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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:EIF4A1-KLF2 (FusionGDB2 ID:25894)

Fusion Gene Summary for EIF4A1-KLF2

check button Fusion gene summary
Fusion gene informationFusion gene name: EIF4A1-KLF2
Fusion gene ID: 25894
HgeneTgene
Gene symbol

EIF4A1

KLF2

Gene ID

1973

10365

Gene nameeukaryotic translation initiation factor 4A1Kruppel like factor 2
SynonymsDDX2A|EIF-4A|EIF4A|eIF-4A-I|eIF4A-ILKLF
Cytomap

17p13.1

19p13.11

Type of geneprotein-codingprotein-coding
Descriptioneukaryotic initiation factor 4A-IATP-dependent RNA helicase eIF4A-1eukaryotic initiation factor 4AIeukaryotic translation initiation factor 4AKrueppel-like factor 2Kruppel-like factor 2 (lung)Kruppel-like factor LKLFlung Kruppel-like factorlung Kruppel-like zinc finger transcription factorlung krueppel-like factor
Modification date2020032220200313
UniProtAcc

P60842

.
Ensembl transtripts involved in fusion geneENST00000380512, ENST00000293831, 
ENST00000577269, ENST00000582746, 
ENST00000581808, 		ENST00000248071, 
ENST00000592003, 
Fusion gene scores* DoF score3 X 2 X 2=123 X 3 X 2=18
# samples 54
** MAII scorelog2(5/12*10)=2.05889368905357
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0		log2(4/18*10)=1.15200309344505
effective Gene in Pan-Cancer Fusion Genes (eGinPCFGs).
DoF>8 and MAII>0
Context

PubMed: EIF4A1 [Title/Abstract] AND KLF2 [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointEIF4A1(7476182)-KLF2(16437666), # samples:1
EIF4A1(7476182)-KLF2(16437667), # samples:1
Anticipated loss of major functional domain due to fusion event.EIF4A1-KLF2 seems lost the major protein functional domain in Hgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
EIF4A1-KLF2 seems lost the major protein functional domain in Hgene partner, which is a essential gene due to the frame-shifted ORF.
EIF4A1-KLF2 seems lost the major protein functional domain in Tgene partner, which is a transcription factor 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
TgeneKLF2

GO:0000122

negative regulation of transcription by RNA polymerase II

26299712

TgeneKLF2

GO:0045429

positive regulation of nitric oxide biosynthetic process

21768538

TgeneKLF2

GO:0045893

positive regulation of transcription, DNA-templated

21063504

TgeneKLF2

GO:0048386

positive regulation of retinoic acid receptor signaling pathway

26416422


check buttonFusion gene breakpoints across EIF4A1 (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 KLF2 (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
ChimerDB4LAMLTCGA-AB-2810EIF4A1chr17

7476182

+KLF2chr19

16437666

+
ChimerDB4LAMLTCGA-AB-2810_700GEAAXX_7EIF4A1chr17

7476182

+KLF2chr19

16437667

+


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Fusion Gene ORF analysis for EIF4A1-KLF2

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-3CDSENST00000380512ENST00000248071EIF4A1chr17

7476182

+KLF2chr19

16437666

+
5UTR-3CDSENST00000380512ENST00000592003EIF4A1chr17

7476182

+KLF2chr19

16437666

+
Frame-shiftENST00000293831ENST00000248071EIF4A1chr17

7476182

+KLF2chr19

16437666

+
Frame-shiftENST00000293831ENST00000592003EIF4A1chr17

7476182

+KLF2chr19

16437666

+
Frame-shiftENST00000577269ENST00000248071EIF4A1chr17

7476182

+KLF2chr19

16437666

+
Frame-shiftENST00000577269ENST00000592003EIF4A1chr17

7476182

+KLF2chr19

16437666

+
Frame-shiftENST00000582746ENST00000248071EIF4A1chr17

7476182

+KLF2chr19

16437666

+
Frame-shiftENST00000582746ENST00000592003EIF4A1chr17

7476182

+KLF2chr19

16437666

+
intron-3CDSENST00000581808ENST00000248071EIF4A1chr17

7476182

+KLF2chr19

16437666

+
intron-3CDSENST00000581808ENST00000592003EIF4A1chr17

7476182

+KLF2chr19

16437666

+
5UTR-3CDSENST00000380512ENST00000248071EIF4A1chr17

7476182

+KLF2chr19

16437667

+
5UTR-3CDSENST00000380512ENST00000592003EIF4A1chr17

7476182

+KLF2chr19

16437667

+
Frame-shiftENST00000293831ENST00000248071EIF4A1chr17

7476182

+KLF2chr19

16437667

+
Frame-shiftENST00000293831ENST00000592003EIF4A1chr17

7476182

+KLF2chr19

16437667

+
Frame-shiftENST00000577269ENST00000248071EIF4A1chr17

7476182

+KLF2chr19

16437667

+
Frame-shiftENST00000577269ENST00000592003EIF4A1chr17

7476182

+KLF2chr19

16437667

+
Frame-shiftENST00000582746ENST00000248071EIF4A1chr17

7476182

+KLF2chr19

16437667

+
Frame-shiftENST00000582746ENST00000592003EIF4A1chr17

7476182

+KLF2chr19

16437667

+
intron-3CDSENST00000581808ENST00000248071EIF4A1chr17

7476182

+KLF2chr19

16437667

+
intron-3CDSENST00000581808ENST00000592003EIF4A1chr17

7476182

+KLF2chr19

16437667

+

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 EIF4A1-KLF2


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)
EIF4A1chr177476182+KLF2chr1916437666+0.70497170.29502836
EIF4A1chr177476182+KLF2chr1916437666+0.70497170.29502836
EIF4A1chr177476182+KLF2chr1916437666+0.70497170.29502836
EIF4A1chr177476182+KLF2chr1916437666+0.70497170.29502836

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 EIF4A1-KLF2


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
EIF4A1

P60842

.
FUNCTION: ATP-dependent RNA helicase which is a subunit of the eIF4F complex involved in cap recognition and is required for mRNA binding to ribosome. In the current model of translation initiation, eIF4A unwinds RNA secondary structures in the 5'-UTR of mRNAs which is necessary to allow efficient binding of the small ribosomal subunit, and subsequent scanning for the initiator codon. {ECO:0000269|PubMed:19153607, ECO:0000269|PubMed:19204291}.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.

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 EIF4A1-KLF2


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 EIF4A1-KLF2


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 EIF4A1-KLF2


check button Drugs targeting genes involved in this fusion gene.
(DrugBank Version 5.1.8 2021-05-08)
PartnerGeneUniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status
HgeneEIF4A1P60842DB09130CopperSmall moleculeApproved|Investigational
HgeneEIF4A1P60842DB09130CopperSmall moleculeApproved|Investigational
HgeneEIF4A1P60842DB09130CopperSmall moleculeApproved|Investigational

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Related Diseases for EIF4A1-KLF2


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneEIF4A1C0019693HIV Infections1CTD_human
HgeneEIF4A1C4505456HIV Coinfection1CTD_human
TgeneKLF2C0009402Colorectal Carcinoma1CTD_human
TgeneKLF2C0009404Colorectal Neoplasms1CTD_human
TgeneKLF2C0024115Lung diseases1CTD_human