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 RPL13
Basic gene info.Gene symbolRPL13
Gene nameribosomal protein L13
SynonymsBBC1|D16S444E|D16S44E|L13
CytomapUCSC genome browser: 16q24.3|17p11.2
Genomic locationchr16 :89627064-89633237
Type of geneprotein-coding
RefGenesNM_000977.3,
NM_001243130.1,NM_001243131.1,NM_033251.2,
Ensembl idENSG00000167526
Description60S ribosomal protein L13OK/SW-cl.46breast basic conserved protein 1
Modification date20141207
dbXrefs MIM : 113703
HGNC : HGNC
Ensembl : ENSG00000167526
HPRD : 06428
Vega : OTTHUMG00000133770
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL13
BioGPS: 6137
Gene Expression Atlas: ENSG00000167526
The Human Protein Atlas: ENSG00000167526
PathwayNCI Pathway Interaction Database: RPL13
KEGG: RPL13
REACTOME: RPL13
ConsensusPathDB
Pathway Commons: RPL13
MetabolismMetaCyc: RPL13
HUMANCyc: RPL13
RegulationEnsembl's Regulation: ENSG00000167526
miRBase: chr16 :89,627,064-89,633,237
TargetScan: NM_000977
cisRED: ENSG00000167526
ContextiHOP: RPL13
cancer metabolism search in PubMed: RPL13
UCL Cancer Institute: RPL13
Assigned class in ccmGDBC

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Phenotypic Information for RPL13(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL13
Familial Cancer Database: RPL13
* 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: RPL13
MedGen: RPL13 (Human Medical Genetics with Condition)
ClinVar: RPL13
PhenotypeMGI: RPL13 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL13

Mutations for RPL13
* 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 RPL13 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BE933378CLPTM113315194549377045494627RPL13306467168962876689629419
AA063629RPL1323106168962940289629485MALAT199439116526766265268002
BG331404RPL13380802168962734689628148MASP17868053186994622186994641
DW426670ARID5B17154106385395463854091RPL13153281168962934089629468
DB231778RPL131274168962709089627753TNFRSF2127057464725416347277287
CR748210MALAT11341116526766265268002RPL13334417168962940289629485
DB270526RPL13168168962784189627908PTRF69543174057480040575274
AA524181RPL13257168962943189629486MAPKAPK35451735067780550683209
BE796741ENTPD1102125109748532397485346RPL13120751168962713789628145
DA534037DDX54366176250080262502397RPL13366540168963077889630952
BG423236AGRN2681991423991489RPL1361291168962876389629485
BC080536MRP637291371132175081621751651RPL1313722068168962710489629474

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=3

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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=1)
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
chr16:89627460-89627460p.R31R3
chr16:89628065-89628065p.S109F1
chr16:89628094-89628094p.E119K1
chr16:89628158-89628158p.S140Y1
chr16:89628749-89628749p.E143K1
chr16:89627425-89627425p.R20W1
chr16:89628774-89628774p.T151S1
chr16:89628779-89628779p.P153S1
chr16:89627471-89627471p.R35I1
chr16:89628795-89628795p.R158Q1

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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  1        1    2 1
# mutation1  1        1    2 1
nonsynonymous SNV1  1        1    1 1
synonymous SNV                 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
chr16:89628029p.S97Y,RPL131
chr16:89628037p.P100T,RPL131
chr16:89628749p.E143K,RPL131
chr16:89628783p.V154A,RPL131
chr16:89629420p.A202A,RPL131
chr16:89629441p.K209N,RPL131

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 RPL13 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 RPL13

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

GLTSCR2,RPL10,RPL10A,RPL11,RPL13A,RPL13AP20,RPL13AP3,
RPL18,RPL28,RPL29,RPL3,RPL37A,RPL7A,RPLP0,
RPS11,RPS14,RPS19,RPS23,RPS5,RPS8,RPS9
FBL,GNB2L1,RPL10,RPL10A,RPL13,RPL13A,RPL18,
RPL18A,RPL19,RPL29,RPL3,RPL36,RPL7A,RPL8,
RPS14,RPS19,RPS21,RPS2,RPS3,RPS5,RPS8

LRRC75A-AS1,RPL10A,RPL12,RPL13A,RPL13AP3,RPL18,RPL28,
RPL3,RPL41,RPL7A,RPLP0,RPS11,RPS15,RPS16,
RPS19,RPS3,RPS5,RPS8,RPS9,SNRPD2,ZNF581
ATP5G2,RPL10,RPL13A,RPL14,RPL18,RPL18A,RPL19,
RPL29,RPL32,RPL3,RPL36,RPL7A,RPL8,RPLP0,
RPLP1,RPS11,RPS12,RPS3,RPS5,RPS8,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 RPL13
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
DB01248ribosomal protein L13approved; investigationalDocetaxel
DB01041ribosomal protein L13approved; withdrawn; investigationalThalidomide


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Cross referenced IDs for RPL13
* 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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