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 RPS10
Basic gene info.Gene symbolRPS10
Gene nameribosomal protein S10
SynonymsDBA9|S10
CytomapUCSC genome browser: 6p21.31
Genomic locationchr6 :34385230-34393902
Type of geneprotein-coding
RefGenesNM_001014.4,
NM_001203245.2,NM_001204091.1,
Ensembl idENSG00000124614
Description40S ribosomal protein S10
Modification date20141219
dbXrefs MIM : 603632
HGNC : HGNC
Ensembl : ENSG00000124614
HPRD : 04697
Vega : OTTHUMG00000014546
ProteinUniProt: P46783
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS10
BioGPS: 6204
Gene Expression Atlas: ENSG00000124614
The Human Protein Atlas: ENSG00000124614
PathwayNCI Pathway Interaction Database: RPS10
KEGG: RPS10
REACTOME: RPS10
ConsensusPathDB
Pathway Commons: RPS10
MetabolismMetaCyc: RPS10
HUMANCyc: RPS10
RegulationEnsembl's Regulation: ENSG00000124614
miRBase: chr6 :34,385,230-34,393,902
TargetScan: NM_001014
cisRED: ENSG00000124614
ContextiHOP: RPS10
cancer metabolism search in PubMed: RPS10
UCL Cancer Institute: RPS10
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RPS10(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS10
Familial Cancer Database: RPS10
* 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 603632; gene.
613308; phenotype.
Orphanet 124; Blackfan-Diamond anemia.
DiseaseKEGG Disease: RPS10
MedGen: RPS10 (Human Medical Genetics with Condition)
ClinVar: RPS10
PhenotypeMGI: RPS10 (International Mouse Phenotyping Consortium)
PhenomicDB: RPS10

Mutations for RPS10
* 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 RPS10 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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=11)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr6:34392596-34392596p.V58M2
chr6:34392483-34392483p.R95R1
chr6:34392484-34392484p.R95H1
chr6:34392507-34392507p.P87P1
chr6:34385306-34385306p.G159R1
chr6:34392585-34392585p.Q61H1
chr6:34386164-34386164p.S146S1
chr6:34386188-34386188p.K138N1
chr6:34392873-34392873p.N42K1
chr6:34389502-34389502p.?1

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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=0

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample                    
# mutation                    
nonsynonymous SNV                    
synonymous SNV                    
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

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 RPS10 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 RPS10

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

RPL10A,RPL11,RPL13,RPL18,RPL18A,RPL27A,RPL32,
RPL35,RPL36,RPL37A,RPLP0,RPLP2,RPS10,RPS18,
RPS19,RPS27A,RPS8,RPS9,RPSA,RPSAP58,UBA52
RPL10,RPL10A,RPL13A,RPL14,RPL18,RPL29,RPL32,
RPL37,RPS10,RPS11,RPS12,RPS14,RPS16,RPS21,
RPS2,RPS3,RPS5,RPS6,RPS7,RPS8,RPSAP58

EEF1B2,RPL10A,RPL27,RPL32,RPL35,RPL35A,RPL36,
RPL7A,RPS10,RPS13,RPS14,RPS15A,RPS16,RPS18,
RPS29,RPS3,RPS6,RPS7,RPS8,RPS9,RPSAP58
EEF1B2,RPL24,RPL27A,RPL32,RPL35,RPL35A,RPL41,
RPS10,RPS11,RPS13,RPS14,RPS18,RPS21,RPS3,
RPS3A,RPS5,RPS6,RPS7,RPS8,SNRPD2,TPT1
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 RPS10


There's no related Drug.
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Cross referenced IDs for RPS10
* 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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