-3UTRENST00000430069ENST00000442937TBL1XR1chr3

176914909

-LINC00578chr3

177257183

+
intron-3UTRENST00000430069ENST00000442937TBL1XR1chr3

176914909

-LINC00578chr3

177347205

+
intron-3UTRENST00000430069ENST00000442937TBL1XR1chr3

176914908

-LINC00578chr3

177257182

+
intron-3UTRENST00000430069ENST00000442937TBL1XR1chr3

176914908

-LINC00578chr3

177347204

+
intron-3UTRENST00000430069ENST00000442937TBL1XR1chr3

176914908

-LINC00578chr3

177469698

+

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 TBL1XR1-LINC00578


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)
TBL1XR1chr3176914908-LINC00578chr3177347204+0.0005000330.9994999
TBL1XR1chr3176914908-LINC00578chr3177347204+0.0005000330.9994999
TBL1XR1chr3176914908-LINC00578chr3177257182+4.97E-060.999995
TBL1XR1chr3176914908-LINC00578chr3177257182+4.97E-060.999995
TBL1XR1chr3176914908-LINC00578chr3177469698+2.70E-060.99999726
TBL1XR1chr3176914908-LINC00578chr3177347204+0.0005000330.9994999
TBL1XR1chr3176914908-LINC00578chr3177347204+0.0005000330.9994999
TBL1XR1chr3176914908-LINC00578chr3177257182+4.97E-060.999995
TBL1XR1chr3176914908-LINC00578chr3177257182+4.97E-060.999995
TBL1XR1chr3176914908-LINC00578chr3177469698+2.70E-060.99999726


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 TBL1XR1-LINC00578


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/:176914908/:177257182)
- 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 TBL1XR1-LINC00578


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 TBL1XR1-LINC00578


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 TBL1XR1-LINC00578


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 TBL1XR1-LINC00578


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTBL1XR1C1865644Plantar Lipomatosis, Unusual Facies, and Developmental Delay5CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneTBL1XR1C4310784MENTAL RETARDATION, AUTOSOMAL DOMINANT 415CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneTBL1XR1C0004352Autistic Disorder1GENOMICS_ENGLAND
HgeneTBL1XR1C0023487Acute Promyelocytic Leukemia1ORPHANET
HgeneTBL1XR1C0033578Prostatic Neoplasms1CTD_human
HgeneTBL1XR1C0345967Malignant mesothelioma1CTD_human
HgeneTBL1XR1C0376358Malignant neoplasm of prostate1CTD_human
HgeneTBL1XR1C1535926Neurodevelopmental Disorders1CTD_human