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	Gene Summary
	Translation studies in PubMed
	Exon Skipping Events
	Expression
	Expression Regulation
	Associated Genes
	Protein 3D Structure
	Protein-Protein Interaction
	Mutations
	Prognostic Analysis
	Gender Association
	Age Association
	Related Drugs
	Related Diseases

Translation Factor: RPS25 (NCBI Gene ID:6230)

Gene Summary

Gene Summary

Gene Information	Gene Name: RPS25
	Gene ID: 6230
	Gene Symbol	RPS25
	Gene ID	6230
	Gene Name	ribosomal protein S25
	Synonyms	S25
	Cytomap	11q23.3
	Type of Gene	protein-coding
	Description	40S ribosomal protein S25small ribosomal subunit protein eS25
	Modification date	20200313
	UniProtAcc	P62851

Child GO biological process term(s) under GO:0006412

GO ID	GO term
GO:0005840	Ribosome
GO:0002181	Cytoplasmic translation
GO:0006412	Translation

Gene ontology of translaction factor with evidence of Inferred from Direct Assay (IDA) from Entrez

Partner

Gene

GO ID

GO term

PubMed ID

Inferred gene age of translation factor.

Gene

Inferred 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

We searched PubMed using 'RPS25[title] AND translation [title] AND human.'

Gene	Title	PMID
RPS25	RPS25 is required for efficient RAN translation of C9orf72 and other neurodegenerative disease-associated nucleotide repeats	31358992

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Exon Skipping Events

Skipped 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.

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.

ENST

Exon skip start (DNA)

Exon Skip end (DNA)

ORF

Exon skipping position in the amino acid sequence.

ENST

Exon 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)

Potentially (partially) lost protein functional features of UniProt.

UniProtAcc

Exon skip start (AA)

Exon Skip end (AA)

Function feature start (AA)

Function feature end (AA)

Functional feature type

Functional feature desc.

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Expression

Gene expression level across TCGA pancancer

Gene expression level across GTEx pantissue

Expression level of gene isoforms across TCGA pancancer

Expression level of gene isoforms across GTEx pantissue

Cancer(tissue) type-specific expression level of Translation factor using z-score distriution

Differential expression between tumor and matched normal (in the cancer types with more than 10 matched samples)

Cancer type	Translation factor	FC	adj.pval
HNSC	RPS25	2.24439018636525	1.07420805761649e-06

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Expression Regulation

Translation factor expression regulation through miRNA binding

Cancer type

Gene

miRNA

TargetScan binding score (Context++ score percentile)

Coefficient

Pvalue

Translation factor expression regulation through methylation in the promoter of Translation factor

Cancer type

Gene

methyl group b

methyl group a

DEG pval

avg methyl in b

avg methyl in a

avg exp in b

avg exp in a

Translation factor expression regulation through methylation in the gene body of Translation factor (positive regulation)

Cancer type

Gene

methyl group b

methyl group a

DEG pval

avg methyl in b

avg methyl in a

avg exp in b

avg exp in a

Translation factor expression regulation through copy number variation of Translation factor

Cancer type	Gene	Coefficient	Pvalue
KICH	RPS25	0.047102987	0.003837106
BRCA	RPS25	0.054877262	0.021086917

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Associated Genes

Strongly correlated genes belong to cellular important gene groups with RPS25 (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)

Cancer type	Gene group	Translation factor	Correlated gene	Coefficient	Pvalue
CHOL	Cell metabolism gene	RPS25	FAU	0.818349341	6.63E-12
DLBC	Cell metabolism gene	RPS25	TIMM9	0.820585051	9.41E-13
DLBC	CGC	RPS25	NACA	0.808080109	3.84E-12
GBM	Cell metabolism gene	RPS25	FAU	0.801620195	7.93E-40
LGG	Cell metabolism gene	RPS25	FAU	0.839383512	6.58E-142
LGG	CGC	RPS25	NACA	0.856248254	1.37E-153
LGG	TSG	RPS25	GAS5	0.823079582	7.77E-132
PAAD	Cell metabolism gene	RPS25	FAU	0.840729659	4.18E-50
PRAD	CGC	RPS25	NACA	0.826836377	4.54E-139
PRAD	TSG	RPS25	GAS5	0.811651146	4.73E-130
UVM	Cell metabolism gene	RPS25	POLR1D	0.818385902	1.88E-20
UVM	CGC	RPS25	NACA	0.868635924	1.67E-25
UVM	TSG	RPS25	GLTSCR2	0.815523789	3.26E-20
UVM	TSG	RPS25	GAS5	0.824506937	5.58E-21

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Protein structure

Protein 3D structure
Visit iCn3D.

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Protein-Protein Interaction

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))

Overlap 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))

* Edge colors based on TCGA cancer types.

