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 RPL18A
Basic gene info.Gene symbolRPL18A
Gene nameribosomal protein L18a
SynonymsL18A
CytomapUCSC genome browser: 19p13
Genomic locationchr19 :17970730-17974124
Type of geneprotein-coding
RefGenesNM_000980.3,
Ensembl idENSG00000105640
Description60S ribosomal protein L18aribosomal protein L18a-like protein
Modification date20141207
dbXrefs MIM : 604178
HGNC : HGNC
Ensembl : ENSG00000105640
HPRD : 16045
Vega : OTTHUMG00000183445
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL18A
BioGPS: 6142
Gene Expression Atlas: ENSG00000105640
The Human Protein Atlas: ENSG00000105640
PathwayNCI Pathway Interaction Database: RPL18A
KEGG: RPL18A
REACTOME: RPL18A
ConsensusPathDB
Pathway Commons: RPL18A
MetabolismMetaCyc: RPL18A
HUMANCyc: RPL18A
RegulationEnsembl's Regulation: ENSG00000105640
miRBase: chr19 :17,970,730-17,974,124
TargetScan: NM_000980
cisRED: ENSG00000105640
ContextiHOP: RPL18A
cancer metabolism search in PubMed: RPL18A
UCL Cancer Institute: RPL18A
Assigned class in ccmGDBC

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Phenotypic Information for RPL18A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL18A
Familial Cancer Database: RPL18A
* 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: RPL18A
MedGen: RPL18A (Human Medical Genetics with Condition)
ClinVar: RPL18A
PhenotypeMGI: RPL18A (International Mouse Phenotyping Consortium)
PhenomicDB: RPL18A

Mutations for RPL18A
* 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 RPL18A 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=2

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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=2)
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
chr19:17974034-17974034p.P165T2
chr19:17973750-17973750p.R118C2
chr19:17972952-17972952p.R83H1
chr19:17973996-17973996p.F152S1
chr19:17972957-17972957p.D85N1
chr19:17974005-17974005p.P155L1
chr19:17972140-17972140p.T19T1
chr19:17972970-17972970p.G89D1
chr19:17972151-17972151p.H23P1
chr19:17972988-17972988p.R95Q1

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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 3   11       12 3
# mutation 2 2   11       12 3
nonsynonymous SNV 2 2   11          2
synonymous SNV                12 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
chr19:17972210p.R43C2
chr19:17972970p.T19T1
chr19:17973010p.P25T1
chr19:17972140p.P26H1
chr19:17973794p.L27L1
chr19:17972156p.R31Q1
chr19:17974037p.V39I1
chr19:17972160p.R83C1
chr19:17972164p.R83H1
chr19:17972175p.G89D1

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 RPL18A 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 RPL18A

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

EEF1G,RPL10,RPL10A,RPL11,RPL13,RPL18A,RPL27A,
RPL31,RPL32,RPL36,RPL37A,RPLP0,RPLP2,RPS10,
RPS12,RPS19,RPS21,RPS8,RPS9,UBA52,USE1
VPS51___IFT46,EXOSC5,RPL10,RPL13,RPL13A,RPL18,RPL18A,
RPL19,RPL28,RPL29,RPL35,RPL36,RPL37,RPL37A,
RPL8,RPS15,RPS16,RPS19,RPS21,RPS5,RPS9

DHRS4L1,EEF1A1,EEF1A1P9,HIST1H4K,LOC100130932,LOC407835,PPIAL4C,
PPIAL4G,RPL13AP20,RPL13AP6,RPL18A,RPL21,RPL39,RPL41,
RPL7,RPS3A,RPSA,RPSAP58,RPSAP9,TRAPPC5,ZNF90
PHB2,RPL10,RPL13A,RPL18,RPL18A,RPL19,RPL29,
RPL32,RPL35,RPL7A,RPL8,RPLP0,RPLP1,RPS11,
RPS14,RPS21,RPS3,RPS5,RPS8,RPS9,RPSAP58
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 RPL18A


There's no related Drug.
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Cross referenced IDs for RPL18A
* 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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