Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 RPS11
Basic gene info.Gene symbolRPS11
Gene nameribosomal protein S11
SynonymsS11
CytomapUCSC genome browser: 19q13.3
Genomic locationchr19 :49999633-50002944
Type of geneprotein-coding
RefGenesNM_001015.4,
Ensembl idENSG00000142534
Description40S ribosomal protein S11
Modification date20141207
dbXrefs MIM : 180471
HGNC : HGNC
Ensembl : ENSG00000142534
HPRD : 01599
Vega : OTTHUMG00000183156
ProteinUniProt: P62280
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS11
BioGPS: 6205
Gene Expression Atlas: ENSG00000142534
The Human Protein Atlas: ENSG00000142534
PathwayNCI Pathway Interaction Database: RPS11
KEGG: RPS11
REACTOME: RPS11
ConsensusPathDB
Pathway Commons: RPS11
MetabolismMetaCyc: RPS11
HUMANCyc: RPS11
RegulationEnsembl's Regulation: ENSG00000142534
miRBase: chr19 :49,999,633-50,002,944
TargetScan: NM_001015
cisRED: ENSG00000142534
ContextiHOP: RPS11
cancer metabolism search in PubMed: RPS11
UCL Cancer Institute: RPS11
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RPS11(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS11
Familial Cancer Database: RPS11
* 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 180471; gene.
Orphanet
DiseaseKEGG Disease: RPS11
MedGen: RPS11 (Human Medical Genetics with Condition)
ClinVar: RPS11
PhenotypeMGI: RPS11 (International Mouse Phenotyping Consortium)
PhenomicDB: RPS11

Mutations for RPS11
* 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 RPS11 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CF130421GOLGA3409612133402787133402844RPS1195375195000120150002946
BM822653NDUFB412843120315228120320086RPS11285450194999968850000575
U52144RPS111176195000276950002945IDH21681591159062721090633860
AA368503DLK1112514101201247101201371RPS11121325195000056150001280
AI589684RPS1128113195000286150002946LIPC112334155880518558805407

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=9

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=16)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr19:50000581-50000581p.E49A9
chr19:50000783-50000783p.E52Q3
chr19:50001200-50001200p.R84G1
chr19:49999721-49999721p.D3G1
chr19:50001234-50001234p.Y95C1
chr19:50000450-50000450p.?1
chr19:50001265-50001265p.R105R1
chr19:50001293-50001293p.P115S1
chr19:50001297-50001297p.C116F1
chr19:50000787-50000790p.G53fs*241

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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   2    1  11 1 21 1
# mutation   2    1  11 1 21 1
nonsynonymous SNV   1    1  11 1 11 1
synonymous SNV   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
chr19:50000840p.R71W2
chr19:50000830p.R69P1
chr19:50000835p.R84G1
chr19:50001200p.V87A1
chr19:50001210p.Y95C1
chr19:50001234p.R105R1
chr19:50001265p.P115S1
chr19:50001293p.T137A1
chr19:50002824p.G150S1
chr19:50002863p.S67S1

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 RPS11 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 RPS11

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

RPL10,RPL11,RPL12,RPL13A,RPL13AP20,RPL18,RPL24,
RPL27A,RPL28,RPL29,RPL31,RPL32,RPL37A,RPLP2,
RPS11,RPS14,RPS19,RPS2,RPS5,RPS8,RPS9
EEF1A1P9,GNB2L1,RPL10,RPL11,RPL13,RPL14,RPL18,
RPL19,RPL24,RPL27A,RPL32,RPL36,RPL37,RPL38,
RPL7A,RPS11,RPS14,RPS16,RPS7,RPS8,SNRPD2

RPL10A,RPL13A,RPL18,RPL28,RPL32,RPL35A,RPL36,
RPLP0,RPS11,RPS13,RPS14,RPS15A,RPS16,RPS18,
RPS19,RPS3,RPS5,RPS6,RPS9,SNRPD2,ZNF581
RPL15,RPL19,RPL24,RPL27A,RPL29,RPL32,RPL35,
RPL35A,RPL41,RPL7A,RPL8,RPLP1,RPS10,RPS11,
RPS13,RPS14,RPS3,RPS5,RPS6,RPS8,SNRPD2
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 RPS11


There's no related Drug.
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Cross referenced IDs for RPS11
* 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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