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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:TWF1-IRAK4 (FusionGDB2 ID:95501)

Fusion Gene Summary for TWF1-IRAK4

check button Fusion gene summary
Fusion gene informationFusion gene name: TWF1-IRAK4
Fusion gene ID: 95501
HgeneTgene
Gene symbol

TWF1

IRAK4

Gene ID

5756

51135

Gene nametwinfilin actin binding protein 1interleukin 1 receptor associated kinase 4
SynonymsA6|PTK9IPD1|IRAK-4|NY-REN-64|REN64
Cytomap

12q12

12q12

Type of geneprotein-codingprotein-coding
Descriptiontwinfilin-1A6 protein tyrosine kinasePTK9 protein tyrosine kinase 9protein A6protein tyrosine kinase 9twinfilin, actin-binding protein, homolog 1interleukin-1 receptor-associated kinase 4renal carcinoma antigen NY-REN-64
Modification date2020032920200313
UniProtAcc.

Q9NWZ3

Ensembl transtripts involved in fusion geneENST00000552521, ENST00000325127, 
ENST00000395510, ENST00000547564, 
ENST00000548315, 		ENST00000431837, 
ENST00000440781, ENST00000448290, 
ENST00000551736, 
Fusion gene scores* DoF score2 X 2 X 2=85 X 5 X 5=125
# samples 26
** MAII scorelog2(2/8*10)=1.32192809488736log2(6/125*10)=-1.05889368905357
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TWF1 [Title/Abstract] AND IRAK4 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTWF1(44196089)-IRAK4(44180202), # 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
HgeneTWF1

GO:0043538

regulation of actin phosphorylation

10406962


check buttonFusion gene breakpoints across TWF1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across IRAK4 (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4STADTCGA-BR-8296-01ATWF1chr12

44196089

-IRAK4chr12

44180202

+


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Fusion Gene ORF analysis for TWF1-IRAK4

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-3CDSENST00000552521ENST00000431837TWF1chr12

44196089

-IRAK4chr12

44180202

+
5UTR-3CDSENST00000552521ENST00000440781TWF1chr12

44196089

-IRAK4chr12

44180202

+
5UTR-3CDSENST00000552521ENST00000448290TWF1chr12

44196089

-IRAK4chr12

44180202

+
5UTR-3CDSENST00000552521ENST00000551736TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000325127ENST00000431837TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000325127ENST00000440781TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000325127ENST00000448290TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000325127ENST00000551736TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000395510ENST00000431837TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000395510ENST00000440781TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000395510ENST00000448290TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000395510ENST00000551736TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000547564ENST00000431837TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000547564ENST00000440781TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000547564ENST00000448290TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000547564ENST00000551736TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000548315ENST00000431837TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000548315ENST00000440781TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000548315ENST00000448290TWF1chr12

44196089

-IRAK4chr12

44180202

+
In-frameENST00000548315ENST00000551736TWF1chr12

44196089

-IRAK4chr12

44180202

+

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 TWF1-IRAK4


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)
TWF1chr1244196086-IRAK4chr1244180201+0.0031064480.9968935
TWF1chr1244196086-IRAK4chr1244180201+0.0031064480.9968935

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.
genomic feature

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 TWF1-IRAK4


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/chr12:44196089/chr12:44180202)
- 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
.IRAK4

