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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:HDAC1-PTPRU (FusionGDB2 ID:35672)

Fusion Gene Summary for HDAC1-PTPRU

check button Fusion gene summary
Fusion gene informationFusion gene name: HDAC1-PTPRU
Fusion gene ID: 35672
HgeneTgene
Gene symbol

HDAC1

PTPRU

Gene ID

3065

10076

Gene namehistone deacetylase 1protein tyrosine phosphatase receptor type U
SynonymsGON-10|HD1|KDAC1|RPD3|RPD3L1FMI|PCP-2|PTP|PTP-J|PTP-PI|PTP-RO|PTPPSI|PTPRO|PTPU2|R-PTP-PSI|R-PTP-U|hPTP-J
Cytomap

1p35.2-p35.1

1p35.3

Type of geneprotein-codingprotein-coding
Descriptionhistone deacetylase 1reduced potassium dependency, yeast homolog-like 1receptor-type tyrosine-protein phosphatase UPTP piReceptor protein tyrosine phosphatase hPTP-Jpancreatic carcinoma phosphatase 2pi R-PTP-Psiprotein-tyrosine phosphatase Jprotein-tyrosine phosphatase piprotein-tyrosine phosphatase receptor omicronr
Modification date2020032720200313
UniProtAcc

Q13547

.
Ensembl transtripts involved in fusion geneENST00000373548, ENST00000373541, 
ENST00000490081, 		ENST00000345512, 
ENST00000373779, ENST00000356870, 
ENST00000323874, ENST00000428026, 
ENST00000460170, ENST00000415600, 
Fusion gene scores* DoF score13 X 9 X 9=10535 X 5 X 5=125
# samples 176
** MAII scorelog2(17/1053*10)=-2.63089878488802
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(6/125*10)=-1.05889368905357
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: HDAC1 [Title/Abstract] AND PTPRU [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointHDAC1(32768334)-PTPRU(29581787), # samples:2
Anticipated loss of major functional domain due to fusion event.HDAC1-PTPRU seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
HDAC1-PTPRU seems lost the major protein functional domain in Hgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
HDAC1-PTPRU seems lost the major protein functional domain in Hgene partner, which is a epigenetic factor due to the frame-shifted ORF.
HDAC1-PTPRU seems lost the major protein functional domain in Tgene partner, which is a essential gene due to the frame-shifted ORF.
HDAC1-PTPRU seems lost the major protein functional domain in Tgene partner, which is a IUPHAR drug target due to the frame-shifted ORF.
* 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
HgeneHDAC1

GO:0000122

negative regulation of transcription by RNA polymerase II

18854353

HgeneHDAC1

GO:0006476

protein deacetylation

17172643|23629966

HgeneHDAC1

GO:0045893

positive regulation of transcription, DNA-templated

16762839

HgeneHDAC1

GO:0045944

positive regulation of transcription by RNA polymerase II

16762839

HgeneHDAC1

GO:0060766

negative regulation of androgen receptor signaling pathway

15919722

HgeneHDAC1

GO:0070932

histone H3 deacetylation

12590135

HgeneHDAC1

GO:0070933

histone H4 deacetylation

12590135

TgenePTPRU

GO:0006470

protein dephosphorylation

12501215

TgenePTPRU

GO:0008285

negative regulation of cell proliferation

16574648

TgenePTPRU

GO:0030336

negative regulation of cell migration

12501215|16574648

TgenePTPRU

GO:0034394

protein localization to cell surface

16574648

TgenePTPRU

GO:0090090

negative regulation of canonical Wnt signaling pathway

16574648

TgenePTPRU

GO:2000049

positive regulation of cell-cell adhesion mediated by cadherin

16574648


check buttonFusion gene breakpoints across HDAC1 (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 PTPRU (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
ChimerDB4OVTCGA-09-1673-01AHDAC1chr1

