Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

Home

Search

Download

 Statistics

Help

About Us

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 RPL13A
Basic gene info.Gene symbolRPL13A
Gene nameribosomal protein L13a
SynonymsL13A|TSTA1
CytomapUCSC genome browser: 19q13.3
Genomic locationchr19 :49990864-49995564
Type of geneprotein-coding
RefGenesNM_001270491.1,
NM_012423.3,NR_073024.1,
Ensembl idENSG00000142541
Description23 kDa highly basic protein60S ribosomal protein L13atissue specific transplantation antigen 1
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000142541
HPRD : 11775
Vega : OTTHUMG00000134289
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL13A
BioGPS: 23521
Gene Expression Atlas: ENSG00000142541
The Human Protein Atlas: ENSG00000142541
PathwayNCI Pathway Interaction Database: RPL13A
KEGG: RPL13A
REACTOME: RPL13A
ConsensusPathDB
Pathway Commons: RPL13A
MetabolismMetaCyc: RPL13A
HUMANCyc: RPL13A
RegulationEnsembl's Regulation: ENSG00000142541
miRBase: chr19 :49,990,864-49,995,564
TargetScan: NM_001270491
cisRED: ENSG00000142541
ContextiHOP: RPL13A
cancer metabolism search in PubMed: RPL13A
UCL Cancer Institute: RPL13A
Assigned class in ccmGDBC

Top
Phenotypic Information for RPL13A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL13A
Familial Cancer Database: RPL13A
* 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: RPL13A
MedGen: RPL13A (Human Medical Genetics with Condition)
ClinVar: RPL13A
PhenotypeMGI: RPL13A (International Mouse Phenotyping Consortium)
PhenomicDB: RPL13A

Mutations for RPL13A
* 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 RPL13A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
EC557264RPL13A168194999373849993805GTF2IP16212877460140474601470
BP333446RPL13A1251194999513549995386KAZN24326211530603415306053
BG255829BHLHE401348350246685025014RPL13A343638194999375849994768
AX747058ANKRD5212297125663633356645863RPL13A22942707194999380149995097
BM677070RPL13A12150194999542749995565ACTG1144683177947872379479353
BM723492RPL13A1101194999311749993526ARL6IP510124336915398969154131
X06537RPL13A1163194999514749995310LCAT1511447166797378667977957
BU683473RPL13A1669194999551249995565FZD7636842202902537202903164
BM838228RPL13A194194948755449492308ACTG194601178150997181512890

check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

Top
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.

Top
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

Top
check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=8)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=0)
There's no deleted snv.There's no inserted snv.

Top
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
chr19:49993823-49993823p.R82R2
chr19:49994304-49994304p.R117Q2
chr19:49995055-49995055p.H199Y2
chr19:49993501-49993501p.V34A1
chr19:49993780-49993780p.R68Q1
chr19:49995067-49995067p.V203L1
chr19:49993505-49993505p.V35V1
chr19:49993509-49993509p.R37G1
chr19:49994111-49994111p.P111L1
chr19:49993523-49993523p.I41M1

Top
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 32 1 1    2    42 4
# mutation 32 1 1    2    42 5
nonsynonymous SNV 32 1 1    1    22 1
synonymous SNV           1    2  4
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])

Top
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
chr19:49993501p.N4K,RPL13A1
chr19:49993803p.P15S,RPL13A1
chr19:49993505p.P50L,RPL13A1
chr19:49994111p.Y51Y,RPL13A1
chr19:49993509p.L19L1
chr19:49994115p.R56W,RPL13A1
chr19:49993523p.G30S1
chr19:49994303p.R56Q,RPL13A1
chr19:49993541p.V34A1
chr19:49994304p.L68L,RPL13A1

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 RPL13A 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]

Top
Gene Expression for RPL13A

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))
Top
check002.gifCNV vs Gene Expression Plot
* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types


Top
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

Top
check002.gifInteracting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top
Pharmacological Information for RPL13A
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 L13aexperimentalAlpha-Hydroxy-Beta-Phenyl-Propionic Acid
DB07374ribosomal protein L13aexperimentalANISOMYCIN
DB08437ribosomal protein L13aexperimentalPUROMYCIN


Top
Cross referenced IDs for RPL13A
* 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



Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @
Site Policies | State of Texas