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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:TPX2-ACLY (FusionGDB2 ID:HG22974TG47)

Fusion Gene Summary for TPX2-ACLY

check button Fusion gene summary
Fusion gene informationFusion gene name: TPX2-ACLY
Fusion gene ID: hg22974tg47
HgeneTgene
Gene symbol

TPX2

ACLY

Gene ID

22974

47

Gene nameTPX2 microtubule nucleation factorATP citrate lyase
SynonymsC20orf1|C20orf2|DIL-2|DIL2|FLS353|GD:C20orf1|HCA519|HCTP4|REPP86|p100ACL|ATPCL|CLATP
Cytomap('TPX2')('ACLY')

20q11.21

17q21.2

Type of geneprotein-codingprotein-coding
Descriptiontargeting 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 ATP-citrate synthaseATP-citrate (pro-S-)-lyasecitrate cleavage enzyme
Modification date2020031320200313
UniProtAcc.

P53396

Ensembl transtripts involved in fusion geneENST00000300403, ENST00000340513, 
Fusion gene scores* DoF score21 X 15 X 15=472513 X 13 X 6=1014
# samples 4015
** MAII scorelog2(40/4725*10)=-3.56224242422107
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/1014*10)=-2.75702324650746
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

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

Most frequent breakpointTPX2(30330450)-ACLY(40070153), # samples:3
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
HgeneTPX2

GO:0007020

microtubule nucleation

26414402

HgeneTPX2

GO:0007026

negative regulation of microtubule depolymerization

26414402

HgeneTPX2

GO:0032147

activation of protein kinase activity

14580337|19801554

HgeneTPX2

GO:0090307

mitotic spindle assembly

26165940

TgeneACLY

GO:0006085

acetyl-CoA biosynthetic process

1371749

TgeneACLY

GO:0006101

citrate metabolic process

1371749

TgeneACLY

GO:0006107

oxaloacetate metabolic process

1371749

TgeneACLY

GO:0008610

lipid biosynthetic process

23932781



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-BR-8077-01ATPX2chr20

30330450

+ACLYchr17

40070149

-
ChimerDB4STADTCGA-BR-8077-01ATPX2chr20

30330450

-ACLYchr17

40070153

-
ChimerDB4STADTCGA-BR-8077-01ATPX2chr20

30330450

+ACLYchr17

40070153

-
ChimerDB4STADTCGA-BR-8077TPX2chr20

30330450

+ACLYchr17

40070149

-


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Fusion Gene ORF analysis for TPX2-ACLY

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-5UTRENST00000300403ENST00000352035TPX2chr20

30330450

+ACLYchr17

40070153

-
5UTR-5UTRENST00000300403ENST00000352035TPX2chr20

30330450

+ACLYchr17

40070149

-
5UTR-5UTRENST00000300403ENST00000353196TPX2chr20

30330450

+ACLYchr17

40070153

-
5UTR-5UTRENST00000300403ENST00000353196TPX2chr20

30330450

+ACLYchr17

40070149

-
5UTR-5UTRENST00000300403ENST00000393896TPX2chr20

30330450

+ACLYchr17

40070153

-
5UTR-5UTRENST00000300403ENST00000393896TPX2chr20

30330450

+ACLYchr17

40070149

-
5UTR-5UTRENST00000300403ENST00000537919TPX2chr20

30330450

+ACLYchr17

40070153

-
5UTR-5UTRENST00000300403ENST00000537919TPX2chr20

30330450

+ACLYchr17

40070149

-
5UTR-5UTRENST00000300403ENST00000590151TPX2chr20

30330450

+ACLYchr17

40070153

-
5UTR-5UTRENST00000300403ENST00000590151TPX2chr20

30330450

+ACLYchr17

40070149

-
5UTR-5UTRENST00000340513ENST00000352035TPX2chr20

30330450

+ACLYchr17

40070153

-
5UTR-5UTRENST00000340513ENST00000352035TPX2chr20

30330450

+ACLYchr17

40070149

-
5UTR-5UTRENST00000340513ENST00000353196TPX2chr20

30330450

+ACLYchr17

40070153

-
5UTR-5UTRENST00000340513ENST00000353196TPX2chr20

30330450

+ACLYchr17

40070149

-
5UTR-5UTRENST00000340513ENST00000393896TPX2chr20

30330450

+ACLYchr17

40070153

-
5UTR-5UTRENST00000340513ENST00000393896TPX2chr20

30330450

+ACLYchr17

40070149

-
5UTR-5UTRENST00000340513ENST00000537919TPX2chr20

30330450

+ACLYchr17

40070153

-
5UTR-5UTRENST00000340513ENST00000537919TPX2chr20

30330450

+ACLYchr17

40070149

-
5UTR-5UTRENST00000340513ENST00000590151TPX2chr20

30330450

+ACLYchr17

40070153

-
5UTR-5UTRENST00000340513ENST00000590151TPX2chr20

30330450

+ACLYchr17

40070149

-
5UTR-intronENST00000300403ENST00000588779TPX2chr20

30330450

+ACLYchr17

40070153

-
5UTR-intronENST00000300403ENST00000588779TPX2chr20

30330450

+ACLYchr17

40070149

-
5UTR-intronENST00000340513ENST00000588779TPX2chr20

30330450

+ACLYchr17

40070153

-
5UTR-intronENST00000340513ENST00000588779TPX2chr20

30330450

+ACLYchr17

40070149

-

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 TPX2-ACLY


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)


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Fusion Protein Features for TPX2-ACLY


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/:30330450/:40070153)
- 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
.ACLY

P53396

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: Catalyzes the cleavage of citrate into oxaloacetate and acetyl-CoA, the latter serving as common substrate for de novo cholesterol and fatty acid synthesis. {ECO:0000269|PubMed:10653665, ECO:0000269|PubMed:1371749, ECO:0000269|PubMed:19286649, ECO:0000269|PubMed:23932781, ECO:0000269|PubMed:9116495}.

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 TPX2-ACLY


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 TPX2-ACLY


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 TPX2-ACLY


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
TgeneACLYP53396DB11936Bempedoic acidInhibitorSmall moleculeApproved|Investigational

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Related Diseases for TPX2-ACLY


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneTPX2C2239176Liver carcinoma1CTD_human
TgeneC0018801Heart failure1CTD_human
TgeneC0018802Congestive heart failure1CTD_human
TgeneC0023212Left-Sided Heart Failure1CTD_human
TgeneC0028754Obesity1CTD_human
TgeneC0235527Heart Failure, Right-Sided1CTD_human
TgeneC1959583Myocardial Failure1CTD_human
TgeneC1961112Heart Decompensation1CTD_human
TgeneC2239176Liver carcinoma1CTD_human