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Center for Computational Systems Medicine
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Gene Summary

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Translation studies in PubMed

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Exon Skipping Events

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Expression

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Expression Regulation

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Associated Genes

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Protein 3D Structure

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Protein-Protein Interaction

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Mutations

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Prognostic Analysis

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Gender Association

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Age Association

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Related Drugs

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Related Diseases

Translation Factor: RPS4Y1 (NCBI Gene ID:6192)


Gene Summary

check button Gene Summary
Gene InformationGene Name: RPS4Y1
Gene ID: 6192
Gene Symbol

RPS4Y1

Gene ID

6192

Gene Nameribosomal protein S4 Y-linked 1
SynonymsRPS4Y|S4
Cytomap

Yp11.2

Type of Geneprotein-coding
Description40S ribosomal protein S4, Y isoform 140S ribosomal protein S4, Yribosomal protein S4, Y-linkedribosomal protein S4Ysmall ribosomal subunit protein eS4
Modification date20200313
UniProtAcc

P22090


check button Child GO biological process term(s) under GO:0006412
GO IDGO term
GO:0005840Ribosome
GO:0006412Translation


check button Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID


check button Inferred gene age of translation factor.
GeneInferred gene age group among (0 - 67.6], (67.6 - 355.7], (355.7 - 733], (733 - 1119.25], >1119.25


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Translation Studies in PubMed

check button We searched PubMed using 'RPS4Y1[title] AND translation [title] AND human.'
GeneTitlePMID
RPS4Y1..


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Exon Skipping Events

check buttonSkipped exons in TCGA and GTEx based on Ensembl gene isoform structure.
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.
For more annotations, please visit our ExonSkipDB.
all structure

check button Open reading frame (ORF) analsis of exon skipping events 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.
ENSTExon skip start (DNA)Exon Skip end (DNA)ORF
ENST0000025078427136862713784Frame-shift
ENST0000025078427226402722812Frame-shift
ENST0000025078427331282733286Frame-shift

check button Exon skipping position in the amino acid sequence.
ENSTExon skip start (DNA)Exon Skip end (DNA)Len(transcript seq)Exon skip start (mRNA)Exon Skip end (mRNA)Len(amino acid seq)Exon skip start (AA)Exon Skip end (AA)

check button Potentially (partially) lost protein functional features of UniProt.
UniProtAccExon skip start (AA)Exon Skip end (AA)Function feature start (AA)Function feature end (AA)Functional feature typeFunctional feature desc.


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Expression


check buttonGene expression level across TCGA pancancer
all structure

check buttonGene expression level across GTEx pantissue
all structure

check buttonExpression level of gene isoforms across TCGA pancancer
all structure

check buttonExpression level of gene isoforms across GTEx pantissue
all structure

check buttonCancer(tissue) type-specific expression level of Translation factor using z-score distriution
all structure

check buttonDifferential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)
all structure
Cancer typeTranslation factorFCadj.pval


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Expression Regulation


check buttonTranslation factor expression regulation through miRNA binding
Cancer typeGenemiRNATargetScan binding score (Context++ score percentile)CoefficientPvalue


check buttonTranslation factor expression regulation through methylation in the promoter of Translation factor
Cancer typeGenemethyl group bmethyl group aDEG pvalavg methyl in bavg methyl in aavg exp in bavg exp in a

check buttonTranslation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)
Cancer typeGenemethyl group bmethyl group aDEG pvalavg methyl in bavg methyl in aavg exp in bavg exp in a

check buttonTranslation factor expression regulation through copy number variation of Translation factor
Cancer typeGeneCoefficientPvalue

