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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:APOA1-FARP1 (FusionGDB2 ID:HG335TG10160)

Fusion Gene Summary for APOA1-FARP1

check button Fusion gene summary
Fusion gene informationFusion gene name: APOA1-FARP1
Fusion gene ID: hg335tg10160
HgeneTgene
Gene symbol

APOA1

FARP1

Gene ID

335

10160

Gene nameapolipoprotein A1FERM, ARH/RhoGEF and pleckstrin domain protein 1
SynonymsHPALP2|apo(a)CDEP|FARP1-IT1|PLEKHC2|PPP1R75
Cytomap('APOA1')('FARP1')

11q23.3

13q32.2

Type of geneprotein-codingprotein-coding
Descriptionapolipoprotein A-Iapo-AIepididymis secretory sperm binding proteinFERM, ARHGEF and pleckstrin domain-containing protein 1FERM, RhoGEF (ARHGEF) and pleckstrin domain protein 1 (chondrocyte-derived)FERM, RhoGEF and pleckstrin domain-containing protein 1PH domain-containing family C member 2chondrocyte-derived ezrin-li
Modification date2020032920200313
UniProtAcc

P02647

.
Ensembl transtripts involved in fusion geneENST00000236850, ENST00000359492, 
ENST00000375320, ENST00000375323, 
ENST00000375329, 
Fusion gene scores* DoF score9 X 5 X 3=13519 X 19 X 8=2888
# samples 922
** MAII scorelog2(9/135*10)=-0.584962500721156
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(22/2888*10)=-3.71449531336251
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: APOA1 [Title/Abstract] AND FARP1 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAPOA1(116706808)-FARP1(99087897), # 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
HgeneAPOA1

