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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:METAP1-EIF4E (FusionGDB2 ID:53008)

Fusion Gene Summary for METAP1-EIF4E

check button Fusion gene summary
Fusion gene informationFusion gene name: METAP1-EIF4E
Fusion gene ID: 53008
HgeneTgene
Gene symbol

METAP1

EIF4E

Gene ID

23173

1977

Gene namemethionyl aminopeptidase 1eukaryotic translation initiation factor 4E
SynonymsMAP1A|MetAP1AAUTS19|CBP|EIF4E1|EIF4EL1|EIF4F|eIF-4E
Cytomap

4q23

4q23

Type of geneprotein-codingprotein-coding
Descriptionmethionine aminopeptidase 1MAP 1metAP 1peptidase M 1eukaryotic translation initiation factor 4EeIF-4F 25 kDa subuniteukaryotic translation initiation factor 4E-like 1mRNA cap-binding protein
Modification date2020031320200322
UniProtAcc

P53582

Q9NRA8

Ensembl transtripts involved in fusion geneENST00000296411, ENST00000506548, 
ENST00000544031, 
ENST00000504472, 
ENST00000280892, ENST00000450253, 
ENST00000504432, ENST00000505992, 
Fusion gene scores* DoF score3 X 3 X 3=274 X 3 X 3=36
# samples 34
** MAII scorelog2(3/27*10)=0.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
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: METAP1 [Title/Abstract] AND EIF4E [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointMETAP1(99917018)-EIF4E(99823133), # samples:3
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
TgeneEIF4E

GO:0006417

regulation of translation

22578813


check buttonFusion gene breakpoints across METAP1 (5'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

check buttonFusion gene breakpoints across EIF4E (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure

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
ChimerDB4BRCATCGA-E2-A1IL-01AMETAP1chr4

99917018

+EIF4Echr4

99823133

-
ChimerDB4GBMTCGA-28-5215-01AMETAP1chr4

99917018

+EIF4Echr4

99823133

-


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Fusion Gene ORF analysis for METAP1-EIF4E

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-5UTRENST00000296411ENST00000504472METAP1chr4

99917018

+EIF4Echr4

99823133

-
In-frameENST00000296411ENST00000280892METAP1chr4

99917018

+EIF4Echr4

99823133

-
In-frameENST00000296411ENST00000450253METAP1chr4

99917018

+EIF4Echr4

99823133

-
In-frameENST00000296411ENST00000504432METAP1chr4

99917018

+EIF4Echr4

99823133

-
In-frameENST00000296411ENST00000505992METAP1chr4

99917018

+EIF4Echr4

99823133

-
intron-3CDSENST00000506548ENST00000280892METAP1chr4

99917018

+EIF4Echr4

99823133

-
intron-3CDSENST00000506548ENST00000450253METAP1chr4

99917018

+EIF4Echr4

99823133

-
intron-3CDSENST00000506548ENST00000504432METAP1chr4

99917018

+EIF4Echr4

99823133

-
intron-3CDSENST00000506548ENST00000505992METAP1chr4

99917018

+EIF4Echr4

99823133

-
intron-3CDSENST00000544031ENST00000280892METAP1chr4

99917018

+EIF4Echr4

99823133

-
intron-3CDSENST00000544031ENST00000450253METAP1chr4

99917018

+EIF4Echr4

99823133

-
intron-3CDSENST00000544031ENST00000504432METAP1chr4

99917018

+EIF4Echr4

99823133

-
intron-3CDSENST00000544031ENST00000505992METAP1chr4

99917018

+EIF4Echr4

99823133

-
intron-5UTRENST00000506548ENST00000504472METAP1chr4

99917018

+EIF4Echr4

99823133

-
intron-5UTRENST00000544031ENST00000504472METAP1chr4

99917018

+EIF4Echr4

99823133

-

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 METAP1-EIF4E


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.
genomic feature

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 METAP1-EIF4E


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/chr4:99917018/chr4:99823133)
- 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
METAP1

