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Center for Computational Systems Medicine level1
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Fusion Gene Summary

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Fusion Gene Sample Information

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Fusion ORF Analysis

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Fusion Amino Acid Sequences

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Fusion Protein Functional Features

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Fusion Protein-Protein Interaction

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Related drugs with this fusion protein

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Related disease with this fusion protein

Fusion Protein:CLU-RPS4X

Fusion Protein Summary

check button Fusion gene summary
Fusion partner gene informationFusion gene name: CLU-RPS4X
FusionPDB ID: 17461
FusionGDB2.0 ID: 17461
HgeneTgene
Gene symbol

CLU

RPS4X

Gene ID

1191

6191

Gene nameclusterinribosomal protein S4 X-linked
SynonymsAAG4|APO-J|APOJ|CLI|CLU1|CLU2|KUB1|NA1/NA2|SGP-2|SGP2|SP-40|TRPM-2|TRPM2CCG2|DXS306|RPS4|S4|SCAR|SCR10
Cytomap

8p21.1

Xq13.1

Type of geneprotein-codingprotein-coding
Descriptionclusterinaging-associated protein 4apolipoprotein Jcomplement cytolysis inhibitorcomplement lysis inhibitorcomplement-associated protein SP-40,40epididymis secretory sperm binding proteinku70-binding protein 1sulfated glycoprotein 2testosterone-r40S ribosomal protein S4, X isoformcell cycle gene 2ribosomal protein S4X isoformsingle copy abundant mRNA proteinsingle-copy abundant mRNAsmall ribosomal subunit protein eS4
Modification date2020032720200313
UniProtAcc

Q15846

.
Ensembl transtripts involved in fusion geneENST idsENST00000316403, ENST00000405140, 
ENST00000523500, ENST00000546343, 
ENST00000560366, 		ENST00000486733, 
ENST00000373626, ENST00000316084, 
Fusion gene scores for assessment (based on all fusion genes of FusionGDB 2.0)* DoF score38 X 38 X 12=1732820 X 17 X 7=2380
# samples 4922
** MAII scorelog2(49/17328*10)=-5.14417958860576
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0		log2(22/2380*10)=-3.43538614467065
possibly effective Gene in Pan-Cancer Fusion Genes (peGinPCFGs).
DoF>8 and MAII<0
Context (manual curation of fusion genes in FusionPDB)

PubMed: CLU [Title/Abstract] AND RPS4X [Title/Abstract] AND fusion [Title/Abstract]

Most frequent breakpoint (based on all fusion genes of FusionGDB 2.0)CLU(27461808)-RPS4X(71493239), # samples:1
Anticipated loss of major functional domain due to fusion event.CLU-RPS4X seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
CLU-RPS4X seems lost the major protein functional domain in Hgene partner, which is a CGC by not retaining the major functional domain in the partially deleted in-frame ORF.
CLU-RPS4X seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
CLU-RPS4X seems lost the major protein functional domain in Hgene partner, which is a essential gene by not retaining the major functional domain in the partially deleted in-frame ORF.
CLU-RPS4X seems lost the major protein functional domain in Hgene partner, which is a tumor suppressor due to the frame-shifted ORF.
CLU-RPS4X seems lost the major protein functional domain in Tgene partner, which is a cell metabolism gene due to the frame-shifted ORF.
CLU-RPS4X seems lost the major protein functional domain in Tgene 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
HgeneCLU

GO:0000902

cell morphogenesis

15857407

HgeneCLU

GO:0001774

microglial cell activation

15857407

HgeneCLU

GO:0017038

protein import

24446231

HgeneCLU

GO:0031333

negative regulation of protein complex assembly

22179788|23106396

HgeneCLU

GO:0031334

positive regulation of protein complex assembly

22179788

HgeneCLU

GO:0032760

positive regulation of tumor necrosis factor production

15857407

HgeneCLU

GO:0045429

positive regulation of nitric oxide biosynthetic process

15857407

HgeneCLU

GO:0050821

protein stabilization

11123922|12176985

HgeneCLU

GO:0051131

chaperone-mediated protein complex assembly

17412999

HgeneCLU

GO:0051788

response to misfolded protein

19996109

HgeneCLU

GO:0061077

chaperone-mediated protein folding

11123922

HgeneCLU

GO:0061518

microglial cell proliferation

15857407

HgeneCLU

GO:1900221

regulation of amyloid-beta clearance

24446231

HgeneCLU

GO:1901214

regulation of neuron death

17412999

HgeneCLU

GO:1901216

positive regulation of neuron death

15857407

HgeneCLU

GO:1902430

negative regulation of amyloid-beta formation

12047389|17412999

HgeneCLU

GO:1905907

negative regulation of amyloid fibril formation

22179788


check buttonFusion gene breakpoints across CLU (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 RPS4X (3'-gene)
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
all structure


