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 RPL10
Basic gene info.Gene symbolRPL10
Gene nameribosomal protein L10
SynonymsAUTSX5|DXS648|DXS648E|L10|NOV|QM
CytomapUCSC genome browser: Xq28
Genomic locationchrX :153626570-153630680
Type of geneprotein-coding
RefGenesNM_001256577.1,
NM_001256580.1,NM_006013.3,
Ensembl idENSG00000268963
Description60S ribosomal protein L10Wilms tumor-related proteinlaminin receptor homologtumor suppressor QM
Modification date20141219
dbXrefs MIM : 312173
HGNC : HGNC
Ensembl : ENSG00000147403
HPRD : 02421
Vega : OTTHUMG00000033189
ProteinUniProt: P27635
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL10
BioGPS: 6134
Gene Expression Atlas: ENSG00000268963
The Human Protein Atlas: ENSG00000268963
PathwayNCI Pathway Interaction Database: RPL10
KEGG: RPL10
REACTOME: RPL10
ConsensusPathDB
Pathway Commons: RPL10
MetabolismMetaCyc: RPL10
HUMANCyc: RPL10
RegulationEnsembl's Regulation: ENSG00000268963
miRBase: chrX :153,626,570-153,630,680
TargetScan: NM_001256577
cisRED: ENSG00000268963
ContextiHOP: RPL10
cancer metabolism search in PubMed: RPL10
UCL Cancer Institute: RPL10
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RPL10(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL10
Familial Cancer Database: RPL10
* 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 300847; phenotype.
312173; gene.
Orphanet 106; Autism.
DiseaseKEGG Disease: RPL10
MedGen: RPL10 (Human Medical Genetics with Condition)
ClinVar: RPL10
PhenotypeMGI: RPL10 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL10

Mutations for RPL10
* 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 RPL10 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI698719RPL103379X153629208153629254MLL270436124943518749435977
CB162793CYB5A1305187192078971928412RPL10301555X153630508153630762
DW421192RPL1068232X153627678153627842POLA1231298X2480674724806814
CB164490CYB5A1305187192078971928412RPL10301592X153630471153630762
AW581181RPL1013247X153628766153629004RNF213234295177831897178319032
BQ771607RPL101872X153629200153629254CSNK2A267548165819556158196042
BC015618RPL1044549X153628152153629254POLA25503007116502945165065088
AA813916RPL1055107X153629200153629254SCLY922412239007418239007567
AI499133RPL102781X153629200153629254IQGAP27146457571562975716022

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=18)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr23:153627713-153627713p.S20P2
chr23:153628932-153628932p.R153C2
chr23:153626863-153626863p.M1I1
chr23:153629057-153629057p.K169N1
chr23:153627911-153627911p.E56K1
chr23:153628824-153628824p.G117S1
chr23:153626864-153626864p.G2S1
chr23:153629100-153629100p.M184L1
chr23:153628162-153628162p.I70T1
chr23:153628830-153628830p.F119L1

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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
# sample22131 2  1 32   45 5
# mutation22131 2  1 32   45 7
nonsynonymous SNV21131 2  1 2    35 4
synonymous SNV 1         12   1  3
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
chrX:153629109p.E151K,RPL102
chrX:153628932p.R117C,RPL102
chrX:153626864p.G2S,RPL101
chrX:153629057p.L55F,RPL101
chrX:153627882p.R115I,RPL101
chrX:153628874p.A6T,RPL101
chrX:153626876p.P57P,RPL101
chrX:153627911p.R7S,RPL101
chrX:153628886p.I63T,RPL101
chrX:153626879p.P16L,RPL101

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 RPL10 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 RPL10

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

EEF1A1P9,EEF1B2,GNB2L1,RPL10,RPL10A,RPL11,RPL13A,
RPL17,RPL31,RPL3,RPL37A,RPL41,RPL6,RPL7A,
RPS10,RPS14,RPS18,RPS23,RPS4X,RPS8,RPS9
EEF1B2,EEF1G,FBL,GNB2L1,RPL10,RPL10A,RPL12,
RPL14,RPL5,RPL6,RPL7A,RPLP0,RPS14,RPS18,
RPS2,RPS3,RPS4X,RPS5,RPS6,RPS8,RPSAP58

EEF1A1,EEF1B2,RPL10A,RPL12,RPL15,RPL32,RPL36,
RPL5,RPL7A,RPS10,RPS11,RPS14,RPS15A,RPS18,
RPS23,RPS29,RPS3,RPS3A,RPS6,RPS8,RPS9
BOD1,C12orf57,DPH5,EEF1A1P9,RPL10,RPL10A,RPL15,
RPL24,RPL29,RPL32,RPL35A,RPL41,RPL5,RPL7A,
RPS11,RPS13,RPS14,RPS3A,RPS5,RPS6,RPS8
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 RPL10


There's no related Drug.
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Cross referenced IDs for RPL10
* 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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