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 RPS16
Basic gene info.Gene symbolRPS16
Gene nameribosomal protein S16
SynonymsS16
CytomapUCSC genome browser: 19q13.1
Genomic locationchr19 :39923846-39926618
Type of geneprotein-coding
RefGenesNM_001020.4,
Ensembl idENSG00000105193
Description40S ribosomal protein S16
Modification date20141207
dbXrefs MIM : 603675
HGNC : HGNC
Ensembl : ENSG00000105193
HPRD : 04724
Vega : OTTHUMG00000182972
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS16
BioGPS: 6217
Gene Expression Atlas: ENSG00000105193
The Human Protein Atlas: ENSG00000105193
PathwayNCI Pathway Interaction Database: RPS16
KEGG: RPS16
REACTOME: RPS16
ConsensusPathDB
Pathway Commons: RPS16
MetabolismMetaCyc: RPS16
HUMANCyc: RPS16
RegulationEnsembl's Regulation: ENSG00000105193
miRBase: chr19 :39,923,846-39,926,618
TargetScan: NM_001020
cisRED: ENSG00000105193
ContextiHOP: RPS16
cancer metabolism search in PubMed: RPS16
UCL Cancer Institute: RPS16
Assigned class in ccmGDBC

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Phenotypic Information for RPS16(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS16
Familial Cancer Database: RPS16
* 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: RPS16
MedGen: RPS16 (Human Medical Genetics with Condition)
ClinVar: RPS16
PhenotypeMGI: RPS16 (International Mouse Phenotyping Consortium)
PhenomicDB: RPS16

Mutations for RPS16
* 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 RPS16 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
CB528938RPS1618168193992386439924014GABARAPL1165720121037066210374746
BG773769ACTB2272755689575570222RPS16272538193992432339926573
BE843019RPS1619249193992392239924349UBD2503556827387830817
BG473536ACTB2273755689575570222RPS16273685193992398239926573
BE732178ACTB1248755689575570201RPS16248764193992387239926573
BG998400LRRC382519411380200113802168RPS16195305193992619139926301
BE621901RPS161325193992386639924390MCM5321842223580257035808549
BU620241RPS1618276193992386439924320CCND1274583116946825769468566
BE904292RPS161536193992386139926575FBL525708194033133740337034
AI114445RPS16186193992633639926560FGA817544155506702155507364
BC070487ZNFX1-AS140571204789519147905797RPS16572832193992431239926556
BQ218778ZNFX1-AS137568204789519147905797RPS16569833193992431339926556
CF128699RPS1619560193992386439926587HIST1H1C55768962605633326056469
BE906373RPS161502193992388939926573NOL749656961361562313615696

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=11

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=19)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr19:39924056-39924056p.V100M11
chr19:39926521-39926521p.G5G3
chr19:39924389-39924389p.V55I2
chr19:39924156-39924156p.?2
chr19:39924009-39924009p.Y115Y1
chr19:39926258-39926258p.L47V1
chr19:39926340-39926340p.A19A1
chr19:39926509-39926509p.S9S1
chr19:39924185-39924185p.A91V1
chr19:39924197-39924197p.S87F1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample12 1       2    3  1
# mutation12 1       2    3  1
nonsynonymous SNV 1 1       1    1  1
synonymous SNV11         1    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
chr19:39924346p.I68I1
chr19:39924348p.V55I1
chr19:39924389p.L47V1
chr19:39926258p.R37R1
chr19:39926288p.A19A1
chr19:39926340p.D116Y1
chr19:39924008p.Y115Y1
chr19:39924009p.S87F1
chr19:39924197p.K73K1
chr19:39924333p.R69L1

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 RPS16 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 RPS16

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

EIF3K,FBL,MRPS12,NFKBIB,PAF1,POLR2I,RPL18A,
RPL37,RPLP2,RPS10,RPS16,RPS19,RPS21,SARS2,
SDHAF1,SIRT2,SNRPD2,SUPT5H,TIMM50,TMEM147,YIF1B
C12orf10,FAU,PHB2,RPL10,RPL11,RPL13,RPL18,
RPL18A,RPL19,RPL28,RPL29,RPL35,RPL36,RPL37,
RPL37A,RPL8,RPS11,RPS15,RPS16,RPS21,RPS9

RPL10A,RPL13A,RPL18,RPL27,RPL28,RPL35,RPL36,
RPLP0,RPS10,RPS11,RPS14,RPS15,RPS16,RPS19,
RPS29,RPS3,RPS5,RPS8,RPS9,SNRPD2,UBA52
ANAPC11,EEF1A1,FAU,RPL18A,RPL19,RPL29,RPL32,
RPL35,RPL35A,RPL38,RPL7A,RPL8,RPLP1,RPS10,
RPS11,RPS13,RPS16,RPS3,RPS5,RPS9,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 RPS16


There's no related Drug.
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Cross referenced IDs for RPS16
* 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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