Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Gene Summary

Phenotypic Information (metabolism pathway, cancer, disease, phenome)

Mutations: SVs, CNVs, SNVs

Gene expression: GE, Protein, DEGE, CNV vs GE

Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG

Pharmacological Information: Drug-Gene Network

Cross referenced IDs

Gene Summary for RPS3
Basic gene info.Gene symbolRPS3
Gene nameribosomal protein S3
SynonymsS3
CytomapUCSC genome browser: 11q13.3-q13.5
Genomic locationchr11 :75110534-75133345
Type of geneprotein-coding
RefGenesNM_001005.4,
NM_001256802.1,NM_001260506.1,NM_001260507.1,
Ensembl idENSG00000149273
Description40S ribosomal protein S3IMR-90 ribosomal protein S3
Modification date20141207
dbXrefs MIM : 600454
HGNC : HGNC
Ensembl : ENSG00000149273
HPRD : 10941
Vega : OTTHUMG00000165448
ProteinUniProt: P23396
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS3
BioGPS: 6188
Gene Expression Atlas: ENSG00000149273
The Human Protein Atlas: ENSG00000149273
PathwayNCI Pathway Interaction Database: RPS3
KEGG: RPS3
REACTOME: RPS3
ConsensusPathDB
Pathway Commons: RPS3
MetabolismMetaCyc: RPS3
HUMANCyc: RPS3
RegulationEnsembl's Regulation: ENSG00000149273
miRBase: chr11 :75,110,534-75,133,345
TargetScan: NM_001005
cisRED: ENSG00000149273
ContextiHOP: RPS3
cancer metabolism search in PubMed: RPS3
UCL Cancer Institute: RPS3
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RPS3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS3
Familial Cancer Database: RPS3
* This gene is included in those cancer gene databases.

.

Oncogene 1

Tumor Suppressor gene 2

Cancer Gene Census 3

CancerGenes 4

Network of Cancer Gene 5

Significant driver gene in

Therapeutic Vulnerabilities in Cancer1

cf) number; DB name
1 Oncogene; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
2 Tumor Suppressor gene; https://bioinfo.uth.edu/TSGene/,
3 Cancer Gene Census; http://www.nature.com/nrc/journal/v4/n3/abs/nrc1299.html,
4 CancerGenes; http://nar.oxfordjournals.org/content/35/suppl_1/D721.long,
5 Network of Cancer Gene; http://ncg.kcl.ac.uk/index.php,
1Therapeutic Vulnerabilities in Cancer; http://cbio.mskcc.org/cancergenomics/statius/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 600454; gene.
Orphanet
DiseaseKEGG Disease: RPS3
MedGen: RPS3 (Human Medical Genetics with Condition)
ClinVar: RPS3
PhenotypeMGI: RPS3 (International Mouse Phenotyping Consortium)
PhenomicDB: RPS3

Mutations for RPS3
* Under tables are showing count per each tissue to give us broad intuition about tissue specific mutation patterns.You can go to the detailed page for each mutation database's web site.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPS3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AK172736ANK311228106226725762493082RPS312211441117511576775116732
BM823567VSIG1176X107322056107322131RPS377433117511056375113468
DA636472RPS31141117511546975115609ARMC5140522163147129631473701
BG028694SET15649131454995131457000RPS3560641117511586175116688
BM856177VSIG1176X107322056107322131RPS377319117511056375112736
BP262829RPS31318117511056275113427C7orf3131256772521961925219874
BM844689RPS310291117511056375112774CLDN428139277324583473245945
BQ084066VSIG1176X107322056107322131RPS377266117511056375111868
BQ084386VSIG1176X107322056107322131RPS377217117511056375111819
BC017103MOB218301115764951577324RPS38311633117511060075116733

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2                
GAIN (# sample)2                
LOSS (# sample)                 
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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check002.gifSNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation

 : Non-synonymous mutation, : Synonymous mutation, Circle size denotes number of samples.
Maximum mutation count=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=15)
Stat. for Synonymous SNVs
(# total SNVs=7)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

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check002.gifTop 10 SNVs Having the Most Samples in COSMIC data
* When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site,primary_histology,mutation(aa),pubmedID.
GRCh37 positionMutation(aa)Unique sampleID count
chr11:75115193-75115193p.S160S1
chr11:75112674-75112675p.?1
chr11:75115202-75115202p.P163P1
chr11:75112684-75112684p.R54R1
chr11:75115222-75115222p.T170I1
chr11:75112734-75112734p.A71D1
chr11:75115230-75115230p.R173C1
chr11:75111750-75111750p.G15R1
chr11:75113406-75113406p.E89A1
chr11:75115745-75115745p.L190V1

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check002.gifSNV Counts per Each Loci in TCGA data