GO:0002740

negative regulation of cytokine secretion involved in immune response

12458630

HgeneAPOA1

GO:0006656

phosphatidylcholine biosynthetic process

4335615

HgeneAPOA1

GO:0007179

transforming growth factor beta receptor signaling pathway

23726972

HgeneAPOA1

GO:0007186

G protein-coupled receptor signaling pathway

16443932

HgeneAPOA1

GO:0007229

integrin-mediated signaling pathway

23726972

HgeneAPOA1

GO:0010804

negative regulation of tumor necrosis factor-mediated signaling pathway

21571275

HgeneAPOA1

GO:0010873

positive regulation of cholesterol esterification

4335615

HgeneAPOA1

GO:0010875

positive regulation of cholesterol efflux

27472885

HgeneAPOA1

GO:0010903

negative regulation of very-low-density lipoprotein particle remodeling

14967812

HgeneAPOA1

GO:0018158

protein oxidation

12576517

HgeneAPOA1

GO:0018206

peptidyl-methionine modification

12576517

HgeneAPOA1

GO:0030301

cholesterol transport

10559507

HgeneAPOA1

GO:0032489

regulation of Cdc42 protein signal transduction

16443932

HgeneAPOA1

GO:0033344

cholesterol efflux

11162594|14703508|15358760|16443932|21481393

HgeneAPOA1

GO:0033700

phospholipid efflux

11162594|14703508

HgeneAPOA1

GO:0034115

negative regulation of heterotypic cell-cell adhesion

21571275

HgeneAPOA1

GO:0034375

high-density lipoprotein particle remodeling

21481393

HgeneAPOA1

GO:0034380

high-density lipoprotein particle assembly

190223

HgeneAPOA1

GO:0035025

positive regulation of Rho protein signal transduction

23726972

HgeneAPOA1

GO:0042632

cholesterol homeostasis

21571275

HgeneAPOA1

GO:0050713

negative regulation of interleukin-1 beta secretion

12458630

HgeneAPOA1

GO:0050728

negative regulation of inflammatory response

21571275

HgeneAPOA1

GO:0050766

positive regulation of phagocytosis

20495215

HgeneAPOA1

GO:0050821

protein stabilization

17655203|20495215

HgeneAPOA1

GO:0050919

negative chemotaxis

23726972

HgeneAPOA1

GO:0051345

positive regulation of hydrolase activity

7638166

HgeneAPOA1

GO:0051496

positive regulation of stress fiber assembly

23726972

HgeneAPOA1

GO:0055091

phospholipid homeostasis

21571275

HgeneAPOA1

GO:0060354

negative regulation of cell adhesion molecule production

21571275

HgeneAPOA1

GO:0060761

negative regulation of response to cytokine stimulus

21571275

HgeneAPOA1

GO:0070328

triglyceride homeostasis

21571275

HgeneAPOA1

GO:0070371

ERK1 and ERK2 cascade

23726972

HgeneAPOA1

GO:1900026

positive regulation of substrate adhesion-dependent cell spreading

23726972

HgeneAPOA1

GO:1902995

positive regulation of phospholipid efflux

27472885

TgeneFARP1

GO:0010923

negative regulation of phosphatase activity

19389623



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
ChimerDB4LIHCTCGA-RC-A7S9-01AAPOA1chr11

116706808

-FARP1chr13

99087897

+


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Fusion Gene ORF analysis for APOA1-FARP1

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
intron-3CDSENST00000236850ENST00000319562APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-3CDSENST00000236850ENST00000376586APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-3CDSENST00000236850ENST00000595437APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-3CDSENST00000359492ENST00000319562APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-3CDSENST00000359492ENST00000376586APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-3CDSENST00000359492ENST00000595437APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-3CDSENST00000375320ENST00000319562APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-3CDSENST00000375320ENST00000376586APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-3CDSENST00000375320ENST00000595437APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-3CDSENST00000375323ENST00000319562APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-3CDSENST00000375323ENST00000376586APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-3CDSENST00000375323ENST00000595437APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-3CDSENST00000375329ENST00000319562APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-3CDSENST00000375329ENST00000376586APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-3CDSENST00000375329ENST00000595437APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-intronENST00000236850ENST00000376581APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-intronENST00000236850ENST00000593990APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-intronENST00000359492ENST00000376581APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-intronENST00000359492ENST00000593990APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-intronENST00000375320ENST00000376581APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-intronENST00000375320ENST00000593990APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-intronENST00000375323ENST00000376581APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-intronENST00000375323ENST00000593990APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-intronENST00000375329ENST00000376581APOA1chr11

116706808

-FARP1chr13

99087897

+
intron-intronENST00000375329ENST00000593990APOA1chr11

116706808

-FARP1chr13

99087897

+

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 APOA1-FARP1


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 APOA1-FARP1


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/:116706808/:99087897)
- 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
APOA1

P02647

.
FUNCTION: Participates in the reverse transport of cholesterol from tissues to the liver for excretion by promoting cholesterol efflux from tissues and by acting as a cofactor for the lecithin cholesterol acyltransferase (LCAT). As part of the SPAP complex, activates spermatozoa motility. {ECO:0000269|PubMed:1909888}.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


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Fusion Gene Sequence for APOA1-FARP1


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 APOA1-FARP1


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 APOA1-FARP1


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneAPOA1P02647DB14548Zinc sulfate, unspecified formInducer|LigandSmall moleculeApproved|Experimental
HgeneAPOA1P02647DB01593ZincSmall moleculeApproved|Investigational
HgeneAPOA1P02647DB09130CopperSmall moleculeApproved|Investigational
HgeneAPOA1P02647DB14487Zinc acetateSmall moleculeApproved|Investigational
HgeneAPOA1P02647DB14533Zinc chlorideInducer|LigandSmall moleculeApproved|Investigational

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Related Diseases for APOA1-FARP1