* 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 type	Translation factor	Interacting protein coding gene	FC	adj.pval
KIRP	RPS25	RPL18A	-1.51651392808885	0.00016188295558095
KICH	RPS25	RPS27A	1.75396693785956	0.000187873840332031
KIRP	RPS25	RPS16	-1.35957043617517	0.00019507110118866
COAD	RPS25	RPS3	1.48730375143014	0.000411599874496461
KIRP	RPS25	RPS11	-1.01861570565103	0.00105937570333481
LIHC	RPS25	RPL8	-4.84588284974558	0.00110314154326131
PRAD	RPS25	RPL18A	1.40600175748499	0.00205137828390396
KICH	RPS25	RPL19	1.36901182894089	0.00250792503356934
KICH	RPS25	RPS12	1.26997381758431	0.00308787822723389
LUAD	RPS25	RPL19	-1.31398026615725	0.00993159558412698
THCA	RPS25	RPS16	-6.16322798156577	0.0115764821363307
BLCA	RPS25	RPS12	-1.47804673440421	0.0204124450683594
BLCA	RPS25	RPS27A	-1.04747470069188	0.0258216857910156
HNSC	RPS25	RPS3	-4.73505819095135	0.0273726439852453
COAD	RPS25	RPS11	1.35307548998204	0.0312207043170929
LUSC	RPS25	RPL19	-2.14669889516666	0.044366810398747
KIRC	RPS25	RPL19	-2.73485271276676	1.33980982873695e-10
BRCA	RPS25	RPS12	-4.91239327478244	1.85340619742495e-09
KIRP	RPS25	RPL37	-1.17421621947139	2.26888805627823e-05
KIRC	RPS25	RPL35	-1.06475238059392	2.72286325678163e-08
KIRC	RPS25	RPL8	-1.18252459971773	5.64962994208288e-07
KIRP	RPS25	RPL8	-1.53003692350119	6.0301274061203e-05
KIRC	RPS25	RPS16	-1.66149869889384	7.8509870430991e-09
BRCA	RPS25	RPS27A	-4.28512148200424	7.8788217967112e-14
KIRC	RPS25	RPL37	-2.87198822058464	8.03913394748564e-12
KIRP	RPS25	RPL35	-1.52981101975496	9.0546440333128e-05
KIRC	RPS25	RPS3	-1.29560847926387	9.05905681935088e-10
KIRC	RPS25	RPL18A	-4.43079304960843	9.2516163152192e-11

Protein-protein interactors with this translation factor (BIOGRID-3.4.160)

PPI interactors with RPS25

UPF2, SGSM2, HAP1, CDC5L, POU5F1, EBNA-LP, RAD21, CUL3, CUL4B, CUL5, CUL2, CUL1, COPS5, CAND1, MDM2, CRK, APP, RPL12, RPS16, RPL13, RPL10A, RPL11, RPL15, RPL18, RPL19, RPL21, RPL24, RPL27A, RPL37A, RPL6, RPL7A, RPLP2, RPS20, RPS23, RPS2, RPS3A, RPS6, RPS8, RPSA, RPS28, RPL14, RPS4X, RPS3, RPL23A, RPL5, RPL4, RPL7, RPL23, RPS13, RPS19, RPS10, RPS17, RPS14, RPL36, RPS24, RPLP1, RPS15, RPS9, RPS7, RPLP0, RPS26, RPL38, RPL17, RPS21, ILF3, HNRNPM, RPLP0P6, RPS27L, DDX24, HSPA5, PRPF8, RPL10L, GNB2L1, NACA2, SMURF1, FN1, VCAM1, UBL4A, ITGA4, PAN2, CD81, IGSF8, ICAM1, TARDBP, PARK2, RPS12, RPS15A, EIF3A, EIF3E, EIF3L, FAU, RPL8, RPS18, RPS29, RPS5, WIBG, SERBP1, TSR1, rev, ZBTB1, AURKB, CDKN1A, CEP250, CEP57, CEP76, TP53, TUBG1, TUBGCP3, VCP, HUWE1, THAP1, PHF6, CUL7, WDR76, ABCE1, RPS6KB2, HNRNPU, RPL10, RPL13A, RPL27, RPL28, RPL29, RPL30, RPL35, RPL35A, RPL3L, RPL9, RPS11, RPL18A, RPL22, RPL26, RPL3, RPL31, RPL34, LOC101929876, RPS27, UBA52, SFN, NTRK1, PTEN, EWSR1, XPO1, AHSA1, NPM1, NOP56, KIF2C, EXOSC1, Eif3a, Rpl35, Srp72, Rrbp1, MCM2, Mdm2, RC3H1, CRBN, RRS1, NCL, CYLD, TRIM25, HEY1, BRCA1, LMNA, FBXO7, WDR77, DIMT1, KRAS, PCBP1, VPS4B, EFTUD2, AAR2, PIH1D1, TNIP2, CHD3, CHD4, LARP7, RNF31, TNF, SPDL1, RIOK1, HEXIM1, MEPCE, RNF123, SENP2, AGR2, RECQL4, DCPS, GPC1, REST, MYC, CDK9, Prkaa1, Prkab1, KRT17, METTL14, EIF4B, RC3H2, PHB, DISC1, USP14, NR2C2, PPP1CC, HDAC2, ZDHHC18, ZDHHC23, VRK1, HIST1H4A, SNRNP70, ITFG1, ARAF, HMGB1, BIRC3, NFX1, WWP2, TRIM28, HMBOX1, C11orf57, TSPYL2, STAC3, ZBTB14, HOMEZ, ARIH2, PLEKHA4, YAP1, TFCP2, FANCD2, HCVgp1, ZC3H18, HNRNPA1L2, PEX5L, MAP3K4, PHLDB1, HIST2H2AB, LMO7, ORF8, NEK4, DUX4, CIT, FASN, INS, Rnf183, RBM45, Apc2, RBM39, RIN3, DNAJA3, DNAJB4, DNAJB5, SPOP, UFL1, DDRGK1, TRIM37, SLC26A4-AS1, UBQLN1, FZR1, PAGE4, NUDCD2, HIST1H1B, SPRTN, BTF3, SLFN11, FBXW7, RCHY1, CCNF, OPTN, PSMD9, KLF4,

