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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:LPP-F2 (FusionGDB2 ID:49314)

Fusion Gene Summary for LPP-F2

check button Fusion gene summary
Fusion gene informationFusion gene name: LPP-F2
Fusion gene ID: 49314
HgeneTgene
Gene symbol

LPP

F2

Gene ID

4026

2147

Gene nameLIM domain containing preferred translocation partner in lipomacoagulation factor II, thrombin
Synonyms-PT|RPRGL2|THPH1
Cytomap

3q27.3-q28

11p11.2

Type of geneprotein-codingprotein-coding
Descriptionlipoma-preferred partnerLIM proteinlipoma preferred partnerprothrombinprepro-coagulation factor IIprothrombin B-chainserine proteasethrombin factor II
Modification date2020031320200329
UniProtAcc.

P55085

Ensembl transtripts involved in fusion geneENST00000448637, ENST00000312675, 
ENST00000543006, ENST00000471917, 
ENST00000311907, ENST00000530231, 
Fusion gene scores* DoF score41 X 30 X 15=184503 X 4 X 3=36
# samples 524
** MAII scorelog2(52/18450*10)=-5.14896538280667
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(4/36*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: LPP [Title/Abstract] AND F2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointLPP(188059507)-F2(46741252), # 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
TgeneF2

GO:0001934

positive regulation of protein phosphorylation

7559487

TgeneF2

GO:0007166

cell surface receptor signaling pathway

1672265

TgeneF2

GO:0009611

response to wounding

9639571

TgeneF2

GO:0030168

platelet activation

9038223

TgeneF2

GO:0030194

positive regulation of blood coagulation

9038223

TgeneF2

GO:0032967

positive regulation of collagen biosynthetic process

9639571

TgeneF2

GO:0042730

fibrinolysis

12855810

TgeneF2

GO:0045861

negative regulation of proteolysis

1695900

TgeneF2

GO:0048712

negative regulation of astrocyte differentiation

1691280

TgeneF2

GO:0051281

positive regulation of release of sequestered calcium ion into cytosol

1672265|19052258

TgeneF2

GO:0051480

regulation of cytosolic calcium ion concentration

19052258

TgeneF2

GO:0051838

cytolysis by host of symbiont cells

20421939

TgeneF2

GO:0061844

antimicrobial humoral immune response mediated by antimicrobial peptide

20421939

TgeneF2

GO:0070945

neutrophil mediated killing of gram-negative bacterium

20421939

TgeneF2

GO:0090218

positive regulation of lipid kinase activity

11309392

TgeneF2

GO:1900016

negative regulation of cytokine production involved in inflammatory response

20421939

TgeneF2

GO:1900182

positive regulation of protein localization to nucleus

11309392

TgeneF2

GO:1900738

positive regulation of phospholipase C-activating G protein-coupled receptor signaling pathway

20164183

TgeneF2

GO:2000379

positive regulation of reactive oxygen species metabolic process

17275676


check buttonFusion gene breakpoints across LPP (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 F2 (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-13-0760LPPchr3

188059507

+F2chr11

46741251

+
ChimerDB4OVTCGA-13-0760-01ALPPchr3

188059507

+F2chr11

46741252

+
ChimerDB4OVTCGA-13-0760-01ALPPchr3

187943315

+F2chr11

46741252

+
ChimerDB4OVTCGA-13-0760-01ALPPchr3

188059507

-F2chr11

46741252

+


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Fusion Gene ORF analysis for LPP-F2

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-3CDSENST00000448637ENST00000311907LPPchr3

