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 RPS6
Basic gene info.Gene symbolRPS6
Gene nameribosomal protein S6
SynonymsS6
CytomapUCSC genome browser: 9p21
Genomic locationchr9 :19376253-19380235
Type of geneprotein-coding
RefGenesNM_001010.2,
Ensembl idENSG00000137154
Description40S ribosomal protein S6phosphoprotein NP33
Modification date20141207
dbXrefs MIM : 180460
HGNC : HGNC
Ensembl : ENSG00000137154
HPRD : 01592
Vega : OTTHUMG00000019642
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS6
BioGPS: 6194
Gene Expression Atlas: ENSG00000137154
The Human Protein Atlas: ENSG00000137154
PathwayNCI Pathway Interaction Database: RPS6
KEGG: RPS6
REACTOME: RPS6
ConsensusPathDB
Pathway Commons: RPS6
MetabolismMetaCyc: RPS6
HUMANCyc: RPS6
RegulationEnsembl's Regulation: ENSG00000137154
miRBase: chr9 :19,376,253-19,380,235
TargetScan: NM_001010
cisRED: ENSG00000137154
ContextiHOP: RPS6
cancer metabolism search in PubMed: RPS6
UCL Cancer Institute: RPS6
Assigned class in ccmGDBC

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Phenotypic Information for RPS6(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS6
Familial Cancer Database: RPS6
* 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
Orphanet
DiseaseKEGG Disease: RPS6
MedGen: RPS6 (Human Medical Genetics with Condition)
ClinVar: RPS6
PhenotypeMGI: RPS6 (International Mouse Phenotyping Consortium)
PhenomicDB: RPS6

Mutations for RPS6
* 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 RPS6 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE257666RPS61152491937662819379618C14orf132524621149655885296558949
CD520454RPS6219091937843719378818MAP2K1182216156673879166738825
AA026363RPS61224191937625319376587POSTN236458133813733238138699
BF843060RPS6825091937661119378762IVL2453211152884030152884106
AW973590RPS6114091937632419376568NPAS21394622101541622101554305
BG874971NUP1601237114780045347800689RPS623242191937846119378842
BF514651RPS61733091937625319378387GANAB329405116240692862407163
BF814502RPS6731291937872219379594MALAT1304530116526652565266751
BF814212MALAT1220357116526652565266662RPS634956091937881519379594
BQ378142RPS6238491937836719379509NARS2371514117827717778277320
AA553904RPS6621091937625919376568NPAS22094352101541622101549457
BF815928RPS61133191937870519379594MALAT1323571116526652565266773
BF815926MALAT135369116526652565266860RPS636166191937872619379594
BG575834RPS6114391937845819378792CASP81258282202098783202105638
T59674RPS6115091937625319376507RPL27150432174115047241152121
AW970974RPS611148091937690519377274RPS647654091937684419376908
AV697913RPS615129691937625319376507NDST32873104118999891118999914

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
There's no copy number variation information in COSMIC data for this gene.

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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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=21)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr9:19376575-19376575p.R191C2
chr9:19378870-19378870p.P62H1
chr9:19376334-19376334p.S236C1
chr9:19378872-19378872p.F61F1
chr9:19376343-19376343p.R233I1
chr9:19376648-19376648p.G166G1
chr9:19379494-19379494p.E43E1
chr9:19376346-19376346p.R232H1
chr9:19378393-19378393p.V157F1
chr9:19379526-19379526p.A33T1

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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
# sample52 3       12   11 6
# mutation52 3       12   11 6
nonsynonymous SNV32 2       11   11 6
synonymous SNV2  1        1       
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
chr9:19376346p.A229S1
chr9:19378843p.E222D1
chr9:19376351p.R216K1
chr9:19378869p.L194L1
chr9:19376356p.I192V1
chr9:19378870p.G166G1
chr9:19376375p.S148F1
chr9:19379526p.T127N1
chr9:19376499p.K93N1
chr9:19379552p.G71D1

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 RPS6 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 RPS6

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.
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check002.gifProtein Expression Plot (RPPA)
*RPPA protein expression data were extracted from TCPA (The Cancer Proteome Atlas). Normalized data based on replicated based normalization (RBN) was used to draw following figures.

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

RPL11,RPL12,RPL14,RPL24,RPL27A,RPL29,RPL31,
RPL32,RPL34,RPL35A,RPL37,RPL37A,RPL5,RPL6,
RPL7A,RPS18,RPS19,RPS4X,RPS6,RPS7,RPS8
GNB2L1,RPL10,RPL10A,RPL12,RPL14,RPL24,RPL32,
RPL35A,RPL37,RPL4,RPL5,RPL6,RPLP0,RPS12,
RPS14,RPS18,RPS3A,RPS4X,RPS6,RPS7,RPS8

EEF1B2,RPL10A,RPL15,RPL31,RPL32,RPL35,RPL35A,
RPL36,RPL5,RPL7A,RPS10,RPS11,RPS13,RPS14,
RPS15A,RPS18,RPS23,RPS3,RPS6,RPS7,RPS8
TMEM261,EEF1B2,MED28,RPL24,RPL27A,RPL35,RPL41,
RPL5,RPS10,RPS11,RPS14,RPS18,RPS3,RPS3A,
RPS5,RPS6,RPS7,RPS8,RPSAP58,SNRPD2,TMEM14B
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 RPS6
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB00877ribosomal protein S6approved; investigationalSirolimus


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Cross referenced IDs for RPS6
* 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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