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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: RPS15A (NCBI Gene ID:6210)


Gene Summary

check button Gene Summary
Gene InformationGene Name: RPS15A
Gene ID: 6210
Gene Symbol

RPS15A

Gene ID

6210

Gene Nameribosomal protein S15a
SynonymsDBA20|S15a
Cytomap

16p12.3

Type of Geneprotein-coding
Description40S ribosomal protein S15asmall ribosomal subunit protein uS8up-regulated by HBV X protein
Modification date20200313
UniProtAcc

P62244


check button Child GO biological process term(s) under GO:0006412
GO IDGO term
GO:0005840Ribosome
GO:0002181Cytoplasmic translation
GO:0006412Translation


check button Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez
PartnerGeneGO IDGO termPubMed ID
HgeneRPS15A

GO:0008284

positive regulation of cell proliferation

15108328

HgeneRPS15A

GO:0009615

response to virus

15108328

HgeneRPS15A

GO:0045787

positive regulation of cell cycle

15108328



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
RPS15A>1119.25


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Translation Studies in PubMed

check button We searched PubMed using 'RPS15A[title] AND translation [title] AND human.'
GeneTitlePMID
RPS15A..


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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
ENST000003229891879938418799464Frame-shift
ENST000005633901879938418799464Frame-shift
ENST000005654201879938418799464Frame-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
BRCARPS15A-1.394031743096990.000110797167056844
STADRPS15A1.101409977860820.0148032568395138
BLCARPS15A-3.679196907429660.0445594787597656
KIRCRPS15A-4.142526239920162.15831756070263e-10
KIRPRPS15A-1.511451014173854.02145087718964e-06


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Expression Regulation


check buttonTranslation factor expression regulation through miRNA binding
Cancer typeGenemiRNATargetScan binding score (Context++ score percentile)CoefficientPvalue
READRPS15Ahsa-miR-186-5p73-0.309688412852970.00566088307863855


check buttonTranslation factor expression regulation through methylation in the promoter of Translation factor
all structure
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)
all structure
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
all structure
Cancer typeGeneCoefficientPvalue
ESCARPS15A-0.093173840.009710429
MESORPS15A0.0638789150.042422633