P53582

EIF4E

Q9NRA8

FUNCTION: Cotranslationally removes the N-terminal methionine from nascent proteins. The N-terminal methionine is often cleaved when the second residue in the primary sequence is small and uncharged (Met-Ala-, Cys, Gly, Pro, Ser, Thr, or Val). Required for normal progression through the cell cycle. {ECO:0000255|HAMAP-Rule:MF_03174, ECO:0000269|PubMed:16274222, ECO:0000269|PubMed:17114291}.FUNCTION: EIF4E-binding protein that regulates translation and stability of mRNAs in processing bodies (P-bodies) (PubMed:16157702, PubMed:24335285, PubMed:27342281, PubMed:32354837). Plays a key role in P-bodies to coordinate the storage of translationally inactive mRNAs in the cytoplasm and prevent their degradation (PubMed:24335285, PubMed:32354837). Acts as a binding platform for multiple RNA-binding proteins: promotes deadenylation of mRNAs via its interaction with the CCR4-NOT complex, and blocks decapping via interaction with eIF4E (EIF4E and EIF4E2), thereby protecting deadenylated and repressed mRNAs from degradation (PubMed:27342281, PubMed:32354837). Component of a multiprotein complex that sequesters and represses translation of proneurogenic factors during neurogenesis (By similarity). Promotes miRNA-mediated translational repression (PubMed:24335285, PubMed:27342281, PubMed:28487484). Required for the formation of P-bodies (PubMed:16157702, PubMed:22966201, PubMed:27342281, PubMed:32354837). Involved in mRNA translational repression mediated by the miRNA effector TNRC6B by protecting TNRC6B-targeted mRNAs from decapping and subsequent decay (PubMed:32354837). Also acts as a nucleoplasmic shuttling protein, which mediates the nuclear import of EIF4E and DDX6 by a piggy-back mechanism (PubMed:10856257, PubMed:28216671). {ECO:0000250|UniProtKB:Q9EST3, ECO:0000269|PubMed:10856257, ECO:0000269|PubMed:16157702, ECO:0000269|PubMed:22966201, ECO:0000269|PubMed:24335285, ECO:0000269|PubMed:27342281, ECO:0000269|PubMed:28216671, ECO:0000269|PubMed:28487484, ECO:0000269|PubMed:32354837}.

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
TgeneEIF4Echr4:99917018chr4:99823133ENST0000028089207102_10326238.0Region7-methylguanosine-containing mRNA cap binding
TgeneEIF4Echr4:99917018chr4:99823133ENST0000028089207132_13926238.0RegionEIF4EBP1/2/3 binding
TgeneEIF4Echr4:99917018chr4:99823133ENST0000028089207157_16226238.0Region7-methylguanosine-containing mRNA cap binding
TgeneEIF4Echr4:99917018chr4:99823133ENST000002808920737_4026238.0RegionEIF4EBP1/2/3 binding
TgeneEIF4Echr4:99917018chr4:99823133ENST000002808920756_5726238.0Region7-methylguanosine-containing mRNA cap binding
TgeneEIF4Echr4:99917018chr4:99823133ENST000002808920773_7726238.0RegionEIF4EBP1/2/3 binding
TgeneEIF4Echr4:99917018chr4:99823133ENST0000045025307102_1036218.0Region7-methylguanosine-containing mRNA cap binding
TgeneEIF4Echr4:99917018chr4:99823133ENST0000045025307132_1396218.0RegionEIF4EBP1/2/3 binding
TgeneEIF4Echr4:99917018chr4:99823133ENST0000045025307157_1626218.0Region7-methylguanosine-containing mRNA cap binding
TgeneEIF4Echr4:99917018chr4:99823133ENST000004502530737_406218.0RegionEIF4EBP1/2/3 binding
TgeneEIF4Echr4:99917018chr4:99823133ENST000004502530756_576218.0Region7-methylguanosine-containing mRNA cap binding
TgeneEIF4Echr4:99917018chr4:99823133ENST000004502530773_776218.0RegionEIF4EBP1/2/3 binding
TgeneEIF4Echr4:99917018chr4:99823133ENST0000050599208102_1036249.0Region7-methylguanosine-containing mRNA cap binding
TgeneEIF4Echr4:99917018chr4:99823133ENST0000050599208132_1396249.0RegionEIF4EBP1/2/3 binding
TgeneEIF4Echr4:99917018chr4:99823133ENST0000050599208157_1626249.0Region7-methylguanosine-containing mRNA cap binding
TgeneEIF4Echr4:99917018chr4:99823133ENST000005059920837_406249.0RegionEIF4EBP1/2/3 binding
TgeneEIF4Echr4:99917018chr4:99823133ENST000005059920856_576249.0Region7-methylguanosine-containing mRNA cap binding
TgeneEIF4Echr4:99917018chr4:99823133ENST000005059920873_776249.0RegionEIF4EBP1/2/3 binding

- In-frame and not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneMETAP1chr4:99917018chr4:99823133ENST00000296411+1119_5238387.0RegionZinc finger-like%3B important for proper ribosome association


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Fusion Gene Sequence for METAP1-EIF4E


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 METAP1-EIF4E


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 METAP1-EIF4E


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 METAP1-EIF4E


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