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 RPS12
Basic gene info.Gene symbolRPS12
Gene nameribosomal protein S12
SynonymsS12
CytomapUCSC genome browser: 6q23.2
Genomic locationchr6 :133135707-133138703
Type of geneprotein-coding
RefGenesNM_001016.3,
Ensembl idENSG00000112306
Description40S ribosomal protein S12
Modification date20141207
dbXrefs MIM : 603660
HGNC : HGNC
HPRD : 04714
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS12
BioGPS: 6206
Gene Expression Atlas: ENSG00000112306
The Human Protein Atlas: ENSG00000112306
PathwayNCI Pathway Interaction Database: RPS12
KEGG: RPS12
REACTOME: RPS12
ConsensusPathDB
Pathway Commons: RPS12
MetabolismMetaCyc: RPS12
HUMANCyc: RPS12
RegulationEnsembl's Regulation: ENSG00000112306
miRBase: chr6 :133,135,707-133,138,703
TargetScan: NM_001016
cisRED: ENSG00000112306
ContextiHOP: RPS12
cancer metabolism search in PubMed: RPS12
UCL Cancer Institute: RPS12
Assigned class in ccmGDBC

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Phenotypic Information for RPS12(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS12
Familial Cancer Database: RPS12
* 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: RPS12
MedGen: RPS12 (Human Medical Genetics with Condition)
ClinVar: RPS12
PhenotypeMGI: RPS12 (International Mouse Phenotyping Consortium)
PhenomicDB: RPS12

Mutations for RPS12
* 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 RPS12 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA436799RPS121656133137948133138012SERINC1645916122775296122792957
AI394068RPS124656133138642133138703NIPAL36023512474578024745955
CD050400RPS12195166133135708133138698PAK4515565193966999439670044
BP319882RPS1215056133135708133138703SMYD35055821246433107246433184

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 # sample        1        
GAIN (# sample)                 
LOSS (# sample)        1        
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=13

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=5)
Stat. for Synonymous SNVs
(# total SNVs=16)
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
chr6:133138146-133138146p.I94I13
chr6:133137703-133137703p.?2
chr6:133138134-133138134p.G90G2
chr6:133136223-133136223p.D43N1
chr6:133137658-133137658p.L64L1
chr6:133137686-133137686p.Q73R1
chr6:133138123-133138123p.E87K1
chr6:133138636-133138636p.S118S1
chr6:133136170-133136171p.L26fs*321
chr6:133136205-133136205p.E37K1

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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        11    1 3
# mutation  1        11    1 3
nonsynonymous SNV           11      3
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
chr6:133138134p.G90G2
chr6:133137686p.Q73R1
chr6:133138165p.R101S1
chr6:133138166p.R101H1
chr6:133138636p.S118S1
chr6:133136205p.E37K1
chr6:133136222p.L42F1
chr6:133136223p.D43N1

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 RPS12 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 RPS12

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

EEF1A1P9,EEF1G,RPL10A,RPL11,RPL13,RPL17,RPL18A,
RPL27A,RPL31,RPL32,RPL36,RPL37A,RPL6,RPLP0,
RPS10,RPS12,RPS18,RPS27A,RPS8,RPSAP58,UBA52
EEF1A1P9,RPL10,RPL14,RPL29,RPL31,RPL32,RPL35A,
RPL37,RPL4,RPL5,RPL6,RPLP0,RPS12,RPS14,
RPS23,RPS27A,RPS6,RPS7,RPS8,RPSA,RPSAP58

GAS5,LRRC75A-AS1,RPL10A,RPL12,RPL13A,RPL26,RPL31,
RPL35A,RPL36,RPL37A,RPL7A,RPLP0,RPS10,RPS11,
RPS12,RPS16,RPS17,RPS18,RPS23,RPS25,RPS27A
EEF1A1,RPL10,RPL10A,RPL14,RPL15,RPL19,RPL30,
RPL32,RPL3,RPL38,RPL6,RPL7A,RPLP0,RPS11,
RPS12,RPS13,RPS23,RPS25,RPS3,RPS5,RPS8
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 RPS12


There's no related Drug.
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Cross referenced IDs for RPS12
* 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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