Fusion Gene Studies
in Kim Lab

FusionBase FusionGDB FusionGDB2 FusionPDB FusionNeoAntigen FusionAI FusionNW FGviewer Publication Contact
FusionGDB Logo

Home

Download

Statistics

Examples

Help

Contact

Center for Computational Systems Medicine
leaf

Fusion Gene Summary

leaf

Fusion Gene ORF analysis

leaf

Fusion Genomic Features

leaf

Fusion Protein Features

leaf

Fusion Gene Sequence

leaf

Fusion Gene PPI analysis

leaf

Related Drugs

leaf

Related Diseases

Fusion gene:F5-PTP4A1 (FusionGDB2 ID:HG2153TG7803)

Fusion Gene Summary for F5-PTP4A1

check button Fusion gene summary
Fusion gene informationFusion gene name: F5-PTP4A1
Fusion gene ID: hg2153tg7803
HgeneTgene
Gene symbol

F5

PTP4A1

Gene ID

2153

7803

Gene namecoagulation factor Vprotein tyrosine phosphatase 4A1
SynonymsFVL|PCCF|RPRGL1|THPH2HH72|PRL-1|PRL1|PTP(CAAX1)|PTPCAAX1
Cytomap('F5')('PTP4A1')

1q24.2

6q12

Type of geneprotein-codingprotein-coding
Descriptioncoagulation factor Vactivated protein c cofactorcoagulation factor V (proaccelerin, labile factor)coagulation factor V jinjiang A2 domainfactor V Leidenprotein tyrosine phosphatase type IVA 1PVT1/PTP4A1 fusionphosphatase of regenerating liver 1protein tyrosine phosphatase type IVA protein 1protein tyrosine phosphatase type IVA, member 1protein-tyrosine phosphatase of regenerating liver 1
Modification date2020031520200320
UniProtAcc

P12259

.
Ensembl transtripts involved in fusion geneENST00000367796, ENST00000367797, 
ENST00000546081, 
Fusion gene scores* DoF score2 X 3 X 2=1215 X 5 X 5=375
# samples 211
** MAII scorelog2(2/12*10)=0.736965594166206
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
log2(11/375*10)=-1.76938707185858
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: F5 [Title/Abstract] AND PTP4A1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointF5(169512840)-PTP4A1(64291324), # 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


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


Top

Fusion Gene ORF analysis for F5-PTP4A1

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

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

Top

Fusion Genomic Features for F5-PTP4A1


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)


Top

Fusion Protein Features for F5-PTP4A1


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/:169512840/:64291324)
- 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
F5

P12259

.
FUNCTION: Central regulator of hemostasis. It serves as a critical cofactor for the prothrombinase activity of factor Xa that results in the activation of prothrombin to thrombin.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


Top

Fusion Gene Sequence for F5-PTP4A1


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.

Top

Fusion Gene PPI Analysis for F5-PTP4A1


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


Top

Related Drugs for F5-PTP4A1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneF5P12259DB11312Protein CInactivatorBiotechApproved
HgeneF5P12259DB11571Human thrombinActivatorBiotechApproved
HgeneF5P12259DB11572Thrombin alfaActivatorBiotechApproved
HgeneF5P12259DB13149Protein S humanAntagonistBiotechApproved
HgeneF5P12259DB05777Thrombomodulin AlfaBiotechApproved|Investigational
HgeneF5P12259DB11300ThrombinActivatorBiotechApproved|Investigational
HgeneF5P12259DB13151Anti-inhibitor coagulant complexAgonistBiotechApproved|Investigational
HgeneF5P12259DB00055Drotrecogin alfaMultitargetBiotechApproved|Investigational|Withdrawn

Top

Related Diseases for F5-PTP4A1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneF5C1861171THROMBOPHILIA DUE TO ACTIVATED PROTEIN C RESISTANCE (disorder)24CLINGEN;CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneF5C0042487Venous Thrombosis5CTD_human
HgeneF5C0149871Deep Vein Thrombosis5CTD_human
HgeneF5C0015499Hereditary Factor V Deficiency3CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
HgeneF5C0019154Hepatic Vein Thrombosis2CTD_human;ORPHANET
HgeneF5C0040038Thromboembolism2CTD_human
HgeneF5C0040053Thrombosis2CTD_human
HgeneF5C0087086Thrombus2CTD_human
HgeneF5C0856761Budd-Chiari Syndrome2CTD_human;ORPHANET
HgeneF5C1861172Venous Thromboembolism2CTD_human
HgeneF5C0005779Blood Coagulation Disorders1CTD_human
HgeneF5C0007102Malignant tumor of colon1CTD_human
HgeneF5C0007786Brain Ischemia1CTD_human
HgeneF5C0009375Colonic Neoplasms1CTD_human
HgeneF5C0023890Liver Cirrhosis1CTD_human
HgeneF5C0027051Myocardial Infarction1CTD_human
HgeneF5C0032580Adenomatous Polyposis Coli1CTD_human
HgeneF5C0035328Retinal Vein Occlusion1CTD_human
HgeneF5C0038454Cerebrovascular accident1CTD_human
HgeneF5C0239946Fibrosis, Liver1CTD_human
HgeneF5C0267412Mesenteric Venous Thrombosis1CTD_human
HgeneF5C0338575Sagittal Sinus Thrombosis1CTD_human
HgeneF5C0751823Septic Phlebitis, Sagittal Sinus1CTD_human
HgeneF5C0751824Sagittal Sinus Thrombophlebitis1CTD_human
HgeneF5C0751956Acute Cerebrovascular Accidents1CTD_human
HgeneF5C0917798Cerebral Ischemia1CTD_human
HgeneF5C1412000Mesenteric vascular insufficiency1CTD_human
HgeneF5C1527411Thrombosis of retinal vein1CTD_human
HgeneF5C1853831Bleeding Disorder, East Texas Type1ORPHANET
HgeneF5C2584620Thrombophilia, hereditary1CTD_human
HgeneF5C2713442Polyposis, Adenomatous Intestinal1CTD_human
HgeneF5C2713443Familial Intestinal Polyposis1CTD_human
HgeneF5C3852984Acute Mesenteric Arterial Embolus1CTD_human
HgeneF5C3852985Occlusive Mesenteric Arterial Ischemia1CTD_human
HgeneF5C3852986Nonocclusive Mesenteric Ischemia1CTD_human
HgeneF5C3852987Acute Mesenteric Arterial Thrombosis1CTD_human
TgeneC0001973Alcoholic Intoxication, Chronic2PSYGENET