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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:EEF2-CKS1B (FusionGDB2 ID:HG1938TG1163)

Fusion Gene Summary for EEF2-CKS1B

check button Fusion gene summary
Fusion gene informationFusion gene name: EEF2-CKS1B
Fusion gene ID: hg1938tg1163
HgeneTgene
Gene symbol

EEF2

CKS1B

Gene ID

1938

1163

Gene nameeukaryotic translation elongation factor 2CDC28 protein kinase regulatory subunit 1B
SynonymsEEF-2|EF-2|EF2|SCA26CKS1|PNAS-16|PNAS-18|ckshs1
Cytomap('EEF2')('CKS1B')

19p13.3

1q21.3

Type of geneprotein-codingprotein-coding
Descriptionelongation factor 2epididymis secretory sperm binding proteinpolypeptidyl-tRNA translocasecyclin-dependent kinases regulatory subunit 1CDC2-associated protein CKS1CDC28 protein kinase 1BNB4 apoptosis/differentiation related proteincell division control protein CKS1
Modification date2020031320200313
UniProtAcc..
Ensembl transtripts involved in fusion geneENST00000309311, ENST00000600720, 
Fusion gene scores* DoF score44 X 37 X 16=260487 X 8 X 6=336
# samples 569
** MAII scorelog2(56/26048*10)=-5.53960196732128
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
log2(9/336*10)=-1.90046432644909
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context

PubMed: EEF2 [Title/Abstract] AND CKS1B [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpointEEF2(3977816)-CKS1B(154947117), # 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


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
ChimerDB4OVTCGA-09-2056EEF2chr19

3977816

-CKS1Bchr1

154947117

+


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Fusion Gene ORF analysis for EEF2-CKS1B

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-intronENST00000309311ENST00000308987EEF2chr19

3977816

-CKS1Bchr1

154947117

+
5CDS-intronENST00000309311ENST00000368436EEF2chr19

3977816

-CKS1Bchr1

154947117

+
5CDS-intronENST00000309311ENST00000368439EEF2chr19

3977816

-CKS1Bchr1

154947117

+
5CDS-intronENST00000309311ENST00000471245EEF2chr19

3977816

-CKS1Bchr1

154947117

+
5CDS-intronENST00000309311ENST00000600888EEF2chr19

3977816

-CKS1Bchr1

154947117

+
intron-intronENST00000600720ENST00000308987EEF2chr19

3977816

-CKS1Bchr1

154947117

+
intron-intronENST00000600720ENST00000368436EEF2chr19

3977816

-CKS1Bchr1

154947117

+
intron-intronENST00000600720ENST00000368439EEF2chr19

3977816

-CKS1Bchr1

154947117

+
intron-intronENST00000600720ENST00000471245EEF2chr19

3977816

-CKS1Bchr1

154947117

+
intron-intronENST00000600720ENST00000600888EEF2chr19

3977816

-CKS1Bchr1

154947117

+

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 EEF2-CKS1B


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 EEF2-CKS1B


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/:3977816/:154947117)
- 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 EEF2-CKS1B


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 EEF2-CKS1B


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 EEF2-CKS1B


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 EEF2-CKS1B


check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneEEF2C0001418Adenocarcinoma1CTD_human
HgeneEEF2C0006142Malignant neoplasm of breast1CTD_human
HgeneEEF2C0007134Renal Cell Carcinoma1CTD_human
HgeneEEF2C0024121Lung Neoplasms1CTD_human
HgeneEEF2C0027626Neoplasm Invasiveness1CTD_human
HgeneEEF2C0027627Neoplasm Metastasis1CTD_human
HgeneEEF2C0029408Degenerative polyarthritis1CTD_human
HgeneEEF2C0086743Osteoarthrosis Deformans1CTD_human
HgeneEEF2C0205641Adenocarcinoma, Basal Cell1CTD_human
HgeneEEF2C0205642Adenocarcinoma, Oxyphilic1CTD_human
HgeneEEF2C0205643Carcinoma, Cribriform1CTD_human
HgeneEEF2C0205644Carcinoma, Granular Cell1CTD_human
HgeneEEF2C0205645Adenocarcinoma, Tubular1CTD_human
HgeneEEF2C0242379Malignant neoplasm of lung1CTD_human
HgeneEEF2C0279702Conventional (Clear Cell) Renal Cell Carcinoma1CTD_human
HgeneEEF2C0678222Breast Carcinoma1CTD_human
HgeneEEF2C1257931Mammary Neoplasms, Human1CTD_human
HgeneEEF2C1266042Chromophobe Renal Cell Carcinoma1CTD_human
HgeneEEF2C1266043Sarcomatoid Renal Cell Carcinoma1CTD_human
HgeneEEF2C1266044Collecting Duct Carcinoma of the Kidney1CTD_human
HgeneEEF2C1306837Papillary Renal Cell Carcinoma1CTD_human
HgeneEEF2C1458155Mammary Neoplasms1CTD_human
HgeneEEF2C1836395SPINOCEREBELLAR ATAXIA 261CTD_human;ORPHANET;UNIPROT
HgeneEEF2C4704874Mammary Carcinoma, Human1CTD_human