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 RPL14
Basic gene info.Gene symbolRPL14
Gene nameribosomal protein L14
SynonymsCAG-ISL-7|CTG-B33|L14|RL14|hRL14
CytomapUCSC genome browser: 3p22-p21.2
Genomic locationchr3 :40498829-40503859
Type of geneprotein-coding
RefGenesNM_001034996.2,
NM_003973.4,
Ensembl idENSG00000188846
Description60S ribosomal protein L14
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000188846
HPRD : 10617
Vega : OTTHUMG00000156046
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL14
BioGPS: 9045
Gene Expression Atlas: ENSG00000188846
The Human Protein Atlas: ENSG00000188846
PathwayNCI Pathway Interaction Database: RPL14
KEGG: RPL14
REACTOME: RPL14
ConsensusPathDB
Pathway Commons: RPL14
MetabolismMetaCyc: RPL14
HUMANCyc: RPL14
RegulationEnsembl's Regulation: ENSG00000188846
miRBase: chr3 :40,498,829-40,503,859
TargetScan: NM_001034996
cisRED: ENSG00000188846
ContextiHOP: RPL14
cancer metabolism search in PubMed: RPL14
UCL Cancer Institute: RPL14
Assigned class in ccmGDBC

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Phenotypic Information for RPL14(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL14
Familial Cancer Database: RPL14
* 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: RPL14
MedGen: RPL14 (Human Medical Genetics with Condition)
ClinVar: RPL14
PhenotypeMGI: RPL14 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL14

Mutations for RPL14
* 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 RPL14 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BG519661RPL1427634050356740503641MED1271399X7036176170362299
BP334301RPL14139934049880140503146SENP639057967641170576411897
BC051312NCOR21158912124904505124979906RPL141589181734050353940503767
BC033087NCOR21175212124904505125002840RPL141752197534050354240503765
AA912468RPL14249534050369640503767H19923151120184342018658
BC010079E2F410965166722608867229791RPL14957117434050354240503759
AV738739RPL14226434050347840503739RPL1426539534050289840503136
BU608656RPL14135734050345740503501RPL144934634050348540503767
CD251046POMC121722538751025391431RPL1421244634050353040503764
BU630143RPL141425134050353440503771S100A162457161153579639153580112

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=0

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=0)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no ns-snv.There's no s-snv.
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

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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   31      41   11 2
# mutation   31      41   11 2
nonsynonymous SNV   2       31   1  2
synonymous SNV   11      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
chr3:40499409p.R11L,RPL142
chr3:40500174p.A76T,RPL141
chr3:40502923p.R90Q,RPL141
chr3:40502966p.R121R,RPL141
chr3:40503438p.A169A,RPL141
chr3:40503582p.P179S,RPL141
chr3:40503610p.A183T,RPL141
chr3:40503622p.A188V,RPL141
chr3:40499405p.G10C,RPL141
chr3:40503638p.G10G,RPL141

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 RPL14 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 RPL14

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

NACA,RPL11,RPL12,RPL14,RPL15,RPL18,RPL24,
RPL27A,RPL29,RPL32,RPL34,RPL37,RPL37A,RPLP1,
RPLP2,RPS14,RPS23,RPS2,RPS8,RPSA,RPSAP58
EEF1B2,GNB2L1,RPL10,RPL10A,RPL12,RPL14,RPL29,
RPL32,RPL37,RPL4,RPL5,RPL6,RPL7A,RPLP0,
RPS11,RPS14,RPS2,RPS6,RPS7,RPS8,RPSAP58

GNB2L1,RPL12,RPL14,RPL15,RPL24,RPL29,RPL31,
RPL32,RPL35A,RPL37,RPL37A,RPL7A,RPS13,RPS14,
RPS18,RPS23,RPS25,RPS6,RPS8,RPSA,RPSAP58
EEF1A1,EEF1A1P9,RPL10,RPL14,RPL15,RPL19,RPL29,
RPL32,RPL3,RPL38,RPL5,RPL7A,RPLP0,RPLP1,
RPS11,RPS12,RPS13,RPS3,RPS5,RPS8,RSL1D1
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 RPL14


There's no related Drug.
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Cross referenced IDs for RPL14
* 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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