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Associated Genes


check button Strongly correlated genes belong to cellular important gene groups with RPS15A (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
DLBCCell metabolism geneRPS15ATBCA0.8026200516.86E-12
DLBCCell metabolism geneRPS15ADGUOK0.8050644085.30E-12
DLBCCell metabolism geneRPS15APOLR2F0.8126870612.31E-12
DLBCCell metabolism geneRPS15APGLS0.81475551.84E-12
DLBCCell metabolism geneRPS15AGFER0.8173733021.36E-12
DLBCCell metabolism geneRPS15ATIMM90.8228742747.19E-13
DLBCCell metabolism geneRPS15ATOMM220.8330428182.07E-13
DLBCCell metabolism geneRPS15ANME20.8468223533.34E-14
DLBCCell metabolism geneRPS15APFDN50.8563039018.56E-15
DLBCCell metabolism geneRPS15AFAU0.8723041466.78E-16
DLBCCell metabolism geneRPS15ASNRPD20.8923927881.66E-17
DLBCCGCRPS15ANACA0.8854627696.44E-17
DLBCEpifactorRPS15AFBL0.8271245684.32E-13
DLBCTFRPS15ANME20.8468223533.34E-14
DLBCTSGRPS15AHINT10.8064057814.59E-12
DLBCTSGRPS15AGADD45GIP10.8333700731.99E-13
DLBCTSGRPS15AGNB2L10.9147389321.00E-19
GBMCell metabolism geneRPS15ALSM10.8040999383.05E-40
GBMCell metabolism geneRPS15APFDN50.8096540073.41E-41
GBMCell metabolism geneRPS15ASSR40.8121925381.22E-41
GBMCell metabolism geneRPS15AZNRD10.8136831446.66E-42
GBMCell metabolism geneRPS15ASNRPD20.8145177384.72E-42
GBMCell metabolism geneRPS15APIGC0.8153219653.39E-42
GBMCell metabolism geneRPS15AFAU0.8169541481.72E-42
GBMCell metabolism geneRPS15APSMA50.8175466021.34E-42
GBMCell metabolism geneRPS15ASNRPG0.8397779545.85E-47
GBMCell metabolism geneRPS15ASSR20.8515763531.49E-49
GBMTSGRPS15AGAS50.8270164432.22E-44
HNSCCell metabolism geneRPS15APFDN50.8023324951.66E-128
LGGCell metabolism geneRPS15AFAU0.8526686285.47E-151
LGGCGCRPS15ANACA0.828495934.60E-135
LGGTSGRPS15AGAS50.8161602037.19E-128
LGGTSGRPS15AGNB2L10.8790873554.91E-172
PRADCell metabolism geneRPS15ATIMM90.8022657047.05E-125
PRADCGCRPS15ANACA0.8273299222.24E-139
PRADEpifactorRPS15AFBL0.8129411148.73E-131
PRADTSGRPS15AGNB2L10.8074971351.00E-127
THYMCell metabolism geneRPS15APSMB70.8110408771.02E-29
THYMCell metabolism geneRPS15APGLS0.8123735516.96E-30
THYMCell metabolism geneRPS15APOLR2I0.8146099013.64E-30
THYMCell metabolism geneRPS15ATIMM8B0.816263772.24E-30
THYMCell metabolism geneRPS15ATIMM130.8171115661.74E-30
THYMCell metabolism geneRPS15ASSR20.8225652493.37E-31
THYMCell metabolism geneRPS15APFDN50.8285035025.28E-32
THYMCell metabolism geneRPS15ASNRPD20.8337635269.62E-33
THYMCell metabolism geneRPS15AAPRT0.8352374495.90E-33
THYMCell metabolism geneRPS15AFAU0.8416934196.57E-34
THYMCell metabolism geneRPS15ADPM20.8439642122.97E-34
THYMEpifactorRPS15AZNHIT10.8003386631.97E-28
THYMEpifactorRPS15ABRMS10.8052256795.22E-29
THYMEpifactorRPS15ATAF100.8074016662.85E-29
THYMEpifactorRPS15APRPF310.8208192655.74E-31
THYMEpifactorRPS15AFBL0.8395305331.39E-33
THYMTFRPS15AZNF5810.8124386536.83E-30
THYMTFRPS15AREXO40.8175815211.52E-30
THYMTSGRPS15ATSSC40.8039325567.44E-29
THYMTSGRPS15ABRMS10.8052256795.22E-29
THYMTSGRPS15AGNB2L10.8199488317.47E-31
UCSCell metabolism geneRPS15APSMB70.8110408771.02E-29
UCSCell metabolism geneRPS15APGLS0.8123735516.96E-30
UCSCell metabolism geneRPS15APOLR2I0.8146099013.64E-30
UCSCell metabolism geneRPS15ATIMM8B0.816263772.24E-30
UCSCell metabolism geneRPS15ATIMM130.8171115661.74E-30
UCSCell metabolism geneRPS15ASSR20.8225652493.37E-31
UCSCell metabolism geneRPS15APFDN50.8285035025.28E-32
UCSCell metabolism geneRPS15ASNRPD20.8337635269.62E-33
UCSCell metabolism geneRPS15AAPRT0.8352374495.90E-33
UCSCell metabolism geneRPS15AFAU0.8416934196.57E-34
UCSCell metabolism geneRPS15ADPM20.8439642122.97E-34
UCSEpifactorRPS15AZNHIT10.8003386631.97E-28
UCSEpifactorRPS15ABRMS10.8052256795.22E-29
UCSEpifactorRPS15ATAF100.8074016662.85E-29
UCSEpifactorRPS15APRPF310.8208192655.74E-31
UCSEpifactorRPS15AFBL0.8395305331.39E-33
UCSTFRPS15AZNF5810.8124386536.83E-30
UCSTFRPS15AREXO40.8175815211.52E-30
UCSTSGRPS15ATSSC40.8039325567.44E-29
UCSTSGRPS15ABRMS10.8052256795.22E-29
UCSTSGRPS15AGNB2L10.8199488317.47E-31
UVMCell metabolism geneRPS15ATIMM90.8125952035.68E-20
UVMCGCRPS15ANACA0.8230205777.52E-21
UVMTSGRPS15AGAS50.8223228838.65E-21


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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))
all structure