32768334

+PTPRUchr1

29581787

+
ChimerDB4OVTCGA-09-1673-01AHDAC1chr1

32768334

+PTPRUchr1

29581787

+


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Fusion Gene ORF analysis for HDAC1-PTPRU

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
Frame-shiftENST00000373548ENST00000345512HDAC1chr1

32768334

+PTPRUchr1

29581787

+
Frame-shiftENST00000373548ENST00000373779HDAC1chr1

32768334

+PTPRUchr1

29581787

+
Frame-shiftENST00000373548ENST00000356870HDAC1chr1

32768334

+PTPRUchr1

29581787

+
Frame-shiftENST00000373548ENST00000323874HDAC1chr1

32768334

+PTPRUchr1

29581787

+
Frame-shiftENST00000373548ENST00000428026HDAC1chr1

32768334

+PTPRUchr1

29581787

+
Frame-shiftENST00000373548ENST00000460170HDAC1chr1

32768334

+PTPRUchr1

29581787

+
5CDS-intronENST00000373548ENST00000415600HDAC1chr1

32768334

+PTPRUchr1

29581787

+
5UTR-3CDSENST00000373541ENST00000345512HDAC1chr1

32768334

+PTPRUchr1

29581787

+
5UTR-3CDSENST00000373541ENST00000373779HDAC1chr1

32768334

+PTPRUchr1

29581787

+
5UTR-3CDSENST00000373541ENST00000356870HDAC1chr1

32768334

+PTPRUchr1

29581787

+
5UTR-3CDSENST00000373541ENST00000323874HDAC1chr1

32768334

+PTPRUchr1

29581787

+
5UTR-3CDSENST00000373541ENST00000428026HDAC1chr1

32768334

+PTPRUchr1

29581787

+
5UTR-3CDSENST00000373541ENST00000460170HDAC1chr1

32768334

+PTPRUchr1

29581787

+
5UTR-intronENST00000373541ENST00000415600HDAC1chr1

32768334

+PTPRUchr1

29581787

+
intron-3CDSENST00000490081ENST00000345512HDAC1chr1

32768334

+PTPRUchr1

29581787

+
intron-3CDSENST00000490081ENST00000373779HDAC1chr1

32768334

+PTPRUchr1

29581787

+
intron-3CDSENST00000490081ENST00000356870HDAC1chr1

32768334

+PTPRUchr1

29581787

+
intron-3CDSENST00000490081ENST00000323874HDAC1chr1

32768334

+PTPRUchr1

29581787

+
intron-3CDSENST00000490081ENST00000428026HDAC1chr1

32768334

+PTPRUchr1

29581787

+
intron-3CDSENST00000490081ENST00000460170HDAC1chr1

32768334

+PTPRUchr1

29581787

+
intron-intronENST00000490081ENST00000415600HDAC1chr1

32768334

+PTPRUchr1

29581787

+

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 HDAC1-PTPRU


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)
HDAC1chr132768334+PTPRUchr129581786+1.72E-081
HDAC1chr132768334+PTPRUchr129581786+1.72E-081

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 HDAC1-PTPRU


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
HDAC1

Q13547

.
FUNCTION: Responsible for the deacetylation of lysine residues on the N-terminal part of the core histones (H2A, H2B, H3 and H4). Histone deacetylation gives a tag for epigenetic repression and plays an important role in transcriptional regulation, cell cycle progression and developmental events. Histone deacetylases act via the formation of large multiprotein complexes. Deacetylates SP proteins, SP1 and SP3, and regulates their function. Component of the BRG1-RB1-HDAC1 complex, which negatively regulates the CREST-mediated transcription in resting neurons. Upon calcium stimulation, HDAC1 is released from the complex and CREBBP is recruited, which facilitates transcriptional activation. Deacetylates TSHZ3 and regulates its transcriptional repressor activity. Deacetylates 'Lys-310' in RELA and thereby inhibits the transcriptional activity of NF-kappa-B. Deacetylates NR1D2 and abrogates the effect of KAT5-mediated relieving of NR1D2 transcription repression activity. Component of a RCOR/GFI/KDM1A/HDAC complex that suppresses, via histone deacetylase (HDAC) recruitment, a number of genes implicated in multilineage blood cell development. Involved in CIART-mediated transcriptional repression of the circadian transcriptional activator: CLOCK-ARNTL/BMAL1 heterodimer. Required for the transcriptional repression of circadian target genes, such as PER1, mediated by the large PER complex or CRY1 through histone deacetylation. {ECO:0000269|PubMed:12837748, ECO:0000269|PubMed:16478997, ECO:0000269|PubMed:17000776, ECO:0000269|PubMed:17704056, ECO:0000269|PubMed:17996965, ECO:0000269|PubMed:19081374, ECO:0000269|PubMed:19343227}.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 HDAC1-PTPRU


