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 RPS13
Basic gene info.Gene symbolRPS13
Gene nameribosomal protein S13
SynonymsS13
CytomapUCSC genome browser: 11p15
Genomic locationchr11 :17095938-17099220
Type of geneprotein-coding
RefGenesNM_001017.2,
Ensembl idENSG00000110700
Description40S ribosomal protein S13
Modification date20141207
dbXrefs MIM : 180476
HGNC : HGNC
Ensembl : ENSG00000110700
HPRD : 01604
Vega : OTTHUMG00000165988
ProteinUniProt: P62277
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS13
BioGPS: 6207
Gene Expression Atlas: ENSG00000110700
The Human Protein Atlas: ENSG00000110700
PathwayNCI Pathway Interaction Database: RPS13
KEGG: RPS13
REACTOME: RPS13
ConsensusPathDB
Pathway Commons: RPS13
MetabolismMetaCyc: RPS13
HUMANCyc: RPS13
RegulationEnsembl's Regulation: ENSG00000110700
miRBase: chr11 :17,095,938-17,099,220
TargetScan: NM_001017
cisRED: ENSG00000110700
ContextiHOP: RPS13
cancer metabolism search in PubMed: RPS13
UCL Cancer Institute: RPS13
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RPS13(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS13
Familial Cancer Database: RPS13
* 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 180476; gene.
Orphanet
DiseaseKEGG Disease: RPS13
MedGen: RPS13 (Human Medical Genetics with Condition)
ClinVar: RPS13
PhenotypeMGI: RPS13 (International Mouse Phenotyping Consortium)
PhenomicDB: RPS13

Mutations for RPS13
* 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 RPS13 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BQ324806RPS1312380111709665917099010HDGF3725541156713960156714142
BU935289SNRPD14404181919230719209056RPS13403576111709594417096746
BG110883ATXN7L3B1469127493280474933276RPS13461768111709665617098766
BU195584RPS1311440111709664917099201RPS13438788111709664417098793

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=11)
Stat. for Synonymous SNVs
(# total SNVs=3)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=2)
There's no deleted 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
chr11:17096743-17096743p.D108V3
chr11:17097027-17097027p.R99G3
chr11:17098745-17098745p.A41T1
chr11:17098755-17098755p.I37M1
chr11:17098784-17098784p.L28V1
chr11:17096717-17096718p.L117fs*141
chr11:17098982-17098982p.V22V1
chr11:17096718-17096719p.L117fs*141
chr11:17099016-17099016p.L11P1
chr11:17096727-17096727p.F113F1

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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=2

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample1  3  2 1       11 1
# mutation1  3  2 1       11 1
nonsynonymous SNV1  2  2 1       11 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
chr11:17099177p.R99Q1
chr11:17099182p.K70T1
chr11:17095985p.A41A1
chr11:17097026p.A41T1
chr11:17097113p.I37M1
chr11:17098743p.L28V1
chr11:17098745p.R19G1
chr11:17098755p.M4I1
chr11:17098784p.R3C1
chr11:17098993p.A151P1

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 RPS13 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 RPS13

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

EEF1B2,EIF3F,RPL10A,RPL11,RPL14,RPL17,RPL27A,
RPL31,RPL34,RPL37A,RPLP0,RPLP2,RPS13,RPS14,
RPS18,RPS23,RPS25,RPS27A,RPS29,RPS8,RPSAP58
BTF3,C18orf21,C8orf59,COMMD6,EIF3H,EIF3M,HINT1,
RPL15,RPL22,RPL30,RPL32,RPL34,RPL35A,RPL38,
RPL41,RPS13,RPS15A,RPS29,RPS3A,TIMM9,UXT

EEF1B2,RPL10A,RPL14,RPL29,RPL32,RPL35A,RPL36,
RPL37A,RPL38,RPLP2,RPS10,RPS11,RPS13,RPS14,
RPS15A,RPS18,RPS23,RPS25,RPS3,RPS6,RPS8
EEF1A1,EEF1B2,FAU,PFDN5,RPL15,RPL24,RPL27A,
RPL32,RPL35,RPL35A,RPL38,RPL41,RPL5,RPL7A,
RPS10,RPS11,RPS13,RPS3A,RPS5,RPS6,SNRPD2
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 RPS13


There's no related Drug.
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Cross referenced IDs for RPS13
* 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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