Q9NWZ3

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: Serine/threonine-protein kinase that plays a critical role in initiating innate immune response against foreign pathogens. Involved in Toll-like receptor (TLR) and IL-1R signaling pathways (PubMed:17878374). Is rapidly recruited by MYD88 to the receptor-signaling complex upon TLR activation to form the Myddosome together with IRAK2. Phosphorylates initially IRAK1, thus stimulating the kinase activity and intensive autophosphorylation of IRAK1. Phosphorylates E3 ubiquitin ligases Pellino proteins (PELI1, PELI2 and PELI3) to promote pellino-mediated polyubiquitination of IRAK1. Then, the ubiquitin-binding domain of IKBKG/NEMO binds to polyubiquitinated IRAK1 bringing together the IRAK1-MAP3K7/TAK1-TRAF6 complex and the NEMO-IKKA-IKKB complex. In turn, MAP3K7/TAK1 activates IKKs (CHUK/IKKA and IKBKB/IKKB) leading to NF-kappa-B nuclear translocation and activation. Alternatively, phosphorylates TIRAP to promote its ubiquitination and subsequent degradation. Phosphorylates NCF1 and regulates NADPH oxidase activation after LPS stimulation suggesting a similar mechanism during microbial infections. {ECO:0000269|PubMed:11960013, ECO:0000269|PubMed:12538665, ECO:0000269|PubMed:15084582, ECO:0000269|PubMed:17217339, ECO:0000269|PubMed:17337443, ECO:0000269|PubMed:17878374, ECO:0000269|PubMed:17997719, ECO:0000269|PubMed:20400509, ECO:0000269|PubMed:24316379}.

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
TgeneIRAK4chr12:44196089chr12:44180202ENST00000431837811313_316272337.0Nucleotide bindingNote=ATP
TgeneIRAK4chr12:44196089chr12:44180202ENST00000440781710313_316272337.0Nucleotide bindingNote=ATP

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneTWF1chr12:44196089chr12:44180202ENST00000325127-39175_313128385.0DomainADF-H 2
HgeneTWF1chr12:44196089chr12:44180202ENST00000325127-392_139128385.0DomainADF-H 1
HgeneTWF1chr12:44196089chr12:44180202ENST00000395510-39175_31394351.0DomainADF-H 2
HgeneTWF1chr12:44196089chr12:44180202ENST00000395510-392_13994351.0DomainADF-H 1
HgeneTWF1chr12:44196089chr12:44180202ENST00000548315-310175_31394358.0DomainADF-H 2
HgeneTWF1chr12:44196089chr12:44180202ENST00000548315-3102_13994358.0DomainADF-H 1
HgeneTWF1chr12:44196089chr12:44180202ENST00000552521-410175_3130253.0DomainADF-H 2
HgeneTWF1chr12:44196089chr12:44180202ENST00000552521-4102_1390253.0DomainADF-H 1
TgeneIRAK4chr12:44196089chr12:44180202ENST00000431837811186_454272337.0DomainProtein kinase
TgeneIRAK4chr12:44196089chr12:44180202ENST0000043183781120_104272337.0DomainNote=Death
TgeneIRAK4chr12:44196089chr12:44180202ENST00000440781710186_454272337.0DomainProtein kinase
TgeneIRAK4chr12:44196089chr12:44180202ENST0000044078171020_104272337.0DomainNote=Death
TgeneIRAK4chr12:44196089chr12:44180202ENST00000448290912186_454396461.0DomainProtein kinase
TgeneIRAK4chr12:44196089chr12:44180202ENST0000044829091220_104396461.0DomainNote=Death
TgeneIRAK4chr12:44196089chr12:44180202ENST000005517361013186_454396461.0DomainProtein kinase
TgeneIRAK4chr12:44196089chr12:44180202ENST00000551736101320_104396461.0DomainNote=Death
TgeneIRAK4chr12:44196089chr12:44180202ENST00000431837811192_200272337.0Nucleotide bindingATP
TgeneIRAK4chr12:44196089chr12:44180202ENST00000440781710192_200272337.0Nucleotide bindingATP
TgeneIRAK4chr12:44196089chr12:44180202ENST00000448290912192_200396461.0Nucleotide bindingATP
TgeneIRAK4chr12:44196089chr12:44180202ENST00000448290912313_316396461.0Nucleotide bindingNote=ATP
TgeneIRAK4chr12:44196089chr12:44180202ENST000005517361013192_200396461.0Nucleotide bindingATP
TgeneIRAK4chr12:44196089chr12:44180202ENST000005517361013313_316396461.0Nucleotide bindingNote=ATP


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Fusion Gene Sequence for TWF1-IRAK4


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 TWF1-IRAK4


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 TWF1-IRAK4


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 TWF1-IRAK4


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