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 RPS14
Basic gene info.Gene symbolRPS14
Gene nameribosomal protein S14
SynonymsEMTB|S14
CytomapUCSC genome browser: 5q31-q33
Genomic locationchr5 :149823791-149829319
Type of geneprotein-coding
RefGenesNM_001025070.1,
NM_001025071.1,NM_005617.3,
Ensembl idENSG00000164587
Description40S ribosomal protein S14emetine resistance
Modification date20141207
dbXrefs MIM : 130620
HGNC : HGNC
Ensembl : ENSG00000164587
HPRD : 00562
Vega : OTTHUMG00000130080
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS14
BioGPS: 6208
Gene Expression Atlas: ENSG00000164587
The Human Protein Atlas: ENSG00000164587
PathwayNCI Pathway Interaction Database: RPS14
KEGG: RPS14
REACTOME: RPS14
ConsensusPathDB
Pathway Commons: RPS14
MetabolismMetaCyc: RPS14
HUMANCyc: RPS14
RegulationEnsembl's Regulation: ENSG00000164587
miRBase: chr5 :149,823,791-149,829,319
TargetScan: NM_001025070
cisRED: ENSG00000164587
ContextiHOP: RPS14
cancer metabolism search in PubMed: RPS14
UCL Cancer Institute: RPS14
Assigned class in ccmGDBC

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Phenotypic Information for RPS14(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS14
Familial Cancer Database: RPS14
* 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: RPS14
MedGen: RPS14 (Human Medical Genetics with Condition)
ClinVar: RPS14
PhenotypeMGI: RPS14 (International Mouse Phenotyping Consortium)
PhenomicDB: RPS14

Mutations for RPS14
* 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 RPS14 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AF116710WDR2616081224613921224614528RPS1460011345149823801149829294
BU602070RPS1443485149826368149829300RPS19348482194237327142375484
AA450315HDLBP14262242176108242179226RPS144184815149823849149823912
BM680717RPS14191285149823798149823906WDR612773034905038449050987
CN271804METTL4252061825423932542574RPS141972785149823801149823882

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=9)
Stat. for Synonymous SNVs
(# total SNVs=5)
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
chr5:149826385-149826385p.L97L2
chr5:149826426-149826426p.R84G2
chr5:149827164-149827164p.T45A1
chr5:149826398-149826402p.?1
chr5:149827186-149827186p.F37L1
chr5:149826406-149826406p.I90I1
chr5:149827233-149827233p.A22T1
chr5:149826413-149826413p.L88Q1
chr5:149827271-149827271p.K9R1
chr5:149826424-149826424p.R84R1

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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 2    11 1    22  
# mutation 2 1    11 1    12  
nonsynonymous SNV 1 1    11       2  
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
chr5:149826426p.R84G,RPS142
chr5:149826385p.L97L,RPS142
chr5:149826406p.I90I,RPS141
chr5:149826448p.L76F,RPS141
chr5:149826455p.A74G,RPS141
chr5:149827271p.K9R,RPS141
chr5:149827277p.K7R,RPS141
chr5:149825182p.I126I,RPS141
chr5:149826384p.R98W,RPS141

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 RPS14 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 RPS14

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

GNB2L1,PFDN5,RPL10,RPL10A,RPL11,RPL13A,RPL18,
RPL24,RPL27A,RPL29,RPL31,RPL32,RPL34,RPL37A,
RPL7A,RPS11,RPS14,RPS23,RPS4X,RPS8,RPS9
EEF1B2,GNB2L1,RPL10,RPL10A,RPL12,RPL13,RPL13A,
RPL14,RPL18,RPL19,RPL24,RPL29,RPL37,RPL7A,
RPLP0,RPS11,RPS14,RPS2,RPS3,RPS6,RPS8

EEF1B2,HINT1,RPL10A,RPL15,RPL29,RPL32,RPL36,
RPS10,RPS11,RPS14,RPS15A,RPS18,RPS23,RPS3,
RPS3A,RPS6,RPS7,RPS8,RPS9,RPSA,RPSAP58
ATRAID,EEF1B2,MRPL43,LRRC75A-AS1,RPL24,RPL27A,RPL35,
RPS10,RPS11,RPS13,RPS14,RPS18,RPS21,RPS3,
RPS3A,RPS5,RPS6,RPS7,RPS8,TMEM14B,TPT1
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 RPS14


There's no related Drug.
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Cross referenced IDs for RPS14
* 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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