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with RPS4Y1 (coefficient>0.8, pval<0.05, node color based on FC between tumor and matched normal). Significantly associated important genes in the individual cancer types. * Cell metabolism gene: cell metabolism genes from REACTOME (black edge), IUPHAR: drug target genes from IUPHAR (blue edge), Kinase: human kinase genes (brown edge), CGC: cancer gene census genes (orange edge), TSG: tumor suppresor genes (purple edge), Epifactor: epigenetic factors (light blue edge), TF: transcription factors (green)
all structure
Cancer typeGene groupTranslation factorCorrelated geneCoefficientPvalue
ACCEpifactorRPS4Y1UTY0.958703588.48E-44
ACCEpifactorRPS4Y1KDM5D0.9781673372.68E-54
ACCIUPHARRPS4Y1PRKY0.9499749721.16E-40
ACCIUPHARRPS4Y1KDM5D0.9781673372.68E-54
ACCKinaseRPS4Y1PRKY0.9499749721.16E-40
ACCTFRPS4Y1ZFY0.9799141551.12E-55
BLCAEpifactorRPS4Y1UTY0.9200299771.28E-174
BLCAEpifactorRPS4Y1KDM5D0.9432181344.70E-205
BLCAIUPHARRPS4Y1PRKY0.940645644.28E-201
BLCAIUPHARRPS4Y1KDM5D0.9432181344.70E-205
BLCAKinaseRPS4Y1PRKY0.940645644.28E-201
BLCATFRPS4Y1ZFY0.9609414641.13E-238
BRCAEpifactorRPS4Y1UTY0.8924595260
BRCAEpifactorRPS4Y1KDM5D0.9044685950
BRCAIUPHARRPS4Y1KDM5D0.9044685950
BRCATFRPS4Y1ZFY0.8080762419.59E-282
CESCEpifactorRPS4Y1KDM5D0.8180274741.76E-75
CESCIUPHARRPS4Y1KDM5D0.8180274741.76E-75
CHOLEpifactorRPS4Y1KDM5D0.9887351094.16E-37
CHOLEpifactorRPS4Y1UTY0.9920944752.12E-40
CHOLIUPHARRPS4Y1PRKY0.9488355743.78E-23
CHOLIUPHARRPS4Y1KDM5D0.9887351094.16E-37
CHOLKinaseRPS4Y1PRKY0.9488355743.78E-23
CHOLTFRPS4Y1ZFY0.98034456.04E-32
COADEpifactorRPS4Y1UTY0.9468275064.20E-163
COADEpifactorRPS4Y1KDM5D0.9602169513.19E-183
COADIUPHARRPS4Y1PRKY0.9206483241.26E-135
COADIUPHARRPS4Y1KDM5D0.9602169513.19E-183
COADKinaseRPS4Y1PRKY0.9206483241.26E-135
COADTFRPS4Y1ZFY0.9589517614.81E-181
DLBCEpifactorRPS4Y1UTY0.9576108991.67E-26
DLBCEpifactorRPS4Y1KDM5D0.9660575141.10E-28
DLBCIUPHARRPS4Y1PRKY0.9316463817.47E-22
DLBCIUPHARRPS4Y1KDM5D0.9660575141.10E-28
DLBCKinaseRPS4Y1PRKY0.9316463817.47E-22
DLBCTFRPS4Y1ZFY0.9478198051.79E-24
ESCAEpifactorRPS4Y1UTY0.9191188052.07E-80
ESCAEpifactorRPS4Y1KDM5D0.9370599371.36E-90
ESCAIUPHARRPS4Y1KDM5D0.9370599371.36E-90
ESCAIUPHARRPS4Y1PRKY0.9384376971.70E-91
ESCAKinaseRPS4Y1PRKY0.9384376971.70E-91
ESCATFRPS4Y1ZFY0.9811241992.13E-140
