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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:EGFR-PTPRF (FusionGDB2 ID:25478)

Fusion Gene Summary for EGFR-PTPRF

check button Fusion gene summary
Fusion gene informationFusion gene name: EGFR-PTPRF
Fusion gene ID: 25478
HgeneTgene
Gene symbol

EGFR

PTPRF

Gene ID

1956

5792

Gene nameepidermal growth factor receptorprotein tyrosine phosphatase receptor type F
SynonymsERBB|ERBB1|HER1|NISBD2|PIG61|mENABNAH2|LAR
Cytomap

7p11.2

1p34.2

Type of geneprotein-codingprotein-coding
Descriptionepidermal growth factor receptoravian erythroblastic leukemia viral (v-erb-b) oncogene homologcell growth inhibiting protein 40cell proliferation-inducing protein 61epidermal growth factor receptor tyrosine kinase domainerb-b2 receptor tyrosine kinasreceptor-type tyrosine-protein phosphatase FLCA-homologleukocyte antigen-related (LAR) PTP receptorleukocyte antigen-related tyrosine phosphataseleukocyte common antigen relatedprotein tyrosine phosphatase, receptor type, F polypeptidereceptor-linke
Modification date2020032920200313
UniProtAcc

P00533

.
Ensembl transtripts involved in fusion geneENST00000275493, ENST00000454757, 
ENST00000342916, ENST00000344576, 
ENST00000420316, ENST00000442591, 
ENST00000455089, ENST00000463948, 
ENST00000359947, ENST00000438120, 
ENST00000372413, ENST00000372414, 
ENST00000422171, ENST00000496447, 
Fusion gene scores* DoF score41 X 25 X 14=1435010 X 14 X 6=840
# samples 5315
** MAII scorelog2(53/14350*10)=-4.75891456699985
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(15/840*10)=-2.48542682717024
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: EGFR [Title/Abstract] AND PTPRF [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointEGFR(55272979)-PTPRF(43996703), # 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
HgeneEGFR

GO:0001934

positive regulation of protein phosphorylation

20551055

HgeneEGFR

GO:0007165

signal transduction

10572067

HgeneEGFR

GO:0007166

cell surface receptor signaling pathway

7736574

HgeneEGFR

GO:0007173

epidermal growth factor receptor signaling pathway

7736574|12435727

HgeneEGFR

GO:0008283

cell proliferation

17115032

HgeneEGFR

GO:0008284

positive regulation of cell proliferation

7736574

HgeneEGFR

GO:0010750

positive regulation of nitric oxide mediated signal transduction

12828935

HgeneEGFR

GO:0018108

peptidyl-tyrosine phosphorylation

22732145

HgeneEGFR

GO:0030307

positive regulation of cell growth

15467833

HgeneEGFR

GO:0042177

negative regulation of protein catabolic process

17115032

HgeneEGFR

GO:0042327

positive regulation of phosphorylation

15082764

HgeneEGFR

GO:0043406

positive regulation of MAP kinase activity

10572067

HgeneEGFR

GO:0045739

positive regulation of DNA repair

17115032

HgeneEGFR

GO:0045740

positive regulation of DNA replication

17115032

HgeneEGFR

GO:0045944

positive regulation of transcription by RNA polymerase II

20551055

HgeneEGFR

GO:0050679

positive regulation of epithelial cell proliferation

10572067

HgeneEGFR

GO:0050999

regulation of nitric-oxide synthase activity

12828935

HgeneEGFR

GO:0070141

response to UV-A

18483258

HgeneEGFR

GO:0070374

positive regulation of ERK1 and ERK2 cascade

20551055

HgeneEGFR

GO:0071392

cellular response to estradiol stimulus

20551055

HgeneEGFR

GO:1900020

positive regulation of protein kinase C activity

22732145

HgeneEGFR

GO:1903078

positive regulation of protein localization to plasma membrane

22732145

TgenePTPRF

GO:0099560

synaptic membrane adhesion

26321637


check buttonFusion gene breakpoints across EGFR (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 PTPRF (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
ChiTaRS5.0N/ABG005213EGFRchr7

55272979

-PTPRFchr1

43996703

+


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Fusion Gene ORF analysis for EGFR-PTPRF

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-5UTRENST00000275493ENST00000359947EGFRchr7

