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 RPS2
Basic gene info.Gene symbolRPS2
Gene nameribosomal protein S2
SynonymsLLREP3|S2
CytomapUCSC genome browser: 16p13.3
Genomic locationchr16 :2012061-2014827
Type of geneprotein-coding
RefGenesNM_002952.3,
Ensembl idENSG00000140988
Description40S ribosomal protein S240S ribosomal protein S4OK/KNS-cl.6protein LLRep3
Modification date20141207
dbXrefs MIM : 603624
HGNC : HGNC
Ensembl : ENSG00000140988
HPRD : 04690
Vega : OTTHUMG00000128708
ProteinUniProt: P15880
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS2
BioGPS: 6187
Gene Expression Atlas: ENSG00000140988
The Human Protein Atlas: ENSG00000140988
PathwayNCI Pathway Interaction Database: RPS2
KEGG: RPS2
REACTOME: RPS2
ConsensusPathDB
Pathway Commons: RPS2
MetabolismMetaCyc: RPS2
HUMANCyc: RPS2
RegulationEnsembl's Regulation: ENSG00000140988
miRBase: chr16 :2,012,061-2,014,827
TargetScan: NM_002952
cisRED: ENSG00000140988
ContextiHOP: RPS2
cancer metabolism search in PubMed: RPS2
UCL Cancer Institute: RPS2
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RPS2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS2
Familial Cancer Database: RPS2
* 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 CLL 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.nature.com/nature/journal/v505/n7484/full/nature12912.html,
7Therapeutic 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 603624; gene.
Orphanet
DiseaseKEGG Disease: RPS2
MedGen: RPS2 (Human Medical Genetics with Condition)
ClinVar: RPS2
PhenotypeMGI: RPS2 (International Mouse Phenotyping Consortium)
PhenomicDB: RPS2

Mutations for RPS2
* 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 RPS2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=12)
Stat. for Synonymous SNVs
(# total SNVs=9)
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
chr16:2012182-2012182p.Q267*3
chr16:2014591-2014591p.G12G3
chr16:2012609-2012609p.R200G2
chr16:2014528-2014528p.I33I2
chr16:2012794-2012794p.P164P2
chr16:2012222-2012222p.P253P2
chr16:2012592-2012592p.V205V2
chr16:2014271-2014271p.?1
chr16:2014292-2014292p.F84L1
chr16:2012119-2012119p.P288S1

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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
# sample21 3    1       42 2
# mutation21 3    1       42 2
nonsynonymous SNV 1 2    1       21  
synonymous SNV2  1            21 2
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
chr16:2012222p.P253P2
chr16:2012881p.V282M1
chr16:2012119p.L273L1
chr16:2012906p.Q267E1
chr16:2012137p.A243V1
chr16:2013210p.F236F1
chr16:2012162p.K212K1
chr16:2014292p.A207V1
chr16:2012182p.I156I1
chr16:2012253p.G135G1

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 RPS2 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 RPS2

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,RPL10A,RPL11,RPL27A,RPL32,RPL35A,RPL36,
RPL36AL,RPL37A,RPL41,RPLP2,RPS10,RPS11,RPS13,
RPS14,RPS15A,RPS27A,RPS29,RPS9,RPSA,RPSAP58
BTF3,CCT4,DPH5,EIF3M,RPL15,RPL22,RPL24,
RPL26,RPL30,RPL32,RPL35A,RPL38,RPL41,RPL6,
RPS13,RPS15A,RPS24,RPS29,RPS3A,RPS7,UXT

EEF1B2,RPL10A,RPL27,RPL29,RPL35,RPL36,RPL41,
RPLP0,RPS10,RPS14,RPS16,RPS18,RPS29,RPS3,
RPS3A,RPS5,RPS6,RPS8,RPS9,RPSAP58,TIMM9
SMDT1,COX16,EEF1B2,RPL26,RPL32,RPL36,RPL37A,
RPL38,RPL39,RPLP0,RPS10,RPS13,RPS14,RPS18,
RPS21,RPS29,RPS3,TPT1,UQCRH,UQCRHL,UXT
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 RPS2


There's no related Drug.
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Cross referenced IDs for RPS2
* 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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