GBMEpifactorRPS4Y1KDM5D0.9680731364.43E-104
GBMEpifactorRPS4Y1UTY0.9778450752.17E-117
GBMIUPHARRPS4Y1PRKY0.8810105313.82E-57
GBMIUPHARRPS4Y1KDM5D0.9680731364.43E-104
GBMKinaseRPS4Y1PRKY0.8810105313.82E-57
GBMTFRPS4Y1ZFY0.9786070881.15E-118
HNSCEpifactorRPS4Y1UTY0.9192073421.91E-230
HNSCEpifactorRPS4Y1KDM5D0.9361594453.23E-258
HNSCIUPHARRPS4Y1PRKY0.9034474821.27E-209
HNSCIUPHARRPS4Y1KDM5D0.9361594453.23E-258
HNSCKinaseRPS4Y1PRKY0.9034474821.27E-209
HNSCTFRPS4Y1ZFY0.9424811981.36E-270
KICHEpifactorRPS4Y1UTY0.9815939088.75E-66
KICHEpifactorRPS4Y1KDM5D0.9918856441.62E-81
KICHIUPHARRPS4Y1PRKY0.9204990224.36E-38
KICHIUPHARRPS4Y1KDM5D0.9918856441.62E-81
KICHKinaseRPS4Y1PRKY0.9204990224.36E-38
KICHTFRPS4Y1ZFY0.9831525161.76E-67
KIRPEpifactorRPS4Y1UTY0.948494842.63E-162
KIRPEpifactorRPS4Y1KDM5D0.9719720626.77E-204
KIRPIUPHARRPS4Y1PRKY0.8590414012.31E-95
KIRPIUPHARRPS4Y1KDM5D0.9719720626.77E-204
KIRPKinaseRPS4Y1PRKY0.8590414012.31E-95
KIRPTFRPS4Y1ZFY0.9462040912.36E-159
LAMLEpifactorRPS4Y1KDM5D0.9927554772.64E-159
LAMLEpifactorRPS4Y1UTY0.9944651012.87E-169
LAMLIUPHARRPS4Y1PRKY0.9785098063.45E-119
LAMLIUPHARRPS4Y1KDM5D0.9927554772.64E-159
LAMLKinaseRPS4Y1PRKY0.9785098063.45E-119
LAMLTFRPS4Y1ZFY0.9920857294.93E-156
LGGEpifactorRPS4Y1UTY0.9864394180
LGGEpifactorRPS4Y1KDM5D0.9879022060
LGGIUPHARRPS4Y1PRKY0.9432941224.98E-255
LGGIUPHARRPS4Y1KDM5D0.9879022060
LGGKinaseRPS4Y1PRKY0.9432941224.98E-255
LGGTFRPS4Y1ZFY0.9856960380
LIHCEpifactorRPS4Y1KDM5D0.9540065352.23E-222
LIHCEpifactorRPS4Y1UTY0.9553716454.53E-225
LIHCIUPHARRPS4Y1PRKY0.91827291.71E-171
LIHCIUPHARRPS4Y1KDM5D0.9540065352.23E-222
LIHCKinaseRPS4Y1PRKY0.91827291.71E-171
LIHCTFRPS4Y1ZFY0.9418134891.90E-201
LUADEpifactorRPS4Y1KDM5D0.9791146710
LUADEpifactorRPS4Y1UTY0.9802335090
LUADIUPHARRPS4Y1PRKY0.9432727644.95E-277
LUADIUPHARRPS4Y1KDM5D0.9791146710
LUADKinaseRPS4Y1PRKY0.9432727644.95E-277
LUADTFRPS4Y1ZFY0.9847658950
LUSCEpifactorRPS4Y1UTY0.9488652114.37E-278
LUSCEpifactorRPS4Y1KDM5D0.9553086728.27E-294
LUSCIUPHARRPS4Y1PRKY0.8871813643.17E-187
LUSCIUPHARRPS4Y1KDM5D0.9553086728.27E-294
LUSCKinaseRPS4Y1PRKY0.8871813643.17E-187
LUSCTFRPS4Y1ZFY0.966607870
MESOEpifactorRPS4Y1UTY0.9525956841.07E-45
MESOEpifactorRPS4Y1KDM5D0.9856290941.98E-67
MESOIUPHARRPS4Y1PRKY0.9552967099.36E-47
MESOIUPHARRPS4Y1KDM5D0.9856290941.98E-67