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))
all structure
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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))
all structure
Cancer typeTranslation factorInteracting protein coding geneFCadj.pval
KIRPRPS15ARPL18A-1.516513928088850.00016188295558095
KICHRPS15ARPS27A1.753966937859560.000187873840332031
KIRPRPS15ARPS16-1.359570436175170.00019507110118866
COADRPS15ARPS31.487303751430140.000411599874496461
KIRPRPS15ARPS11-1.018615705651030.00105937570333481
LIHCRPS15ARPL8-4.845882849745580.00110314154326131
PRADRPS15ARPL18A1.406001757484990.00205137828390396
KICHRPS15ARPL191.369011828940890.00250792503356934
KICHRPS15ARPS121.269973817584310.00308787822723389
LUADRPS15ARPL19-1.313980266157250.00993159558412698
THCARPS15ARPS16-6.163227981565770.0115764821363307
BLCARPS15ARPS12-1.478046734404210.0204124450683594
BLCARPS15ARPS27A-1.047474700691880.0258216857910156
HNSCRPS15ARPS3-4.735058190951350.0273726439852453
COADRPS15ARPS111.353075489982040.0312207043170929
LUSCRPS15ARPL19-2.146698895166660.044366810398747
KIRCRPS15ARPL19-2.734852712766761.33980982873695e-10
BRCARPS15ARPS12-4.912393274782441.85340619742495e-09
KIRPRPS15ARPL37-1.174216219471392.26888805627823e-05
KIRCRPS15ARPL35-1.064752380593922.72286325678163e-08
KIRCRPS15ARPL8-1.182524599717735.64962994208288e-07
KIRPRPS15ARPL8-1.530036923501196.0301274061203e-05
KIRCRPS15ARPS16-1.661498698893847.8509870430991e-09
BRCARPS15ARPS27A-4.285121482004247.8788217967112e-14
KIRCRPS15ARPL37-2.871988220584648.03913394748564e-12
KIRPRPS15ARPL35-1.529811019754969.0546440333128e-05
KIRCRPS15ARPS3-1.295608479263879.05905681935088e-10
KIRCRPS15ARPL18A-4.430793049608439.2516163152192e-11


check button Protein-protein interactors with this translation factor (BIOGRID-3.4.160)
PPI interactors with RPS15A
EWSR1, ELF5, MGMT, CALM1, CDC37, PCK1, VHL, RAD21, HDGF, CUL3, CUL4A, CUL5, CUL2, CDK2, CUL1, COPS5, COPS6, CAND1, NEDD8, RPL10A, RPL10, RPL11, RPL12, RPL14, RPL15, RPL18A, RPL18, RPL19, RPL21, RPL23, RPL24, RPL27, RPL30, RPL31, RPL37A, RPL4, RPL5, RPL6, RPL7A, RPL7, RPL9, RPS10, RPS11, RPS12, RPS13, RPS14, RPS19, RPS26, RPS3A, RPS3, RPS4X, RPS5, RPS6, RPS7, RPS8, RPSA, RPS23, RPS16, RPS17, RPLP1, RPS24, RPLP2, RPL23A, RPS2, RPLP0, RPS20, RPS15, RPL3, RPL13, RPL38, RPL29, RPS21, RPL17, RPL32, RPS27A, EEF1A1, EEF2, NOP56, FBL, HNRNPU, GNL3, SLC25A5, ILF3, ILF2, NOP58, MOV10, TUFM, NHP2L1, HNRNPM, ACTA2, EIF6, HSP90AA1, RPLP0P6, RPL10L, GALNT2, NOP2, NIFK, MRPS14, UBA2, GNL1, HIST1H2AD, HSPA8, ATP5A1, HNRNPA0, PSMB1, ESR1, SMURF1, FN1, VCAM1, UBL4A, ITGA4, PAN2, PSMC1, PSMC6, PSMD11, PSMD3, FAU, PNO1, PSMD1, RPS18, RPS25, RPS27, RPS27L, RPS29, RPS9, WDR26, WIBG, RPS28, TSR1, ZBTB1, CEP250, CEP57, CEP76, TUBG1, HUWE1, RNF2, EGFR, DIMT1, IMP3, MPHOSPH10, MRPL14, MRPL16, MRPL22, MRPS7, RPL13A, RPL27A, RPL28, RPL34, RPL35, RPL37, DDX18, RPL22, RPL35A, RPL36, RPL8, VAPA, LOC101929876, TUBB, TUBB2B, TUBB4B, UBA52, SFN, PTEN, AHSA1, EXOSC1, Cbx1, Eif3a, Eif3e, Eif3i, Rpl35, Srp72, Rrbp1, UBE3A, MCM2, Ksr1, RHOU, RC3H1, ZNF746, HNRNPA1, CYLD, TRIM25, UBE2A, HEY1, BRCA1, HDAC6, FBXO7, RMND5A, TMPO, ACO2, API5, COPE, CSNK1A1, GSK3A, LARS, ADSL, ADSS, BCL2L1, BMP4, CDK9, CTNNB1, MED12, PCBP1, TGFB1, UBE2L6, PRPF8, AAR2, PIH1D1, EFTUD2, AKTIP, CHD3, CHD4, RIOK1, HEXIM1, MEPCE, LARP7, AGR2, RECQL4, REST, MYC, RPS6KB2, GRWD1, METTL14, KIAA1429, EIF4B, RC3H2, PHB, DISC1, NR2C2, UCHL3, PPP1CC, CTCF, ATXN3, VRK1, VRK3, SNRNP70, ITFG1, ARAF, HMGB1, ABCC6, BIRC3, NFX1, WWP2, SOX2, TRIM28, ARIH2, PLEKHA4, PINK1, YAP1, TFCP2, FANCD2, ZC3H18, ANKRD55, ERCC6, DDX19B, IGF2BP1, NXF1, PARN, DUX4, CIT, ANLN, CHMP4C, ECT2, KIF14, KIF20A, KIF23, PRC1, AUH, LONP1, FASN, CLPP, LRRC59, INS, NDN, BRD4, NINL, CIC, Apc2, TMEM259, RBM39, FBP1, LGALS9, RIN3, DDX58, BAG5, PARK2, UFL1, DDRGK1, COIL, DHFRL1, LAMTOR1, ATG10, ATG3, FZR1, UBC, PAGE4, FAT4, RPSAP58, ZNF346, SPRTN, BTF3, FBXW7, UBR5, nsp1, RCHY1, CCNF, PSMD9, ZEB1,


