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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:AMFR-PLLP (FusionGDB2 ID:HG267TG51090)

Fusion Gene Summary for AMFR-PLLP

check button Fusion gene summary
Fusion gene informationFusion gene name: AMFR-PLLP
Fusion gene ID: hg267tg51090
HgeneTgene
Gene symbol

AMFR

PLLP

Gene ID

267

51090

Gene nameautocrine motility factor receptorplasmolipin
SynonymsGP78|RNF45PMLP|TM4SF11
Cytomap('AMFR')('PLLP')

16q13

16q13

Type of geneprotein-codingprotein-coding
DescriptionE3 ubiquitin-protein ligase AMFRRING finger protein 45RING-type E3 ubiquitin transferase AMFRplasmolipinplasma membrane proteolipid (plasmolipin)transmembrane 4 superfamily member 11 (plasmolipin)
Modification date2020032720200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000290649, ENST00000564283, 
Fusion gene scores* DoF score7 X 5 X 5=1755 X 3 X 5=75
# samples 86
** MAII scorelog2(8/175*10)=-1.12928301694497
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(6/75*10)=-0.321928094887362
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: AMFR [Title/Abstract] AND PLLP [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointAMFR(56435645)-PLLP(57295982), # samples:1
Anticipated loss of major functional domain due to fusion event.AMFR-PLLP seems lost the major protein functional domain in Hgene partner, which is a essential gene 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
HgeneAMFR

GO:0000209

protein polyubiquitination

17310145|19103148

HgeneAMFR

GO:0030433

ubiquitin-dependent ERAD pathway

11724934|17872946

HgeneAMFR

GO:0051865

protein autoubiquitination

24810856

HgeneAMFR

GO:0070936

protein K48-linked ubiquitination

12847084|24424410



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
ChimerDB4SARCTCGA-HS-A5N7-01AAMFRchr16

56435645

-PLLPchr16

57295982

-


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Fusion Gene ORF analysis for AMFR-PLLP

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
5CDS-intronENST00000290649ENST00000569059AMFRchr16

56435645

-PLLPchr16

57295982

-
Frame-shiftENST00000290649ENST00000219207AMFRchr16

56435645

-PLLPchr16

57295982

-
intron-3CDSENST00000564283ENST00000219207AMFRchr16

56435645

-PLLPchr16

57295982

-
intron-intronENST00000564283ENST00000569059AMFRchr16

56435645

-PLLPchr16

57295982

-

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 AMFR-PLLP


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 AMFR-PLLP


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/:56435645/:57295982)
- 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
..
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: 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 AMFR-PLLP


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 AMFR-PLLP


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 AMFR-PLLP


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 AMFR-PLLP


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneAMFRC0002395Alzheimer's Disease1CTD_human
HgeneAMFRC0005684Malignant neoplasm of urinary bladder1CTD_human
HgeneAMFRC0005695Bladder Neoplasm1CTD_human
HgeneAMFRC0011265Presenile dementia1CTD_human
HgeneAMFRC0235874Disease Exacerbation1CTD_human
HgeneAMFRC0276496Familial Alzheimer Disease (FAD)1CTD_human
HgeneAMFRC0494463Alzheimer Disease, Late Onset1CTD_human
HgeneAMFRC0546126Acute Confusional Senile Dementia1CTD_human
HgeneAMFRC0750900Alzheimer's Disease, Focal Onset1CTD_human
HgeneAMFRC0750901Alzheimer Disease, Early Onset1CTD_human
TgeneC0036341Schizophrenia1PSYGENET
TgeneC0345967Malignant mesothelioma1CTD_human