MESOKinaseRPS4Y1PRKY0.9552967099.36E-47
MESOTFRPS4Y1ZFY0.9739980491.37E-56
PAADEpifactorRPS4Y1UTY0.9804082081.17E-129
PAADEpifactorRPS4Y1KDM5D0.9834316173.47E-136
PAADIUPHARRPS4Y1PRKY0.9436621747.33E-89
PAADIUPHARRPS4Y1KDM5D0.9834316173.47E-136
PAADKinaseRPS4Y1PRKY0.9436621747.33E-89
PAADTFRPS4Y1ZFY0.9683857854.39E-111
PCPGEpifactorRPS4Y1UTY0.9790932036.71E-130
PCPGEpifactorRPS4Y1KDM5D0.9832864498.26E-139
PCPGIUPHARRPS4Y1PRKY0.9470528723.27E-93
PCPGIUPHARRPS4Y1KDM5D0.9832864498.26E-139
PCPGKinaseRPS4Y1PRKY0.9470528723.27E-93
PCPGTFRPS4Y1ZFY0.981736762.81E-135
READEpifactorRPS4Y1UTY0.9631475631.48E-60
READEpifactorRPS4Y1KDM5D0.9741597432.24E-68
READIUPHARRPS4Y1PRKY0.9393568661.12E-49
READIUPHARRPS4Y1KDM5D0.9741597432.24E-68
READKinaseRPS4Y1PRKY0.9393568661.12E-49
READTFRPS4Y1ZFY0.9776235991.48E-71
SKCMEpifactorRPS4Y1UTY0.9524232731.06E-245
SKCMEpifactorRPS4Y1KDM5D0.9681705664.42E-286
SKCMIUPHARRPS4Y1PRKY0.9326979343.50E-211
SKCMIUPHARRPS4Y1KDM5D0.9681705664.42E-286
SKCMKinaseRPS4Y1PRKY0.9326979343.50E-211
SKCMTFRPS4Y1ZFY0.9566909224.13E-255
STADEpifactorRPS4Y1UTY0.9616311498.92E-254
STADEpifactorRPS4Y1KDM5D0.9695371667.79E-276
STADIUPHARRPS4Y1PRKY0.9519201662.63E-232
STADIUPHARRPS4Y1KDM5D0.9695371667.79E-276
STADKinaseRPS4Y1PRKY0.9519201662.63E-232
STADTFRPS4Y1ZFY0.9780790311.98E-307
THCAEpifactorRPS4Y1UTY0.9872066770
THCAEpifactorRPS4Y1KDM5D0.9895622810
THCAIUPHARRPS4Y1PRKY0.8644572792.17E-172
THCAIUPHARRPS4Y1KDM5D0.9895622810
THCAKinaseRPS4Y1PRKY0.8644572792.17E-172
THCATFRPS4Y1ZFY0.9841371490
THYMEpifactorRPS4Y1KDM5D0.9849983732.00E-93
THYMEpifactorRPS4Y1UTY0.9874891924.00E-98
THYMIUPHARRPS4Y1PRKY0.9542161899.61E-65
THYMIUPHARRPS4Y1KDM5D0.9849983732.00E-93
THYMKinaseRPS4Y1PRKY0.9542161899.61E-65
THYMTFRPS4Y1SRY0.8456252991.64E-34
THYMTFRPS4Y1ZFY0.9633998621.85E-70
UCSEpifactorRPS4Y1KDM5D0.9849983732.00E-93
UCSEpifactorRPS4Y1UTY0.9874891924.00E-98
UCSIUPHARRPS4Y1PRKY0.9542161899.61E-65
UCSIUPHARRPS4Y1KDM5D0.9849983732.00E-93
UCSKinaseRPS4Y1PRKY0.9542161899.61E-65
UCSTFRPS4Y1SRY0.8456252991.64E-34
UCSTFRPS4Y1ZFY0.9633998621.85E-70
UVMEpifactorRPS4Y1UTY0.9609515722.82E-45
UVMEpifactorRPS4Y1KDM5D0.9788425711.65E-55
UVMIUPHARRPS4Y1PRKY0.8808360424.76E-27
UVMIUPHARRPS4Y1KDM5D0.9788425711.65E-55
UVMKinaseRPS4Y1PRKY0.8808360424.76E-27
UVMTFRPS4Y1ZFY0.9187795713.20E-33


