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 RPL23A
Basic gene info.Gene symbolRPL23A
Gene nameribosomal protein L23a
SynonymsL23A|MDA20
CytomapUCSC genome browser: 17q11.2
Genomic locationchr17 :27046999-27051374
Type of geneprotein-coding
RefGenesNM_000984.5,
Ensembl idENSG00000198242
Description60S ribosomal protein L23amelanoma differentiation-associated gene 20
Modification date20141207
dbXrefs MIM : 602326
HGNC : HGNC
HPRD : 15998
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL23A
BioGPS: 6147
Gene Expression Atlas: ENSG00000198242
The Human Protein Atlas: ENSG00000198242
PathwayNCI Pathway Interaction Database: RPL23A
KEGG: RPL23A
REACTOME: RPL23A
ConsensusPathDB
Pathway Commons: RPL23A
MetabolismMetaCyc: RPL23A
HUMANCyc: RPL23A
RegulationEnsembl's Regulation: ENSG00000198242
miRBase: chr17 :27,046,999-27,051,374
TargetScan: NM_000984
cisRED: ENSG00000198242
ContextiHOP: RPL23A
cancer metabolism search in PubMed: RPL23A
UCL Cancer Institute: RPL23A
Assigned class in ccmGDBC

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Phenotypic Information for RPL23A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL23A
Familial Cancer Database: RPL23A
* 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: RPL23A
MedGen: RPL23A (Human Medical Genetics with Condition)
ClinVar: RPL23A
PhenotypeMGI: RPL23A (International Mouse Phenotyping Consortium)
PhenomicDB: RPL23A

Mutations for RPL23A
* 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 RPL23A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB117326RPL23A144172704759027047633UBC4563912125397790125399196
BP259075CMYA5146057903376279034220RPL23A452574172704786327049817
BG623888RPL23A154172705044927050502NAA15467014140278552140283091
BQ943640CCDC4386356174275637742761280RPL23A357743172704702427049913
AW090311RPL23A1561172705090827050954SPEF25348653565143035651862
BC007583TRBV20-1439851620120622014652RPL23A9851487172704772327050954

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=9)
Stat. for Synonymous SNVs
(# total SNVs=4)
Stat. for Deletions
(# total SNVs=2)
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
chr17:27047808-27047810p.K39delK2
chr17:27047880-27047880p.P61A1
chr17:27049755-27049755p.A75D1
chr17:27049769-27049770p.P80L1
chr17:27047044-27047044p.K7K1
chr17:27050593-27050593p.D131H1
chr17:27047724-27047724p.?1
chr17:27050601-27050601p.E133D1
chr17:27050606-27050606p.K135R1
chr17:27047813-27047813p.K38K1

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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
# sample1  2       311     3
# mutation1  2       311     3
nonsynonymous SNV1  1       2 1     3
synonymous SNV   1       11       
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
chr17:27050601p.Y144D1
chr17:27050613p.L147F1
chr17:27050632p.K38K1
chr17:27050643p.I40T1
chr17:27047813p.R41C1
chr17:27047818p.S43L1
chr17:27047820p.R47W1
chr17:27047827p.P49P1
chr17:27047838p.A75D1
chr17:27047846p.E133D1

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 RPL23A 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 RPL23A

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,ERAL1,FLOT2,IFT20,POLDIP2,RAB34,RPL13,
RPL18A,RPL23A,RPL32,RPL36,RPL41,RPL6,RPLP0,
RPS11,RPS5,SDF2,TLCD1,TMEM199,TRAF4,UBA52
BTF3,CCT4,EEF1A1,RPL10,RPL10A,RPL14,RPL22,
RPL23A,RPL24,RPL30,RPL31,RPL32,RPL34,RPL35A,
RPL37,RPL41,RPL6,RPS15A,RPS27A,RPS4X,RPS7

EEF1G,EIF1,NME2,RPL18A,RPL23,RPL23A,RPL27,
RPL28,RPL38,RPL39,RPL41,RPL7,RPLP0,RPS13,
RPS16,RPS2,RPS29,RPS3,RPS9,TMEM101,UBA52
EEF1A1,EEF1G,EIF3H,GNB2L1,RPL10,RPL13,RPL19,
RPL23A,RPL30,RPL32,RPL3,RPL36,RPL37,RPL37A,
RPL38,RPLP2,RPS12,RPS19,RPS23,RPS25,UBA52
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 RPL23A
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02494ribosomal protein L23aexperimentalAlpha-Hydroxy-Beta-Phenyl-Propionic Acid
DB07374ribosomal protein L23aexperimentalANISOMYCIN
DB08437ribosomal protein L23aexperimentalPUROMYCIN


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Cross referenced IDs for RPL23A
* 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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