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAPOA1C0268389Amyloidosis, familial visceral8CTD_human;GENOMICS_ENGLAND;UNIPROT
HgeneAPOA1C1704429Hypoalphalipoproteinemia, Familial3GENOMICS_ENGLAND;ORPHANET
HgeneAPOA1C0024623Malignant neoplasm of stomach2CTD_human
HgeneAPOA1C0038356Stomach Neoplasms2CTD_human
HgeneAPOA1C0342898Apolipoprotein A-I deficiency2ORPHANET
HgeneAPOA1C1708349Hereditary Diffuse Gastric Cancer2CTD_human
HgeneAPOA1C0001418Adenocarcinoma1CTD_human
HgeneAPOA1C0003129Anoxemia1CTD_human
HgeneAPOA1C0003130Anoxia1CTD_human
HgeneAPOA1C0004943Behcet Syndrome1CTD_human
HgeneAPOA1C0010054Coronary Arteriosclerosis1CTD_human
HgeneAPOA1C0011609Drug Eruptions1CTD_human
HgeneAPOA1C0013604Edema1CTD_human
HgeneAPOA1C0017665Membranous glomerulonephritis1CTD_human
HgeneAPOA1C0019193Hepatitis, Toxic1CTD_human
HgeneAPOA1C0019693HIV Infections1CTD_human
HgeneAPOA1C0020538Hypertensive disease1CTD_human
HgeneAPOA1C0021368Inflammation1CTD_human
HgeneAPOA1C0024121Lung Neoplasms1CTD_human
HgeneAPOA1C0038454Cerebrovascular accident1CTD_human
HgeneAPOA1C0079221Determination of Death1CTD_human
HgeneAPOA1C0086445Idiopathic Membranous Glomerulonephritis1CTD_human
HgeneAPOA1C0151603Anasarca1CTD_human
HgeneAPOA1C0152013Adenocarcinoma of lung (disorder)1CTD_human
HgeneAPOA1C0154251Lipid Metabolism Disorders1CTD_human
HgeneAPOA1C0205641Adenocarcinoma, Basal Cell1CTD_human
HgeneAPOA1C0205642Adenocarcinoma, Oxyphilic1CTD_human
HgeneAPOA1C0205643Carcinoma, Cribriform1CTD_human
HgeneAPOA1C0205644Carcinoma, Granular Cell1CTD_human
HgeneAPOA1C0205645Adenocarcinoma, Tubular1CTD_human
HgeneAPOA1C0242184Hypoxia1CTD_human
HgeneAPOA1C0242379Malignant neoplasm of lung1CTD_human
HgeneAPOA1C0242488Acute Lung Injury1CTD_human
HgeneAPOA1C0345967Malignant mesothelioma1CTD_human
HgeneAPOA1C0376297Cardiac Death1CTD_human
HgeneAPOA1C0406537Morbilliform Drug Reaction1CTD_human
HgeneAPOA1C0700292Hypoxemia1CTD_human
HgeneAPOA1C0751956Acute Cerebrovascular Accidents1CTD_human
HgeneAPOA1C0853897Diabetic Cardiomyopathies1CTD_human
HgeneAPOA1C0860207Drug-Induced Liver Disease1CTD_human
HgeneAPOA1C1262760Hepatitis, Drug-Induced1CTD_human
HgeneAPOA1C1704378Heymann Nephritis1CTD_human
HgeneAPOA1C1848533Ataxia with vitamin E deficiency1CTD_human
HgeneAPOA1C1956346Coronary Artery Disease1CTD_human
HgeneAPOA1C2239176Liver carcinoma1CTD_human
HgeneAPOA1C2362324Pediatric Obesity1CTD_human
HgeneAPOA1C3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneAPOA1C4087498Familial LCAT deficiency1GENOMICS_ENGLAND
HgeneAPOA1C4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneAPOA1C4279912Chemically-Induced Liver Toxicity1CTD_human
HgeneAPOA1C4317171Adolescent Obesity1CTD_human
HgeneAPOA1C4505456HIV Coinfection1CTD_human
HgeneAPOA1C4521075Childhood Overweight1CTD_human
HgeneAPOA1C4553478Infantile Obesity1CTD_human
HgeneAPOA1C4704955Infant Overweight1CTD_human
HgeneAPOA1C4704956Adolescent Overweight1CTD_human
TgeneC0013146Drug abuse1CTD_human
TgeneC0013170Drug habituation1CTD_human
TgeneC0013222Drug Use Disorders1CTD_human
TgeneC0029231Organic Mental Disorders, Substance-Induced1CTD_human
TgeneC0038580Substance Dependence1CTD_human
TgeneC0038586Substance Use Disorders1CTD_human
TgeneC0236969Substance-Related Disorders1CTD_human
TgeneC0740858Substance abuse problem1CTD_human
TgeneC1510472Drug Dependence1CTD_human
TgeneC4316881Prescription Drug Abuse1CTD_human