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Protein structure


check button Protein 3D structure
Visit iCn3D.


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Protein-Protein Interaction


check button Protein-protein interaction networks
* Overlap between up-regulated DEGs (log2FC<-1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))

check buttonOverlap between down-regulated DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network (center: Translation factor, node: DEGs, edges: weighted by -log2(adj.P))
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* Edge colors based on TCGA cancer types.

check button* Overlap between DEGs (log2FC>1 and adj.P<0.05) and STRING PPI network per cancer (center: Translation factor, node: DEGs, node color: log2FC, edges: weighted by -log2(adj.P))
Cancer typeTranslation factorInteracting protein coding geneFCadj.pval


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with RPS4Y1
CALM1, CD81, IGSF8, ICAM1, RNF2, RPS4Y2, PRPS1, CLK1, ZNF746, CYLD, FGF11, ESR2, HEXIM1, MEPCE, LARP7, NR2C2, MEOX2, PLEKHA4, SNIP1, M, nsp13, nsp4, nsp5, nsp6, CIT, ANLN, AURKB, CHMP4B, CHMP4C, ECT2, KIF14, KIF20A, KIF23, PRC1, CBX8, WHSC1L1, AR, ACTR3B, ACOT7, PHYHIPL, CA5B, CCT3, RBKS, NCAPD3, PADI4, C1orf123, NEU2, TMCC2, RPL10A, AGPAT1, HSPBP1, RPS15, ACTR3, ZZEF1, AK3, SSSCA1, PINK1, WRAP53, SLURP1, RPS19, WDR37, SDC3, RPSAP58, FTL, YTHDF1, UGT3A1, HINT3, RPS8, LTV1, ZC3H10, SHMT2, CD55, ALDOA, RPL23A, NEUROG3, HECTD3, SPRTN,


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Mutations


check button Clinically associated variants from ClinVar.
GeneChrPositionRefSeqVarSeqRefSeeqVarTypePathogenicDiseaseVarInfo


check button nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.
all structure


check button SNVs and Indels
GeneCancer typeChromosomeStartEndRefSeeqMutSeqMutation typeAAchange# samples

check buttonCopy number variation (CNV) of RPS4Y1
* Click on the image to open the original image in a new window.
all structure

check buttonFusion gene breakpoints (product of the structural variants (SVs)) across RPS4Y1
* 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 genes with this translation factor from FusionGDB2.0.
FusionGDB2 IDDiseaseSampleHgeneHchrHbpHstrandTgeneTchrTbpTstrand
103203N/ABF340665ACADVLchr177128585+RPS4Y1chrY2758841+
103203N/ABD237243ADIRFchr1088730488+RPS4Y1chrY2758842+
103203N/AAF116711ALBchr474281996-RPS4Y1chrY2709643+
103203N/AAA525486CABLES1chr1820808709-RPS4Y1chrY2734997-
103203PAADTCGA-F2-A7TXDHRSXchrX2209543-RPS4Y1chrY2733129+
103203PAADTCGA-F2-A7TXDHRSXchrY2159542-RPS4Y1chrY2733128+
103203PAADTCGA-F2-A7TX-01ADHRSXchrY2159543-RPS4Y1chrY2733129+
103203N/AEI796321FCHSD2chr1172808161-RPS4Y1chrY2610246+
103203N/AAI147734PIWIL1chr12130893959+RPS4Y1chrY2752404-
103203N/AAW300778RPS19chr1942364325-RPS4Y1chrY2734859+
100335N/ABI047537RPS4Y1chrY2733176+ARGLU1chr13107220075+
97159GBMTCGA-06-0132-01ARPS4Y1chrY2712298+CDH13chr1683158990+
100283STADTCGA-RD-A7BT-01ARPS4Y1chrY2713784+DHRSXchrY2260515-
89814N/AEC580829RPS4Y1chrY2753051-EIF3Dchr2236906903+
97936N/ACB054335RPS4Y1chrY2758836-FNBP1chr9132654163+
77951N/ABI495156RPS4Y1chrY2734988+LINC00366chr1339146582+
77951N/ABQ351516RPS4Y1chrY2733263+MKNK2chr192037878+
103203N/ABF810102RPS4Y1chrY2715654+RPS4Y1chrY2715518-
103203N/ACB049280SMAD2chr1845363929-RPS4Y1chrY2734988-
103203GBMTCGA-06-0132-01ASRCAPchr1630727800+RPS4Y1chrY2722641+
103204N/AEC465045ZRANB2-AS1chr171515651-RPS4Y1chrY2734834+