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Fusion Gene Sample Information

check buttonFusion gene information from FusionGDB2.0.
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
ChimerDB4THCATCGA-DJ-A13V-01ACLUchr8

27461808

-RPS4XchrX

71493239

-


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Fusion ORF Analysis


check buttonFusion information from ORFfinder translation from full-length transcript sequence from FusionPDB.
HenstTenstHgeneHchrHbpHstrandTgeneTchrTbpTstrandSeq length
(transcript)		BP loci
(transcript)		Predicted start
(transcript)		Predicted stop
(transcript)		Seq length
(amino acids)
ENST00000546343CLUchr827461808-ENST00000316084RPS4XchrX71493239-200311141471373408
ENST00000560366CLUchr827461808-ENST00000316084RPS4XchrX71493239-20081119291378449
ENST00000523500CLUchr827461808-ENST00000316084RPS4XchrX71493239-260917206811979432

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
ENST00000546343ENST00000316084CLUchr827461808-RPS4XchrX71493239-0.0050175240.9949825
ENST00000560366ENST00000316084CLUchr827461808-RPS4XchrX71493239-0.0026968550.9973031
ENST00000523500ENST00000316084CLUchr827461808-RPS4XchrX71493239-0.0024135970.99758637

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Fusion Amino Acid Sequences


check button For individual full-length fusion transcript sequence from FusionPDB, we ran ORFfinder and chose the longest ORF among the all predicted ones.
>FusionGDB ID_FusionGDB isoform ID_FGname_Hgene_Hchr_Hbp_Henst_Tgene_Tchr_Tbp_Tenst_length(fusion AA) seq_BP

>17461_17461_1_CLU-RPS4X_CLU_chr8_27461808_ENST00000523500_RPS4X_chrX_71493239_ENST00000316084_length(amino acids)=432AA_BP=346
MLQAAGGRDASRLSSCSHDGLLFSAEACKDSRIGGMMKTLLLFVGLLLTWESGQVLGDQTVSDNELQEMSNQGSKYVNKEIQNAVNGVKQ
IKTLIEKTNEERKTLLSNLEEAKKKKEDALNETRESETKLKELPGVCNETMMALWEECKPCLKQTCMKFYARVCRSGSGLVGRQLEEFLN
QSSPFYFWMNGDRIDSLLENDRQQTHMLDVMQDHFSRASSIIDELFQDRFFTREPQDTYHYLPFSLPHRRPHFFFPKSRIVRSLMPFSPY
EPLNFHAMFQPFLEMIHEAQQAMDIHFHSPAFQHPPTEFIREGDDDRTVCREIRHNSTGCLRMKDQCDKCREILSVGNLCMVTGGANLGR

--------------------------------------------------------------

>17461_17461_2_CLU-RPS4X_CLU_chr8_27461808_ENST00000546343_RPS4X_chrX_71493239_ENST00000316084_length(amino acids)=408AA_BP=322
MEACKDSRIGGMMKTLLLFVGLLLTWESGQVLGDQTVSDNELQEMSNQGSKYVNKEIQNAVNGVKQIKTLIEKTNEERKTLLSNLEEAKK
KKEDALNETRESETKLKELPGVCNETMMALWEECKPCLKQTCMKFYARVCRSGSGLVGRQLEEFLNQSSPFYFWMNGDRIDSLLENDRQQ
THMLDVMQDHFSRASSIIDELFQDRFFTREPQDTYHYLPFSLPHRRPHFFFPKSRIVRSLMPFSPYEPLNFHAMFQPFLEMIHEAQQAMD
IHFHSPAFQHPPTEFIREGDDDRTVCREIRHNSTGCLRMKDQCDKCREILSVGNLCMVTGGANLGRIGVITNRERHPGSFDVVHVKDANG