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 HDAC1-PTPRU


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 HDAC1-PTPRU


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneHDAC1Q13547DB14548Zinc sulfate, unspecified formCofactorSmall moleculeApproved|Experimental
HgeneHDAC1Q13547DB14548Zinc sulfate, unspecified formCofactorSmall moleculeApproved|Experimental
HgeneHDAC1Q13547DB01169Arsenic trioxideSmall moleculeApproved|Investigational
HgeneHDAC1Q13547DB01169Arsenic trioxideSmall moleculeApproved|Investigational
HgeneHDAC1Q13547DB01593ZincCofactorSmall moleculeApproved|Investigational
HgeneHDAC1Q13547DB01593ZincCofactorSmall moleculeApproved|Investigational
HgeneHDAC1Q13547DB02546VorinostatInhibitorSmall moleculeApproved|Investigational
HgeneHDAC1Q13547DB02546VorinostatInhibitorSmall moleculeApproved|Investigational
HgeneHDAC1Q13547DB06176RomidepsinAntagonist|InhibitorSmall moleculeApproved|Investigational
HgeneHDAC1Q13547DB06176RomidepsinAntagonist|InhibitorSmall moleculeApproved|Investigational
HgeneHDAC1Q13547DB08868FingolimodInhibitorSmall moleculeApproved|Investigational
HgeneHDAC1Q13547DB08868FingolimodInhibitorSmall moleculeApproved|Investigational
HgeneHDAC1Q13547DB14487Zinc acetateSmall moleculeApproved|Investigational
HgeneHDAC1Q13547DB14487Zinc acetateSmall moleculeApproved|Investigational
HgeneHDAC1Q13547DB14533Zinc chlorideCofactorSmall moleculeApproved|Investigational
HgeneHDAC1Q13547DB14533Zinc chlorideCofactorSmall moleculeApproved|Investigational

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Related Diseases for HDAC1-PTPRU


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneHDAC1C0036341Schizophrenia2PSYGENET
HgeneHDAC1C0007137Squamous cell carcinoma1CTD_human
HgeneHDAC1C0014175Endometriosis1CTD_human
HgeneHDAC1C0018799Heart Diseases1CTD_human
HgeneHDAC1C0269102Endometrioma1CTD_human
HgeneHDAC1C0340543Familial primary pulmonary hypertension1CTD_human
HgeneHDAC1C0525045Mood Disorders1PSYGENET
HgeneHDAC1C1969342PULMONARY HYPERTENSION, PRIMARY, DEXFENFLURAMINE-ASSOCIATED1CTD_human
HgeneHDAC1C1969343Pulmonary Hypertension, Primary, Fenfluramine-Associated1CTD_human
HgeneHDAC1C2713368Hematopoetic Myelodysplasia1CTD_human
HgeneHDAC1C3203102Idiopathic pulmonary arterial hypertension1CTD_human
HgeneHDAC1C3463824MYELODYSPLASTIC SYNDROME1CTD_human
HgeneHDAC1C3714844Pulmonary Hypertension, Primary, 1, With Hereditary Hemorrhagic Telangiectasia1CTD_human
HgeneHDAC1C4552070Pulmonary Hypertension, Primary, 11CTD_human