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Prognostic Analysis


check button Kaplan-Meier plots with logrank tests of overall survival (OS)
all structure
Cancer typeTranslation factorCoefficentHazard ratioWald test pvalLikelihool ratio pvalLogrank test pval# samples


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Translation factor and Gender


check button Differential gene expression between female and male. (Wilcoxon test, pval<0.05)
all structure
Cancer typeTranslation factorpvaladj.p
TGCTRPS4Y10.01315007891480870.013
ESCARPS4Y11.07130202086949e-189.6e-18
LUSCRPS4Y11.09390469832596e-712.4e-70
LIHCRPS4Y11.15196170977466e-632.3e-62
THYMRPS4Y11.65605361677016e-211.8e-20
COADRPS4Y11.67630067703086e-533e-52
KIRCRPS4Y11.89633269722089e-875.1e-86
UVMRPS4Y11.96021999823571e-141.2e-13
BRCARPS4Y12.1139827627896e-202.1e-19
BLCARPS4Y12.18748701281115e-564.2e-55
KIRPRPS4Y12.33371114703326e-413.7e-40
LGGRPS4Y12.47940778597488e-866.4e-85
LAMLRPS4Y12.50685696211605e-323.8e-31
STADRPS4Y12.53112267444388e-695.3e-68
ACCRPS4Y13.30149139032644e-141.7e-13
PCPGRPS4Y13.34186924324147e-324.7e-31
DLBCRPS4Y13.44060419479513e-091e-08
PAADRPS4Y13.56513630089674e-314.6e-30
READRPS4Y14.03524212666965e-183.2e-17
LUADRPS4Y14.25964790062367e-961.2e-94
HNSCRPS4Y14.34722958285396e-731e-71
SARCRPS4Y14.91567994863942e-458.4e-44
MESORPS4Y15.03758590774822e-102e-09
SKCMRPS4Y15.83143851814514e-751.4e-73
KICHRPS4Y16.85480567396137e-164.8e-15
THCARPS4Y16.98763656566539e-801.7e-78
GBMRPS4Y17.20624186303352e-288.6e-27
CHOLRPS4Y19.25673590399124e-091.9e-08

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Translation factor and Age


check button Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)
all structure
Cancer typeTranslation factorpvaladj.p
STADRPS4Y10.01833634852727670.57
KIRCRPS4Y14.0499515858376e-050.0013
KICHRPS4Y10.01930460052361630.58
CHOLRPS4Y10.02333588490881450.68
HNSCRPS4Y10.01306246195599320.42
READRPS4Y10.02570698049090040.72

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Related Drugs


check button Drugs targeting genes involved in this translation factor.
(DrugBank Version 5.1.8 2021-05-08)
UniProtAccDrugBank IDDrug nameDrug activityDrug typeDrug status

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Related Diseases


check button Diseases associated with this translation factor.
(DisGeNet 4.0)
Disease IDDisease Name# PubMedsDisease source