188059507

+F2chr11

46741251

+
5UTR-3CDSENST00000448637ENST00000530231LPPchr3

188059507

+F2chr11

46741251

+
intron-3CDSENST00000312675ENST00000311907LPPchr3

188059507

+F2chr11

46741251

+
intron-3CDSENST00000312675ENST00000530231LPPchr3

188059507

+F2chr11

46741251

+
5UTR-3CDSENST00000543006ENST00000311907LPPchr3

188059507

+F2chr11

46741251

+
5UTR-3CDSENST00000543006ENST00000530231LPPchr3

188059507

+F2chr11

46741251

+
intron-3CDSENST00000471917ENST00000311907LPPchr3

188059507

+F2chr11

46741251

+
intron-3CDSENST00000471917ENST00000530231LPPchr3

188059507

+F2chr11

46741251

+
5UTR-3CDSENST00000448637ENST00000311907LPPchr3

188059507

+F2chr11

46741252

+
5UTR-3CDSENST00000448637ENST00000530231LPPchr3

188059507

+F2chr11

46741252

+
intron-3CDSENST00000312675ENST00000311907LPPchr3

188059507

+F2chr11

46741252

+
intron-3CDSENST00000312675ENST00000530231LPPchr3

188059507

+F2chr11

46741252

+
5UTR-3CDSENST00000543006ENST00000311907LPPchr3

188059507

+F2chr11

46741252

+
5UTR-3CDSENST00000543006ENST00000530231LPPchr3

188059507

+F2chr11

46741252

+
intron-3CDSENST00000471917ENST00000311907LPPchr3

188059507

+F2chr11

46741252

+
intron-3CDSENST00000471917ENST00000530231LPPchr3

188059507

+F2chr11

46741252

+
intron-3CDSENST00000448637ENST00000311907LPPchr3

187943315

+F2chr11

46741252

+
intron-3CDSENST00000448637ENST00000530231LPPchr3

187943315

+F2chr11

46741252

+
5UTR-3CDSENST00000312675ENST00000311907LPPchr3

187943315

+F2chr11

46741252

+
5UTR-3CDSENST00000312675ENST00000530231LPPchr3

187943315

+F2chr11

46741252

+
5UTR-3CDSENST00000543006ENST00000311907LPPchr3

187943315

+F2chr11

46741252

+
5UTR-3CDSENST00000543006ENST00000530231LPPchr3

187943315

+F2chr11

46741252

+
intron-3CDSENST00000471917ENST00000311907LPPchr3

187943315

+F2chr11

46741252

+
intron-3CDSENST00000471917ENST00000530231LPPchr3

187943315

+F2chr11

46741252

+

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 LPP-F2


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)
LPPchr3188059507+F2chr1146741251+1.08E-091
LPPchr3188059507+F2chr1146741251+1.08E-091
LPPchr3187943315+F2chr1146741251+1.33E-101
LPPchr3188059507+F2chr1146741251+1.08E-091
LPPchr3188059507+F2chr1146741251+1.08E-091
LPPchr3187943315+F2chr1146741251+1.33E-101

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 LPP-F2


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
.F2

P55085

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: Receptor for trypsin and trypsin-like enzymes coupled to G proteins (PubMed:28445455). Its function is mediated through the activation of several signaling pathways including phospholipase C (PLC), intracellular calcium, mitogen-activated protein kinase (MAPK), I-kappaB kinase/NF-kappaB and Rho (PubMed:28445455). Can also be transactivated by cleaved F2R/PAR1. Involved in modulation of inflammatory responses and regulation of innate and adaptive immunity, and acts as a sensor for proteolytic enzymes generated during infection. Generally is promoting inflammation. Can signal synergistically with TLR4 and probably TLR2 in inflammatory responses and modulates TLR3 signaling. Has a protective role in establishing the endothelial barrier; the activity involves coagulation factor X. Regulates endothelial cell barrier integrity during neutrophil extravasation, probably following proteolytic cleavage by PRTN3 (PubMed:23202369). Proposed to have a bronchoprotective role in airway epithelium, but also shown to compromise the airway epithelial barrier by interrupting E-cadherin adhesion (PubMed:10086357). Involved in the regulation of vascular tone; activation results in hypotension presumably mediated by vasodilation. Associates with a subset of G proteins alpha subunits such as GNAQ, GNA11, GNA14, GNA12 and GNA13, but probably not with G(o) alpha, G(i) subunit alpha-1 and G(i) subunit alpha-2. However, according to PubMed:21627585 can signal through G(i) subunit alpha. Believed to be a class B receptor which internalizes as a complex with arrestin and traffic with it to endosomal vesicles, presumably as desensitized receptor, for extended periods of time. Mediates inhibition of TNF-alpha stimulated JNK phosphorylation via coupling to GNAQ and GNA11; the function involves dissociation of RIPK1 and TRADD from TNFR1. Mediates phosphorylation of nuclear factor NF-kappa-B RELA subunit at 'Ser-536'; the function involves IKBKB and is predominantly independent of G proteins. Involved in cellular migration. Involved in cytoskeletal rearrangement and chemotaxis through beta-arrestin-promoted scaffolds; the function is independent of GNAQ and GNA11 and involves promotion of cofilin dephosphorylation and actin filament severing. Induces redistribution of COPS5 from the plasma membrane to the cytosol and activation of the JNK cascade is mediated by COPS5. Involved in the recruitment of leukocytes to the sites of inflammation and is the major PAR receptor capable of modulating eosinophil function such as proinflammatory cytokine secretion, superoxide production and degranulation. During inflammation promotes dendritic cell maturation, trafficking to the lymph nodes and subsequent T-cell activation. Involved in antimicrobial response of innate immune cells; activation enhances phagocytosis of Gram-positive and killing of Gram-negative bacteria. Acts synergistically with interferon-gamma in enhancing antiviral responses. Implicated in a number of acute and chronic inflammatory diseases such as of the joints, lungs, brain, gastrointestinal tract, periodontium, skin, and vascular systems, and in autoimmune disorders. {ECO:0000269|PubMed:10086357, ECO:0000269|PubMed:10725339, ECO:0000269|PubMed:11413129, ECO:0000269|PubMed:11441110, ECO:0000269|PubMed:11447194, ECO:0000269|PubMed:11714832, ECO:0000269|PubMed:12832443, ECO:0000269|PubMed:15155775, ECO:0000269|PubMed:16359518, ECO:0000269|PubMed:16410250, ECO:0000269|PubMed:16478888, ECO:0000269|PubMed:16714334, ECO:0000269|PubMed:17404307, ECO:0000269|PubMed:17500066, ECO:0000269|PubMed:18424071, ECO:0000269|PubMed:18453611, ECO:0000269|PubMed:18474671, ECO:0000269|PubMed:18622013, ECO:0000269|PubMed:19494303, ECO:0000269|PubMed:19781631, ECO:0000269|PubMed:19864598, ECO:0000269|PubMed:19865078, ECO:0000269|PubMed:20826780, ECO:0000269|PubMed:21501162, ECO:0000269|PubMed:23202369, ECO:0000269|PubMed:28445455}.