--------------------------------------------------------------

>17461_17461_3_CLU-RPS4X_CLU_chr8_27461808_ENST00000560366_RPS4X_chrX_71493239_ENST00000316084_length(amino acids)=449AA_BP=363
MQVCSQPQRGCVREQSAINTAPPSAHNAASPGGARGHRVPLTEACKDSRIGGMMKTLLLFVGLLLTWESGQVLGDQTVSDNELQEMSNQG
SKYVNKEIQNAVNGVKQIKTLIEKTNEERKTLLSNLEEAKKKKEDALNETRESETKLKELPGVCNETMMALWEECKPCLKQTCMKFYARV
CRSGSGLVGRQLEEFLNQSSPFYFWMNGDRIDSLLENDRQQTHMLDVMQDHFSRASSIIDELFQDRFFTREPQDTYHYLPFSLPHRRPHF
FFPKSRIVRSLMPFSPYEPLNFHAMFQPFLEMIHEAQQAMDIHFHSPAFQHPPTEFIREGDDDRTVCREIRHNSTGCLRMKDQCDKCREI

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Fusion Protein Functional Features


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/chr8:27461808/chrX:71493239)
- 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
CLU

Q15846

.
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.
- Retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCLUchr8:27461808chrX:71493239ENST00000316403-6978_81311.3333333333333450.0MotifNuclear localization signal
HgeneCLUchr8:27461808chrX:71493239ENST00000405140-6978_81311.3333333333333450.0MotifNuclear localization signal
HgeneCLUchr8:27461808chrX:71493239ENST00000523500-5878_81311.3333333333333450.0MotifNuclear localization signal
HgeneCLUchr8:27461808chrX:71493239ENST00000546343-6978_81322.3333333333333461.0MotifNuclear localization signal
HgeneCLUchr8:27461808chrX:71493239ENST00000560366-6978_81363.3333333333333502.0MotifNuclear localization signal

- Not-retained protein feature among the 13 regional features.
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenProtein featureProtein feature note
HgeneCLUchr8:27461808chrX:71493239ENST00000316403-69443_447311.3333333333333450.0MotifNuclear localization signal
HgeneCLUchr8:27461808chrX:71493239ENST00000405140-69443_447311.3333333333333450.0MotifNuclear localization signal
HgeneCLUchr8:27461808chrX:71493239ENST00000523500-58443_447311.3333333333333450.0MotifNuclear localization signal
HgeneCLUchr8:27461808chrX:71493239ENST00000546343-69443_447322.3333333333333461.0MotifNuclear localization signal
HgeneCLUchr8:27461808chrX:71493239ENST00000560366-69443_447363.3333333333333502.0MotifNuclear localization signal
TgeneRPS4Xchr8:27461808chrX:71493239ENST000003160844742_104177.33333333333334264.0DomainNote=S4 RNA-binding


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Fusion Protein-Protein Interaction


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 from validated records (BIOGRID-3.4.160)
GenePPI interactors


check button Protein-protein interactors based on sequence similarity (STRING)
GeneSTRING network
CLUall structure
RPS4X


check button - Retained interactions in fusion protein (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenStill interaction with


check button - Lost interactions due to fusion (protein functional feature from UniProt).
PartnerGeneHbpTbpENSTStrandBPexonTotalExonProtein feature loci*BPlociTotalLenInteraction lost with


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Related Drugs to CLU-RPS4X


check button Drugs used for this fusion-positive patient.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDrugSourcePMID

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Related Diseases to CLU-RPS4X


check button Diseases that have this fusion gene.
(Manual curation of PubMed, 04-30-2022 + MyCancerGenome)
HgeneTgeneDiseaseSourcePMID

