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 RPS18
Basic gene info.Gene symbolRPS18
Gene nameribosomal protein S18
SynonymsD6S218E|HKE3|KE-3|KE3|S18
CytomapUCSC genome browser: 6p21.3
Genomic locationchr6_ssto_hap7 :4720053-4720706
Type of geneprotein-coding
RefGenesNM_022551.2,
Ensembl idENSG00000231500
Description40S ribosomal protein S18rhabdomyosarcoma antigen MU-RMS-40.21
Modification date20141207
dbXrefs MIM : 180473
HGNC : HGNC
Ensembl : ENSG00000231500
HPRD : 01601
Vega : OTTHUMG00000031053
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS18
BioGPS: 6222
Gene Expression Atlas: ENSG00000231500
The Human Protein Atlas: ENSG00000231500
PathwayNCI Pathway Interaction Database: RPS18
KEGG: RPS18
REACTOME: RPS18
ConsensusPathDB
Pathway Commons: RPS18
MetabolismMetaCyc: RPS18
HUMANCyc: RPS18
RegulationEnsembl's Regulation: ENSG00000231500
miRBase: chr6_ssto_hap7 :4,720,053-4,720,706
TargetScan: NM_022551
cisRED: ENSG00000231500
ContextiHOP: RPS18
cancer metabolism search in PubMed: RPS18
UCL Cancer Institute: RPS18
Assigned class in ccmGDBC

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Phenotypic Information for RPS18(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS18
Familial Cancer Database: RPS18
* 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: RPS18
MedGen: RPS18 (Human Medical Genetics with Condition)
ClinVar: RPS18
PhenotypeMGI: RPS18 (International Mouse Phenotyping Consortium)
PhenomicDB: RPS18

Mutations for RPS18
* 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 RPS18 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW865643RPS18496647203154720408RPS1890343647204054720658

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=10)
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
chr6:33243782-33243782p.Y77C2
chr6:33243620-33243620p.I50T2
chr6:33240411-33240411p.V4M1
chr6:33243622-33243622p.D51N1
chr6:33244018-33244018p.A119A1
chr6:33240412-33240412p.V4A1
chr6:33243639-33243639p.A56A1
chr6:33244047-33244047p.?1
chr6:33240417-33240417p.P6S1
chr6:33243640-33243640p.G57R1

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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
# sample3  2    3   11  51 3
# mutation3  2    3   11  51 3
nonsynonymous SNV3  2        11  1  3
synonymous SNV        3       41  
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
chr6:33240411p.I12I1
chr6:33243970p.R23R1
chr6:33240417p.A32V1
chr6:33244009p.A41A1
chr6:33240427p.D51N1
chr6:33244018p.A56A1
chr6:33240430p.K78N1
chr6:33244172p.L103L1
chr6:33240437p.K116K1
chr6:33244179p.A119A1

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 RPS18 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 RPS18

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,RPL10A,RPL11,RPL12,RPL24,RPL27A,RPL31,
RPL32,RPL35A,RPL37,RPL5,RPL6,RPL7A,RPS10,
RPS11,RPS18,RPS25,RPS2,RPS6,RPS7,RPS8
EEF1B2,EEF1G,EIF3D,FBL,GNB2L1,IMPDH2,NOB1,
RPL10A,RPL12,RPL14,RPL3,RPL4,RPL5,RPL6,
RPL7A,RPLP0,RPS18,RPS2,RPS3,RPS6,RPS8

EEF1B2,LYRM4,RPL10A,RPL15,RPL32,RPL35,RPL35A,
RPL36,RPL37A,RPL5,RPL7A,RPS10,RPS11,RPS13,
RPS14,RPS15A,RPS18,RPS3,RPS6,RPS7,RPS8
TMEM261,DPY30,EEF1B2,NUDCD2,RPL24,RPL27A,RPL35,
RPL41,RPS10,RPS11,RPS14,RPS18,RPS21,RPS3A,
RPS5,RPS6,RPS7,RPS8,RPSAP58,SNRPD2,TMEM14B
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 RPS18


There's no related Drug.
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Cross referenced IDs for RPS18
* 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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