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Mutations

Clinically associated variants from ClinVar.

Gene	Chr	Position	RefSeq	VarSeq	RefSeeq	VarType	Pathogenic	Disease	VarInfo
RPS25	chr11	118886603	G	A	single_nucleotide_variant	Benign	not_provided	SO:0001819\|synonymous_variant	SO:0001819\|synonymous_variant
RPS25	chr11	118889016	G	A	single_nucleotide_variant	Benign	not_provided	SO:0001623\|5_prime_UTR_variant	SO:0001623\|5_prime_UTR_variant
RPS25	chr11	118889028	G	A	single_nucleotide_variant	Benign	not_provided	SO:0001623\|5_prime_UTR_variant	SO:0001623\|5_prime_UTR_variant

nsSNVs with sample frequency (size of circle) from TCGA 33 cancers.

SNVs and Indels

Gene	Cancer type	Chromosome	Start	End	RefSeeq	MutSeq	Mutation type	AAchange	# samples
RPS25	ESCA	chr11	118888677	118888677	G	T	Silent	p.A30A	4
RPS25	UCEC	chr11	118886581	118886581	C	T	Missense_Mutation	p.A118T	3
RPS25	UVM	chr11	118888181	118888181	G	C	Silent	p.L58L	3
RPS25	UCEC	chr11	118886635	118886635	C	G	Missense_Mutation	p.V100L	2
RPS25	UVM	chr11	118888181	118888181	G	C	Silent		2
RPS25	CESC	chr11	118888132	118888132	C	T	Missense_Mutation		2
RPS25	CESC	chr11	118888132	118888132	C	T	Missense_Mutation	p.E75K	1
RPS25	LUAD	chr11	118886586	118886586	C	T	Missense_Mutation	p.G116E	1
RPS25	COAD	chr11	118888732	118888732	G	T	Missense_Mutation	p.A12D	1
RPS25	LUAD	chr11	118888204	118888204	C	G	Missense_Mutation	p.D51H	1
RPS25	THYM	chr11	118888099	118888099	C	T	Missense_Mutation		1
RPS25	HNSC	chr11	118888677	118888677	G	A	Silent		1
RPS25	THYM	chr11	118888242	118888242	C	T	Missense_Mutation	p.G38D	1
RPS25	HNSC	chr11	118888739	118888739	T	C	Missense_Mutation		1
RPS25	THYM	chr11	118888099	118888099	C	T	Missense_Mutation	p.A86T	1
RPS25	HNSC	chr11	118886642	118886642	G	A	Silent		1
RPS25	HNSC	chr11	118888739	118888739	T	C	Missense_Mutation	p.K10E	1
RPS25	HNSC	chr11	118886642	118886642	G	A	Silent	p.I97I	1
RPS25	BLCA	chr11	118889387	118889387	G	C	Missense_Mutation		1
RPS25	HNSC	chr11	118888251	118888251	C	T	Nonsense_Mutation	p.W35*	1
RPS25	LIHC	chr11	118886603	118886603	G	A	Silent		1
RPS25	CESC	chr11	118889067	118889067	G	C	Missense_Mutation		1
RPS25	LIHC	chr11	118888669	118888669	T	-	Splice_Site	p.K34_splice	1

Copy number variation (CNV) of RPS25
* Click on the image to open the original image in a new window.

