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 RPL11
Basic gene info.Gene symbolRPL11
Gene nameribosomal protein L11
SynonymsDBA7|GIG34|L11
CytomapUCSC genome browser: 1p36.1-p35
Genomic locationchr1 :24018268-24022915
Type of geneprotein-coding
RefGenesNM_000975.3,
NM_001199802.1,
Ensembl idENSG00000142676
Description60S ribosomal protein L11CLL-associated antigen KW-12cell growth-inhibiting protein 34
Modification date20141222
dbXrefs MIM : 604175
HGNC : HGNC
Ensembl : ENSG00000142676
HPRD : 10364
Vega : OTTHUMG00000002926
ProteinUniProt: P62913
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL11
BioGPS: 6135
Gene Expression Atlas: ENSG00000142676
The Human Protein Atlas: ENSG00000142676
PathwayNCI Pathway Interaction Database: RPL11
KEGG: RPL11
REACTOME: RPL11
ConsensusPathDB
Pathway Commons: RPL11
MetabolismMetaCyc: RPL11
HUMANCyc: RPL11
RegulationEnsembl's Regulation: ENSG00000142676
miRBase: chr1 :24,018,268-24,022,915
TargetScan: NM_000975
cisRED: ENSG00000142676
ContextiHOP: RPL11
cancer metabolism search in PubMed: RPL11
UCL Cancer Institute: RPL11
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RPL11(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL11
Familial Cancer Database: RPL11
* 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 604175; gene.
612562; phenotype.
Orphanet 124; Blackfan-Diamond anemia.
DiseaseKEGG Disease: RPL11
MedGen: RPL11 (Human Medical Genetics with Condition)
ClinVar: RPL11
PhenotypeMGI: RPL11 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL11

Mutations for RPL11
* 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 RPL11 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AA447363RPL11117412402230024022908KDM5C170448X5322227153222655
CN269184RPL11143812401910024022336TMCO64335455140021281140021725
CB409379RPL11148712401910824022397NDUFB44855733120321083120321171
AU134575RPL11149412401829624022367STRN4489647194722647947228158
BE613010RPL11149612402032324020406EPHX1976871226027547226033006
BQ310852RPL1117012401914624019217RPL116640312401921824022354
CD388242RPL114130212401909824020406TKT30238635325966853259752
BU598868NAA5015593113442278113465099RPL1155673212402229724022905
AU100496FRYL587744853105048531069RPL116830012401913224020764
CV387556ADAMTS21111305178701856178701875RPL1113154412401829624021281

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=17)
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
chr1:24021260-24021260p.I125M3
chr1:24022315-24022315p.A142T2
chr1:24019220-24019220p.L43H2
chr1:24018320-24018320p.?2
chr1:24020362-24020362p.R75*2
chr1:24019138-24019138p.R16C2
chr1:24019179-24019179p.S29S1
chr1:24019189-24019189p.L33M1
chr1:24021271-24021271p.D129V1
chr1:24019195-24019195p.R35*1

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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
# sample2  4    11 2    1  4
# mutation2  4    11 2    1  4
nonsynonymous SNV2  3    11 1    1  3
synonymous SNV   1       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
chr1:24022315p.A142T,RPL112
chr1:24021204p.I125M,RPL111
chr1:24021209p.D129V,RPL111
chr1:24021260p.R146H,RPL111
chr1:24021271p.I151F,RPL111
chr1:24022328p.F166L,RPL111
chr1:24022342p.D171D,RPL111
chr1:24019129p.I173I,RPL111
chr1:24022387p.R13W,RPL111
chr1:24019138p.R16C,RPL111

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 RPL11 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 RPL11

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

RPL11,RPL12,RPL18,RPL24,RPL27A,RPL29,RPL31,
RPL32,RPL34,RPL36,RPL37,RPL37A,RPL6,RPL7A,
RPLP2,RPS11,RPS14,RPS18,RPS23,RPS8,RPS9
RPL10,RPL11,RPL14,RPL19,RPL24,RPL27A,RPL29,
RPL35,RPL36,RPL37,RPL38,RPL5,RPL6,RPL7A,
RPS11,RPS14,RPS16,RPS17,RPS25,RPS6,RPS8

PITHD1,GNB2L1,NACA,RPL11,RPL12,RPL22,RPL26,
RPL31,RPL34,RPL35A,RPL3,RPL37,RPL37A,RPL6,
RPL7A,RPLP2,RPS24,RPS25,RPS2,RPS27A,SYF2
EIF3H,NACA,RPL10,RPL11,RPL12,RPL14,RPL19,
RPL30,RPL31,RPL32,RPL3,RPL4,RPL6,RPL7,
RPL7A,RPS12,RPS20,RPS23,RPS24,RPS25,UBA52
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 RPL11
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA34664; -.
Organism-specific databasesCTD 6135; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02494ribosomal protein L11experimentalAlpha-Hydroxy-Beta-Phenyl-Propionic Acid
DB07374ribosomal protein L11experimentalANISOMYCIN
DB08437ribosomal protein L11experimentalPUROMYCIN


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Cross referenced IDs for RPL11
* 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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