 : non-synonymous mutation, : synonymous mutation, Circle size denotes number of samples.
maximum mutation count=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   3  1 2  4 1  21 7
# mutation   3  1 2  4 1  21 7
nonsynonymous SNV   3  1 2  2 1   1 3
synonymous SNV           2    2  4
cf) Tissue ID; Tissue type (1; BLCA[Bladder Urothelial Carcinoma], 2; BRCA[Breast invasive carcinoma], 3; CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], 4; COAD[Colon adenocarcinoma], 5; GBM[Glioblastoma multiforme], 6; Glioma Low Grade, 7; HNSC[Head and Neck squamous cell carcinoma], 8; KICH[Kidney Chromophobe], 9; KIRC[Kidney renal clear cell carcinoma], 10; KIRP[Kidney renal papillary cell carcinoma], 11; LAML[Acute Myeloid Leukemia], 12; LUAD[Lung adenocarcinoma], 13; LUSC[Lung squamous cell carcinoma], 14; OV[Ovarian serous cystadenocarcinoma ], 15; PAAD[Pancreatic adenocarcinoma], 16; PRAD[Prostate adenocarcinoma], 17; SKCM[Skin Cutaneous Melanoma], 18:STAD[Stomach adenocarcinoma], 19:THCA[Thyroid carcinoma], 20:UCEC[Uterine Corpus Endometrial Carcinoma])

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check002.gifTop 10 SNVs Having the Most Samples in TCGA data
* We represented just top 10 SNVs. When you move the cursor on each content, you can see more deailed mutation information on the Tooltip. Those are primary_site, primary_histology, mutation(aa), pubmedID.
Genomic PositionMutation(aa)Unique sampleID count
chr11:75115230p.R47C,RPS32
chr11:75115793p.N22K,RPS31
chr11:75113455p.P65P,RPS31
chr11:75115797p.R27W,RPS31
chr11:75113456p.D80N,RPS31
chr11:75115888p.L29L,RPS31
chr11:75115080p.H81R,RPS31
chr11:75111750p.A30D,RPS31
chr11:75115084p.P111P,RPS31
chr11:75111773p.R40Q,RPS31

check002.gifOther DBs for Point Mutations
Point Mutation Table of Ensembl: go to Ensembl variation table
Mutation of cBioPortal: go to cBioPortal's Cross-cancer alteration summary

check002.gifCopy Number for RPS3 in TCGA
* Copy number data were extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered on Jan-05-2015. Function ProcessCNAData in TCGA-Assembler package was used to obtain gene-level copy number value which is calculated as the average copy number of the genomic region of a gene.
cf) Tissue ID[Tissue type]: BLCA[Bladder Urothelial Carcinoma], BRCA[Breast invasive carcinoma], CESC[Cervical squamous cell carcinoma and endocervical adenocarcinoma], COAD[Colon adenocarcinoma], GBM[Glioblastoma multiforme], Glioma Low Grade, HNSC[Head and Neck squamous cell carcinoma], KICH[Kidney Chromophobe], KIRC[Kidney renal clear cell carcinoma], KIRP[Kidney renal papillary cell carcinoma], LAML[Acute Myeloid Leukemia], LUAD[Lung adenocarcinoma], LUSC[Lung squamous cell carcinoma], OV[Ovarian serous cystadenocarcinoma ], PAAD[Pancreatic adenocarcinoma], PRAD[Prostate adenocarcinoma], SKCM[Skin Cutaneous Melanoma], STAD[Stomach adenocarcinoma], THCA[Thyroid carcinoma], UCEC[Uterine Corpus Endometrial Carcinoma]

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Gene Expression for RPS3

check002.gifGene Expression in Cancer Cell-lines (CCLE)
* CCLE gene expression data were extracted from CCLE_Expression_Entrez_2012-10-18.res: Gene-centric RMA-normalized mRNA expression data.

check002.gifDifferential Gene Expression in Primary Tumors (TCGA)
* Normalized gene expression data of RNASeqV2 was extracted from TCGA using R package TCGA-Assembler. The URLs of all public data files on TCGA DCC data server were gathered at Jan-05-2015. Only eight cancer types have enough normal control samples for differential expression analysis.
(t test, adjusted p<0.05 (using Benjamini-Hochberg FDR))
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check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


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Gene-Gene Network Information
check002.gifCo-Expressed gene's network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

EEF1A1,EEF1A1P9,EEF1B2,EEF1G,RPL10A,RPL11,RPL17,
RPL22,RPL27,RPL31,RPL34,RPL3,RPL5,RPL6,
RPL7A,RPS14,RPS18,RPS23,RPS3A,RPS4X,RPS8
BTF3,CCT4,DPH5,EEF1B2,NPM1,RPL15,RPL22,
RPL32,RPL35A,RPL41,RPL5,RPL6,RPL7,RPS15A,
RPS23,RPS24,RPS27A,RPS3A,RPS4X,RPS6,RPS7

EEF1A1,EEF1A1P9,EEF1B2,RPL10A,RPL15,RPL18A,RPL35,
RPL41,RPS10,RPS14,RPS18,RPS29,RPS3,RPS3A,
RPS5,RPS6,RPS7,RPS8,RPS9,RPSA,RPSAP58
DPY30,EEF1B2,MED28,PFDN5,RPL24,RPL27A,RPL35,
RPL41,RPL5,RPS10,RPS14,RPS18,RPS3A,RPS5,
RPS6,RPS7,RPS8,RPSAP58,RSL24D1,TMEM14B,TPT1
check002.gifCo-Expressed gene's Protein-protein interaction Network Plot
* Co-Expression network figures were drawn using R package igraph. Only the top 20 genes with the highest correlations were shown.
Red circle: input gene, orange circle: cell metabolism gene, sky circle: other gene

: Open all plots for all cancer types

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check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

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Pharmacological Information for RPS3


There's no related Drug.
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Cross referenced IDs for RPS3
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section

: Open all cross reference information



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