Fusion gene breakpoints (product of the structural variants (SVs)) across RPS25
* Click on the image to open the UCSC genome browser with custom track showing this image in a new window.

Fusion genes with this translation factor from FusionGDB2.0.

FusionGDB2 ID	Disease	Sample	Hgene	Hchr	Hbp	Hstrand	Tgene	Tchr	Tbp	Tstrand
61410	N/A	AA507674	ARL14EPL	chr5	115388018	+	RPS25	chr11	118886422	+
61410	N/A	AA888388	ARL14EPL	chr5	115388014	+	RPS25	chr11	118886422	+
61410	N/A	BM970753	ARL14EPL	chr5	115387887	+	RPS25	chr11	118886422	+
61410	N/A	AA230202	BDNF-AS	chr11	27603245	-	RPS25	chr11	118886422	+
61410	N/A	AA569570	BDNF-AS	chr11	27603268	-	RPS25	chr11	118886422	+
61410	N/A	EC510393	BDNF-AS	chr11	27603647	+	RPS25	chr11	118886470	-
61410	ESCA	TCGA-L5-A4OQ	CCDC84	chr11	118886455	+	RPS25	chr11	118886468	-
61410	N/A	BE857084	CCDC84	chr11	118886468	+	RPS25	chr11	118886551	+
61410	N/A	BQ721711	CLIC4	chr1	25167568	+	RPS25	chr11	118888757	-
61410	N/A	EC560442	FOXP1	chr3	71509554	-	RPS25	chr11	118889035	-
61410	N/A	AA572866	LRRTM3	chr10	68787213	+	RPS25	chr11	118886422	+
61410	N/A	EC573623	MYCBP2	chr13	77732277	-	RPS25	chr11	118886426	+
61410	N/A	FN100183	MYCBP2	chr13	77732276	-	RPS25	chr11	118886424	+
61410	STAD	TCGA-CD-8525-01A	OGFOD2	chr12	123459930	+	RPS25	chr11	118888255	-
77712	N/A	AA177102	RPS25	chr11	118886422	-	ARL14EPL	chr5	115387570	-
77712	N/A	AA525012	RPS25	chr11	118886422	-	ARL14EPL	chr5	115387962	-
77712	N/A	AA528431	RPS25	chr11	118886422	-	ARL14EPL	chr5	115387894	-
77712	N/A	CF123213	RPS25	chr11	118886422	-	ARL14EPL	chr5	115388039	-
77712	N/A	CF123584	RPS25	chr11	118886422	-	ARL14EPL	chr5	115387880	-
77712	N/A	CF123650	RPS25	chr11	118886423	-	ARL14EPL	chr5	115387962	-
90685	N/A	AA572733	RPS25	chr11	118886422	-	BDNF-AS	chr11	27603245	+
93804	N/A	BM972124	RPS25	chr11	118886473	-	CCDC84	chr11	118886451	-
77712	STAD	TCGA-HU-A4GT-01A	RPS25	chr11	118888992	-	GAS5	chr1	173834685	-
91811	STAD	TCGA-CD-8531-01A	RPS25	chr11	118888668	-	GBF1	chr10	104140263	+
94016	GBM	TCGA-14-1034-02B	RPS25	chr11	118888668	-	HYOU1	chr11	118916543	-
78667	STAD	TCGA-R5-A7O7	RPS25	chr11	118888991	-	PGP	chr16	2264054	-
100124	N/A	BP271042	RPS25	chr11	118888201	-	STK4	chr20	43707835	+

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Prognostic Analysis

Kaplan-Meier plots with logrank tests of overall survival (OS)

Cancer type

Translation factor

Coefficent

Hazard ratio

Wald test pval

Likelihool ratio pval

Logrank test pval

# samples

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Translation factor and Gender

Differential gene expression between female and male. (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
BRCA	RPS25	0.021420276710728	0.6

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Translation factor and Age

Differential gene expression between young and old age groups (Wilcoxon test, pval<0.05)

Cancer type	Translation factor	pval	adj.p
LUSC	RPS25	0.0479342620084731	1
BRCA	RPS25	0.00366079454477709	0.12
PAAD	RPS25	0.040003796092789	1

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Related Drugs

Drugs targeting genes involved in this translation factor.
(DrugBank Version 5.1.8 2021-05-08)

UniProtAcc

DrugBank ID

Drug name

Drug activity

Drug type

Drug status

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Related Diseases

Diseases associated with this translation factor.
(DisGeNet 4.0)

Disease ID

Disease Name

# PubMeds

Disease source