55272979

-PTPRFchr1

43996703

+
5CDS-5UTRENST00000275493ENST00000438120EGFRchr7

55272979

-PTPRFchr1

43996703

+
5CDS-5UTRENST00000454757ENST00000359947EGFRchr7

55272979

-PTPRFchr1

43996703

+
5CDS-5UTRENST00000454757ENST00000438120EGFRchr7

55272979

-PTPRFchr1

43996703

+
5CDS-intronENST00000275493ENST00000372413EGFRchr7

55272979

-PTPRFchr1

43996703

+
5CDS-intronENST00000275493ENST00000372414EGFRchr7

55272979

-PTPRFchr1

43996703

+
5CDS-intronENST00000275493ENST00000422171EGFRchr7

55272979

-PTPRFchr1

43996703

+
5CDS-intronENST00000275493ENST00000496447EGFRchr7

55272979

-PTPRFchr1

43996703

+
5CDS-intronENST00000454757ENST00000372413EGFRchr7

55272979

-PTPRFchr1

43996703

+
5CDS-intronENST00000454757ENST00000372414EGFRchr7

55272979

-PTPRFchr1

43996703

+
5CDS-intronENST00000454757ENST00000422171EGFRchr7

55272979

-PTPRFchr1

43996703

+
5CDS-intronENST00000454757ENST00000496447EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-5UTRENST00000342916ENST00000359947EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-5UTRENST00000342916ENST00000438120EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-5UTRENST00000344576ENST00000359947EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-5UTRENST00000344576ENST00000438120EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-5UTRENST00000420316ENST00000359947EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-5UTRENST00000420316ENST00000438120EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-5UTRENST00000442591ENST00000359947EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-5UTRENST00000442591ENST00000438120EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-5UTRENST00000455089ENST00000359947EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-5UTRENST00000455089ENST00000438120EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-5UTRENST00000463948ENST00000359947EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-5UTRENST00000463948ENST00000438120EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000342916ENST00000372413EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000342916ENST00000372414EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000342916ENST00000422171EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000342916ENST00000496447EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000344576ENST00000372413EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000344576ENST00000372414EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000344576ENST00000422171EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000344576ENST00000496447EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000420316ENST00000372413EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000420316ENST00000372414EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000420316ENST00000422171EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000420316ENST00000496447EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000442591ENST00000372413EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000442591ENST00000372414EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000442591ENST00000422171EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000442591ENST00000496447EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000455089ENST00000372413EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000455089ENST00000372414EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000455089ENST00000422171EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000455089ENST00000496447EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000463948ENST00000372413EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000463948ENST00000372414EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000463948ENST00000422171EGFRchr7

55272979

-PTPRFchr1

43996703

+
intron-intronENST00000463948ENST00000496447EGFRchr7

55272979

-PTPRFchr1

43996703

+

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 EGFR-PTPRF


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)

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 EGFR-PTPRF


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/:55272979/:43996703)
- 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
EGFR

P00533

.
FUNCTION: Receptor tyrosine kinase binding ligands of the EGF family and activating several signaling cascades to convert extracellular cues into appropriate cellular responses (PubMed:2790960, PubMed:10805725, PubMed:27153536). Known ligands include EGF, TGFA/TGF-alpha, AREG, epigen/EPGN, BTC/betacellulin, epiregulin/EREG and HBEGF/heparin-binding EGF (PubMed:2790960, PubMed:7679104, PubMed:8144591, PubMed:9419975, PubMed:15611079, PubMed:12297049, PubMed:27153536, PubMed:20837704, PubMed:17909029). Ligand binding triggers receptor homo- and/or heterodimerization and autophosphorylation on key cytoplasmic residues. The phosphorylated receptor recruits adapter proteins like GRB2 which in turn activates complex downstream signaling cascades. Activates at least 4 major downstream signaling cascades including the RAS-RAF-MEK-ERK, PI3 kinase-AKT, PLCgamma-PKC and STATs modules (PubMed:27153536). May also activate the NF-kappa-B signaling cascade (PubMed:11116146). Also directly phosphorylates other proteins like RGS16, activating its GTPase activity and probably coupling the EGF receptor signaling to the G protein-coupled receptor signaling (PubMed:11602604). Also phosphorylates MUC1 and increases its interaction with SRC and CTNNB1/beta-catenin (PubMed:11483589). Positively regulates cell migration via interaction with CCDC88A/GIV which retains EGFR at the cell membrane following ligand stimulation, promoting EGFR signaling which triggers cell migration (PubMed:20462955). Plays a role in enhancing learning and memory performance (By similarity). {ECO:0000250|UniProtKB:Q01279, ECO:0000269|PubMed:10805725, ECO:0000269|PubMed:11116146, ECO:0000269|PubMed:11483589, ECO:0000269|PubMed:11602604, ECO:0000269|PubMed:12297049, ECO:0000269|PubMed:12297050, ECO:0000269|PubMed:12620237, ECO:0000269|PubMed:12873986, ECO:0000269|PubMed:15374980, ECO:0000269|PubMed:15590694, ECO:0000269|PubMed:15611079, ECO:0000269|PubMed:17115032, ECO:0000269|PubMed:17909029, ECO:0000269|PubMed:19560417, ECO:0000269|PubMed:20462955, ECO:0000269|PubMed:20837704, ECO:0000269|PubMed:21258366, ECO:0000269|PubMed:27153536, ECO:0000269|PubMed:2790960, ECO:0000269|PubMed:7679104, ECO:0000269|PubMed:8144591, ECO:0000269|PubMed:9419975}.; FUNCTION: Isoform 2 may act as an antagonist of EGF action.; FUNCTION: (Microbial infection) Acts as a receptor for hepatitis C virus (HCV) in hepatocytes and facilitates its cell entry. Mediates HCV entry by promoting the formation of the CD81-CLDN1 receptor complexes that are essential for HCV entry and by enhancing membrane fusion of cells expressing HCV envelope glycoproteins. {ECO:0000269|PubMed:21516087}.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 EGFR-PTPRF


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 EGFR-PTPRF


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 EGFR-PTPRF


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 EGFR-PTPRF


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource