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 RPL10A
Basic gene info.Gene symbolRPL10A
Gene nameribosomal protein L10a
SynonymsCSA19|Csa-19|L10A|NEDD6
CytomapUCSC genome browser: 6p21.31
Genomic locationchr6 :35436177-35438558
Type of geneprotein-coding
RefGenesNM_007104.4,
Ensembl idENSG00000198755
Description60S ribosomal protein L10aNEDD-6neural precursor cell expressed developmentally down-regulated protein 6
Modification date20141207
dbXrefs MIM : 615660
HGNC : HGNC
Ensembl : ENSG00000198755
HPRD : 10199
Vega : OTTHUMG00000014566
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL10A
BioGPS: 4736
Gene Expression Atlas: ENSG00000198755
The Human Protein Atlas: ENSG00000198755
PathwayNCI Pathway Interaction Database: RPL10A
KEGG: RPL10A
REACTOME: RPL10A
ConsensusPathDB
Pathway Commons: RPL10A
MetabolismMetaCyc: RPL10A
HUMANCyc: RPL10A
RegulationEnsembl's Regulation: ENSG00000198755
miRBase: chr6 :35,436,177-35,438,558
TargetScan: NM_007104
cisRED: ENSG00000198755
ContextiHOP: RPL10A
cancer metabolism search in PubMed: RPL10A
UCL Cancer Institute: RPL10A
Assigned class in ccmGDBC

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Phenotypic Information for RPL10A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL10A
Familial Cancer Database: RPL10A
* 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: RPL10A
MedGen: RPL10A (Human Medical Genetics with Condition)
ClinVar: RPL10A
PhenotypeMGI: RPL10A (International Mouse Phenotyping Consortium)
PhenomicDB: RPL10A

Mutations for RPL10A
* 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 RPL10A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA314410RPL10A514663543618135436754DPP91455701947141424723759

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=8)
Stat. for Synonymous SNVs
(# total SNVs=5)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr6:35436793-35436793p.S50S2
chr6:35438059-35438059p.L138L2
chr6:35436736-35436736p.T31T1
chr6:35438370-35438370p.A166V1
chr6:35436753-35436753p.S37T1
chr6:35438392-35438392p.K173N1
chr6:35436757-35436757p.L38F1
chr6:35438423-35438423p.H184Y1
chr6:35438486-35438486p.Y205D1
chr6:35437187-35437187p.S64Y1

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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
# sample11 2  2  1 1 1 1  12
# mutation11 2  2  1 1 1 1  12
nonsynonymous SNV1  2         1 1  11
synonymous SNV 1    2  1 1       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
chr6:35436736p.T31T2
chr6:35436757p.P135L1
chr6:35437209p.L138F1
chr6:35438049p.L138L1
chr6:35438057p.A166V1
chr6:35438059p.K173N1
chr6:35438370p.H184Y1
chr6:35438392p.L216L1
chr6:35438423p.M1V1
chr6:35436212p.R7R1

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 RPL10A 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 RPL10A

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 RPL10A


There's no related Drug.
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Cross referenced IDs for RPL10A
* 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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