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Mutations


check button Clinically associated variants from ClinVar.
GeneChrPositionRefSeqVarSeqRefSeeqVarTypePathogenicDiseaseVarInfo
RPS15Achr1618799385CTsingle_nucleotide_variantPathogenicDiamond-Blackfan_anemia_20SO:0001819|synonymous_variantSO:0001819|synonymous_variant
RPS15Achr1618799615CAsingle_nucleotide_variantBenignnot_providedSO:0001627|intron_variantSO:0001627|intron_variant
RPS15Achr1618800638GCsingle_nucleotide_variantBenignnot_providedSO:0001627|intron_variantSO:0001627|intron_variant


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


check button SNVs and Indels
GeneCancer typeChromosomeStartEndRefSeeqMutSeqMutation typeAAchange# samples
RPS15AUCECchr161879437118794371CTMissense_Mutationp.R118Q2
RPS15AUCECchr161879439718794397GASilentp.G1092
RPS15AREADchr161879608618796086ACMissense_Mutationp.N91K1
RPS15ASARCchr161880024718800247CTRNANULL1
RPS15ASKCMchr161879434918794349GASilentp.I125I1
RPS15ABLCAchr161879614118796141CAMissense_Mutation1
RPS15AUCECchr161879439718794397GASilentp.G109G1
RPS15AESCAchr161879598218795983-ARNANULL1
RPS15AHNSCchr161879611018796110GCSilent1
RPS15AHNSCchr161879612118796121CTMissense_Mutation1
RPS15AHNSCchr161879611018796110GCSilentp.L83L1
RPS15AHNSCchr161879612118796121CTMissense_Mutationp.D80N1
RPS15ALIHCchr161879944518799445TCSilent1
RPS15ALIHCchr161879611118796111AGMissense_Mutation1

check buttonCopy number variation (CNV) of RPS15A
* 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 RPS15A
* 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
99238N/AAK054921CDR1chrX139866517+RPS15Achr1618801656-
99238COADTCGA-5M-AAT4-01AKIAA0907chr1155884004-RPS15Achr1618801659-
99238N/AAW772792P2RY6chr1172984135-RPS15Achr1618794291+
99238Non-Cancer5381NPGA3chr1160975962+RPS15Achr1618800440-
99238LIHCTCGA-BC-A10T-01APKD1chr162185476-RPS15Achr1618796145-
99238READTCGA-AG-3586PTPRKchr6128505576-RPS15Achr1618800440-
84059BRCATCGA-A2-A0D2-01ARPS15Achr1618796060-ARL6IP1chr1618810156-
90077N/ABM015299RPS15Achr1618794291-CLNS1Achr1177256179+
77428N/ABE737542RPS15Achr1618794290-LEPROTL1chr829974849-
77428N/ACF123929RPS15Achr1618794291-LEPROTL1chr829974886-
92573STADTCGA-CD-5798-01ARPS15Achr1618799385-PICALMchr1185689136-
101492N/ABI856629RPS15Achr1618794285-PNPLA8chr7108138445+
77428STADTCGA-CD-A48C-01ARPS15Achr1618800338-RHOGchr113848287-
89508N/ABI860288RPS15Achr1618794291-TMTC2chr1283489029-
99238BRCATCGA-A2-A0CM-01ASMG1chr1618937272-RPS15Achr1618800440-
99238N/ABE716419SPRR3chr1152976131+RPS15Achr1618800992+
99238N/AAI076857TSNAX-DISC1chr1231713444+RPS15Achr1618794277+
99242N/AAW772569WHSC1chr41900438+RPS15Achr1618794290+


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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
KIRCRPS15A0.006075387420269960.17
ACCRPS15A0.04694242397479891

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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
LUSCRPS15A0.002226699279889540.073
LGGRPS15A0.04468850849526091
BRCARPS15A0.03540706649243081
PAADRPS15A0.007674934441652590.25

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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
C1260899Anemia, Diamond-Blackfan1ORPHANET
C2931850Aase Smith syndrome 21ORPHANET