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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:TM9SF4-TPX2 (FusionGDB2 ID:90646)

Fusion Gene Summary for TM9SF4-TPX2

check button Fusion gene summary
Fusion gene informationFusion gene name: TM9SF4-TPX2
Fusion gene ID: 90646
HgeneTgene
Gene symbol

TM9SF4

TPX2

Gene ID

9777

22974

Gene nametransmembrane 9 superfamily member 4TPX2 microtubule nucleation factor
SynonymsdJ836N17.2C20orf1|C20orf2|DIL-2|DIL2|FLS353|GD:C20orf1|HCA519|HCTP4|REPP86|p100
Cytomap

20q11.21

20q11.21

Type of geneprotein-codingprotein-coding
Descriptiontransmembrane 9 superfamily member 4dinucleotide oxidase disulfide thiol exchanger 3 superfamily member 4transmembrane 9 superfamily protein member 4tumor cannibalism associated protein 1targeting protein for Xklp2TPX2, microtubule-associated protein homologTPX2, microtubule-associated, homologdifferentially expressed in cancerous and non-cancerous lung cells 2differentially expressed in lung cellshepatocellular carcinoma-associated
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000398022, ENST00000217315, 
ENST00000340513, ENST00000300403, 
Fusion gene scores* DoF score20 X 19 X 14=53207 X 12 X 6=504
# samples 2813
** MAII scorelog2(28/5320*10)=-4.24792751344359
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(13/504*10)=-1.95491211047146
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: TM9SF4 [Title/Abstract] AND TPX2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointTM9SF4(30697558)-TPX2(30345209), # 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
HgeneTM9SF4

GO:0001666

response to hypoxia

25961573

TgeneTPX2

GO:0007020

microtubule nucleation

26414402

TgeneTPX2

GO:0007026

negative regulation of microtubule depolymerization

26414402

TgeneTPX2

GO:0032147

activation of protein kinase activity

14580337|19801554

TgeneTPX2

GO:0090307

mitotic spindle assembly

26165940


check buttonFusion gene breakpoints across TM9SF4 (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 TPX2 (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
ChimerDB4STADTCGA-BR-7715TM9SF4chr20

30697558

+TPX2chr20

30345209

+
ChimerDB4STADTCGA-BR-7715TM9SF4chr20

30697558

+TPX2chr20

30345209

+
ChimerDB4STADTCGA-BR-7715TM9SF4chr20

30697558

+TPX2chr20

30330343

+
ChimerDB4STADTCGA-BR-7715-01ATM9SF4chr20

30697558

+TPX2chr20

30345210

+
ChimerDB4BRCATCGA-E2-A1LK-01ATM9SF4chr20

30697842

-TPX2chr20

30354359

+


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Fusion Gene ORF analysis for TM9SF4-TPX2

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
5CDS-5UTRENST00000398022ENST00000340513TM9SF4chr20

30697558

+TPX2chr20

30345209

+
5CDS-5UTRENST00000398022ENST00000300403TM9SF4chr20

30697558

+TPX2chr20

30345209

+
5UTR-5UTRENST00000217315ENST00000340513TM9SF4chr20

30697558

+TPX2chr20

30345209

+
5UTR-5UTRENST00000217315ENST00000300403TM9SF4chr20

30697558

+TPX2chr20

30345209

+
5CDS-5UTRENST00000398022ENST00000340513TM9SF4chr20

30697558

+TPX2chr20

30330343

+
5CDS-5UTRENST00000398022ENST00000300403TM9SF4chr20

30697558

+TPX2chr20

30330343

+
5UTR-5UTRENST00000217315ENST00000340513TM9SF4chr20

30697558

+TPX2chr20

30330343

+
5UTR-5UTRENST00000217315ENST00000300403TM9SF4chr20

30697558

+TPX2chr20

30330343

+
5CDS-5UTRENST00000398022ENST00000340513TM9SF4chr20

30697558

+TPX2chr20

30345210

+
5CDS-5UTRENST00000398022ENST00000300403TM9SF4chr20

30697558

+TPX2chr20

30345210

+
5UTR-5UTRENST00000217315ENST00000340513TM9SF4chr20

30697558

+TPX2chr20

30345210

+
5UTR-5UTRENST00000217315ENST00000300403TM9SF4chr20

30697558

+TPX2chr20

30345210

+
intron-3CDSENST00000398022ENST00000340513TM9SF4chr20

30697842

-TPX2chr20

30354359

+
intron-3CDSENST00000398022ENST00000300403TM9SF4chr20

30697842

-TPX2chr20

30354359

+
5UTR-3CDSENST00000217315ENST00000340513TM9SF4chr20

30697842

-TPX2chr20

30354359

+
5UTR-3CDSENST00000217315ENST00000300403TM9SF4chr20

30697842

-TPX2chr20

30354359

+

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 TM9SF4-TPX2


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)
TM9SF4chr2030697558+TPX2chr2030330343+8.40E-060.99999166
TM9SF4chr2030697558+TPX2chr2030345209+5.62E-060.9999944
TM9SF4chr2030697558+TPX2chr2030345209+5.62E-060.9999944
TM9SF4chr2030697558+TPX2chr2030330343+8.40E-060.99999166
TM9SF4chr2030697558+TPX2chr2030345209+5.62E-060.9999944
TM9SF4chr2030697558+TPX2chr2030345209+5.62E-060.9999944

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 TM9SF4-TPX2


check button Go to

FGviewer for the breakpoints of :-:

.
- FGviewer provides the online visualization of the retention search of the protein functional features across DNA, RNA, protein, and pathological levels.
FGviewer

check buttonMain function of each fusion partner protein. (from UniProt)
HgeneTgene
..
FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.FUNCTION: Might normally function as a transcriptional repressor. EWS-fusion-proteins (EFPS) may play a role in the tumorigenic process. They may disturb gene expression by mimicking, or interfering with the normal function of CTD-POLII within the transcription initiation complex. They may also contribute to an aberrant activation of the fusion protein target genes.

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 TM9SF4-TPX2


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 TM9SF4-TPX2


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 TM9SF4-TPX2


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 TM9SF4-TPX2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
TgeneTPX2C2239176Liver carcinoma1CTD_human