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 LPP-F2


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 LPP-F2


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 LPP-F2


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 LPP-F2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneLPPC0087031Juvenile-Onset Still Disease1CTD_human
HgeneLPPC3495559Juvenile arthritis1CTD_human
HgeneLPPC3714758Juvenile psoriatic arthritis1CTD_human
HgeneLPPC4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
HgeneLPPC4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human
TgeneF2C0020640Inherited Factor II deficiency14CTD_human;GENOMICS_ENGLAND;ORPHANET;UNIPROT
TgeneF2C0040053Thrombosis4CTD_human
TgeneF2C0087086Thrombus4CTD_human
TgeneF2C0027051Myocardial Infarction3CTD_human
TgeneF2C0042487Venous Thrombosis3CTD_human
TgeneF2C0149871Deep Vein Thrombosis3CTD_human
TgeneF2C0007786Brain Ischemia2CTD_human
TgeneF2C0085762Alcohol abuse2PSYGENET
TgeneF2C0272317Hereditary factor II deficiency disease2ORPHANET
TgeneF2C0917798Cerebral Ischemia2CTD_human
TgeneF2C3203356Factor II deficiency2ORPHANET
TgeneF2C4722227Hypoprothrombinemias2CTD_human;GENOMICS_ENGLAND
TgeneF2C0002395Alzheimer's Disease1CTD_human
TgeneF2C0003873Rheumatoid Arthritis1CTD_human
TgeneF2C0005779Blood Coagulation Disorders1CTD_human
TgeneF2C0011265Presenile dementia1CTD_human
TgeneF2C0012739Disseminated Intravascular Coagulation1CTD_human
TgeneF2C0015695Fatty Liver1CTD_human
TgeneF2C0019080Hemorrhage1CTD_human
TgeneF2C0020564Hypertrophy1CTD_human
TgeneF2C0023890Liver Cirrhosis1CTD_human
TgeneF2C0027720Nephrosis1CTD_human
TgeneF2C0027746Nerve Degeneration1CTD_human
TgeneF2C0028754Obesity1CTD_human
TgeneF2C0030524Paratuberculosis1CTD_human
TgeneF2C0036341Schizophrenia1CTD_human
TgeneF2C0037198Sinus Thrombosis, Intracranial1CTD_human
TgeneF2C0038454Cerebrovascular accident1CTD_human
TgeneF2C0040038Thromboembolism1CTD_human
TgeneF2C0085605Liver Failure1CTD_human
TgeneF2C0162819Skin Diseases, Vascular1CTD_human
TgeneF2C0239946Fibrosis, Liver1CTD_human
TgeneF2C0267412Mesenteric Venous Thrombosis1CTD_human
TgeneF2C0276496Familial Alzheimer Disease (FAD)1CTD_human
TgeneF2C0398623Thrombophilia1CTD_human
TgeneF2C0400966Non-alcoholic Fatty Liver Disease1CTD_human
TgeneF2C0494463Alzheimer Disease, Late Onset1CTD_human
TgeneF2C0546126Acute Confusional Senile Dementia1CTD_human
TgeneF2C0750900Alzheimer's Disease, Focal Onset1CTD_human
TgeneF2C0750901Alzheimer Disease, Early Onset1CTD_human
TgeneF2C0751500Petrous Sinus Thrombophlebitis1CTD_human
TgeneF2C0751501Intracranial Sinus Thrombophlebitis1CTD_human
TgeneF2C0751502Petrous Sinus Thrombosis1CTD_human
TgeneF2C0751956Acute Cerebrovascular Accidents1CTD_human
TgeneF2C1412000Mesenteric vascular insufficiency1CTD_human
TgeneF2C1861172Venous Thromboembolism1CTD_human
TgeneF2C2239176Liver carcinoma1CTD_human
TgeneF2C2711227Steatohepatitis1CTD_human
TgeneF2C3241937Nonalcoholic Steatohepatitis1CTD_human
TgeneF2C3852984Acute Mesenteric Arterial Embolus1CTD_human
TgeneF2C3852985Occlusive Mesenteric Arterial Ischemia1CTD_human
TgeneF2C3852986Nonocclusive Mesenteric Ischemia1CTD_human
TgeneF2C3852987Acute Mesenteric Arterial Thrombosis1CTD_human