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 RPS23
Basic gene info.Gene symbolRPS23
Gene nameribosomal protein S23
SynonymsS23
CytomapUCSC genome browser: 5q14.2
Genomic locationchr5 :81569138-81574235
Type of geneprotein-coding
RefGenesNM_001025.4,
Ensembl idENSG00000186468
Description40S ribosomal protein S23homolog of yeast ribosomal protein S28
Modification date20141207
dbXrefs MIM : 603683
HGNC : HGNC
Ensembl : ENSG00000186468
HPRD : 04729
Vega : OTTHUMG00000162557
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS23
BioGPS: 6228
Gene Expression Atlas: ENSG00000186468
The Human Protein Atlas: ENSG00000186468
PathwayNCI Pathway Interaction Database: RPS23
KEGG: RPS23
REACTOME: RPS23
ConsensusPathDB
Pathway Commons: RPS23
MetabolismMetaCyc: RPS23
HUMANCyc: RPS23
RegulationEnsembl's Regulation: ENSG00000186468
miRBase: chr5 :81,569,138-81,574,235
TargetScan: NM_001025
cisRED: ENSG00000186468
ContextiHOP: RPS23
cancer metabolism search in PubMed: RPS23
UCL Cancer Institute: RPS23
Assigned class in ccmGDBC

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Phenotypic Information for RPS23(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS23
Familial Cancer Database: RPS23
* 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: RPS23
MedGen: RPS23 (Human Medical Genetics with Condition)
ClinVar: RPS23
PhenotypeMGI: RPS23 (International Mouse Phenotyping Consortium)
PhenomicDB: RPS23

Mutations for RPS23
* 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 RPS23 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI908980RPS231418858157351481574155RPS24189253107979996079800413
BQ222647RPS23149758157187981574158MRPL3048350529987907199879093
BM785206TUBA1C4389124965886749663672RPS2338345558157188381571955
AI889745NLGN4X144X61437206143763RPS233910858157187981571948
BF154662SNX19124611130750593130753340RPS2323838058157228081573597
CB217558MRPL30214329987907199879093RPS232934558157187981572337
CA429429RPS23138558157187981571951CCDC80835963112358666112359590
AI982804EFNA511375106713905106714041RPS2312448658157129581571656
H17554CUTA1117648656494866157RPS2310150558156996981570373

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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=1)
Stat. for Synonymous SNVs
(# total SNVs=10)
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
chr5:81573670-81573670p.G34G6
chr5:81573514-81573514p.K86K1
chr5:81573573-81573573p.A67T1
chr5:81573622-81573622p.R50R1
chr5:81574149-81574149p.A30A1
chr5:81572042-81572042p.G138G1
chr5:81572228-81572228p.N124H1
chr5:81572316-81572316p.P94P1

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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
# sample  15             2 1
# mutation  25             2 1
nonsynonymous SNV  14             1  
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
chr5:81572316p.P62P1
chr5:81573526p.I50I1
chr5:81573540p.H46Y1
chr5:81573560p.N39T1
chr5:81573573p.A35T1
chr5:81573578p.G33D1
chr5:81573622p.R18R1
chr5:81572042p.G106G1
chr5:81572249p.V85L1
chr5:81572269p.G78D1

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 RPS23 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 RPS23

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,HNRNPA1,NACA,RPL10,RPL10A,RPL11,RPL14,
RPL15,RPL26,RPL29,RPL31,RPL32,RPL34,RPL37A,
RPL6,RPL7A,RPS13,RPS14,RPS23,RPS4X,RPS8
EEF1B2,RPL10,RPL14,RPL22,RPL24,RPL30,RPL31,
RPL32,RPL35A,RPL37,RPL38,RPL41,RPL4,RPL5,
RPL6,RPS12,RPS23,RPS27A,RPS3A,RPS6,RPS7

BTF3,GNB2L1,RPL10A,RPL12,RPL14,RPL15,RPL29,
RPL31,RPL32,RPL35A,RPL36,RPL37,RPL37A,RPL5,
RPL7A,RPS13,RPS14,RPS23,RPS6,RPS8,RPS9
EEF1A1,RPL10,RPL12,RPL15,RPL19,RPL30,RPL32,
RPL35A,RPL3,RPL38,RPL41,RPL6,RPL7A,RPLP1,
RPS11,RPS12,RPS13,RPS23,RPS25,RPS3,RPS9
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 RPS23


There's no related Drug.
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Cross referenced IDs for RPS23
* 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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