check button Diseases associated with fusion partners.
(DisGeNet 4.0)
PartnerGeneDisease IDDisease name# pubmedsSource
HgeneCLUC0022660Kidney Failure, Acute6CTD_human
HgeneCLUC1565662Acute Kidney Insufficiency6CTD_human
HgeneCLUC2609414Acute kidney injury6CTD_human
HgeneCLUC0002395Alzheimer's Disease3CTD_human
HgeneCLUC0011265Presenile dementia3CTD_human
HgeneCLUC0022658Kidney Diseases3CTD_human
HgeneCLUC0276496Familial Alzheimer Disease (FAD)3CTD_human
HgeneCLUC0494463Alzheimer Disease, Late Onset3CTD_human
HgeneCLUC0546126Acute Confusional Senile Dementia3CTD_human
HgeneCLUC0750900Alzheimer's Disease, Focal Onset3CTD_human
HgeneCLUC0750901Alzheimer Disease, Early Onset3CTD_human
HgeneCLUC0013221Drug toxicity2CTD_human
HgeneCLUC0029408Degenerative polyarthritis2CTD_human
HgeneCLUC0041755Adverse reaction to drug2CTD_human
HgeneCLUC0086743Osteoarthrosis Deformans2CTD_human
HgeneCLUC0019193Hepatitis, Toxic1CTD_human
HgeneCLUC0022333Jacksonian Seizure1CTD_human
HgeneCLUC0024141Lupus Erythematosus, Systemic1CTD_human
HgeneCLUC0025202melanoma1CTD_human
HgeneCLUC0027686Pathologic Neovascularization1CTD_human
HgeneCLUC0033578Prostatic Neoplasms1CTD_human
HgeneCLUC0036341Schizophrenia1PSYGENET
HgeneCLUC0036572Seizures1CTD_human
HgeneCLUC0087031Juvenile-Onset Still Disease1CTD_human
HgeneCLUC0149958Complex partial seizures1CTD_human
HgeneCLUC0234533Generalized seizures1CTD_human
HgeneCLUC0234535Clonic Seizures1CTD_human
HgeneCLUC0234985Mental deterioration1CTD_human
HgeneCLUC0242380Libman-Sacks Disease1CTD_human
HgeneCLUC0270824Visual seizure1CTD_human
HgeneCLUC0270844Tonic Seizures1CTD_human
HgeneCLUC0270846Epileptic drop attack1CTD_human
HgeneCLUC0333641Atrophic1CTD_human
HgeneCLUC0338656Impaired cognition1CTD_human
HgeneCLUC0376358Malignant neoplasm of prostate1CTD_human
HgeneCLUC0422850Seizures, Somatosensory1CTD_human
HgeneCLUC0422852Seizures, Auditory1CTD_human
HgeneCLUC0422853Olfactory seizure1CTD_human
HgeneCLUC0422854Gustatory seizure1CTD_human
HgeneCLUC0422855Vertiginous seizure1CTD_human
HgeneCLUC0494475Tonic - clonic seizures1CTD_human
HgeneCLUC0751056Non-epileptic convulsion1CTD_human
HgeneCLUC0751110Single Seizure1CTD_human
HgeneCLUC0751123Atonic Absence Seizures1CTD_human
HgeneCLUC0751494Convulsive Seizures1CTD_human
HgeneCLUC0751495Seizures, Focal1CTD_human
HgeneCLUC0751496Seizures, Sensory1CTD_human
HgeneCLUC0860207Drug-Induced Liver Disease1CTD_human
HgeneCLUC1262760Hepatitis, Drug-Induced1CTD_human
HgeneCLUC1270972Mild cognitive disorder1CTD_human
HgeneCLUC1862939AMYOTROPHIC LATERAL SCLEROSIS 11CTD_human
HgeneCLUC1862941Amyotrophic Lateral Sclerosis, Sporadic1CTD_human
HgeneCLUC3495559Juvenile arthritis1CTD_human
HgeneCLUC3495874Nonepileptic Seizures1CTD_human
HgeneCLUC3658290Drug-Induced Acute Liver Injury1CTD_human
HgeneCLUC3714758Juvenile psoriatic arthritis1CTD_human
HgeneCLUC4048158Convulsions1CTD_human
HgeneCLUC4277682Chemical and Drug Induced Liver Injury1CTD_human
HgeneCLUC4279912Chemically-Induced Liver Toxicity1CTD_human
HgeneCLUC4316903Absence Seizures1CTD_human
HgeneCLUC4317109Epileptic Seizures1CTD_human
HgeneCLUC4317123Myoclonic Seizures1CTD_human
HgeneCLUC4505436Generalized Absence Seizures1CTD_human
HgeneCLUC4551993Amyotrophic Lateral Sclerosis, Familial1CTD_human
HgeneCLUC4552091Polyarthritis, Juvenile, Rheumatoid Factor Negative1CTD_human
HgeneCLUC4704862Polyarthritis, Juvenile, Rheumatoid Factor Positive1CTD_human