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 RPS4X
Basic gene info.Gene symbolRPS4X
Gene nameribosomal protein S4, X-linked
SynonymsCCG2|DXS306|RPS4|S4|SCAR|SCR10
CytomapUCSC genome browser: Xq13.1
Genomic locationchrX :71492452-71497141
Type of geneprotein-coding
RefGenesNM_001007.4,
Ensembl idENSG00000198034
Description40S ribosomal protein S4, X isoformcell cycle gene 2ribosomal protein S4X isoformsingle copy abundant mRNA proteinsingle-copy abundant mRNA
Modification date20141207
dbXrefs MIM : 312760
HGNC : HGNC
HPRD : 02427
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS4X
BioGPS: 6191
Gene Expression Atlas: ENSG00000198034
The Human Protein Atlas: ENSG00000198034
PathwayNCI Pathway Interaction Database: RPS4X
KEGG: RPS4X
REACTOME: RPS4X
ConsensusPathDB
Pathway Commons: RPS4X
MetabolismMetaCyc: RPS4X
HUMANCyc: RPS4X
RegulationEnsembl's Regulation: ENSG00000198034
miRBase: chrX :71,492,452-71,497,141
TargetScan: NM_001007
cisRED: ENSG00000198034
ContextiHOP: RPS4X
cancer metabolism search in PubMed: RPS4X
UCL Cancer Institute: RPS4X
Assigned class in ccmGDBC

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Phenotypic Information for RPS4X(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS4X
Familial Cancer Database: RPS4X
* 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: RPS4X
MedGen: RPS4X (Human Medical Genetics with Condition)
ClinVar: RPS4X
PhenotypeMGI: RPS4X (International Mouse Phenotyping Consortium)
PhenomicDB: RPS4X

Mutations for RPS4X
* 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 RPS4X related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=1)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
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
chr23:71493138-71493138p.D212H1
chr23:71495495-71495495p.Y54C1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample22151   1  1       2
# mutation22151   1  1       2
nonsynonymous SNV12131      1        
synonymous SNV1  2    1          2
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:71493124p.P150P1
chrX:71495568p.L139M1
chrX:71493144p.K120N1
chrX:71496026p.I102M1
chrX:71493153p.E97E1
chrX:71496038p.Y54C1
chrX:71493721p.T33T1
chrX:71493733p.R30C1
chrX:71493768p.D21G1
chrX:71494903p.R255R1

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 RPS4X 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 RPS4X

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

GNB2L1,NACA,RPL10,RPL10A,RPL11,RPL12,RPL14,
RPL15,RPL17,RPL29,RPL31,RPL32,RPL34,RPL3,
RPL6,RPL7A,RPS14,RPS18,RPS23,RPS4X,RPS8
BTF3,CCT4,FBL,GNB2L1,RPL10A,RPL12,RPL14,
RPL22,RPL24,RPL32,RPL35A,RPL41,RPL5,RPL6,
RPS24,RPS27A,RPS3A,RPS4X,RPS6,RPS7,RPS8

EIF1AX,EIF2S3,FAM104B,IGBP1,NDUFB11,PQBP1,RBM3,
RBMX2,RPL10,RPL10A,RPL12,RPL32,RPL37,RPL5,
RPL7A,RPS23,RPS25,RPS4X,RPS8,SLC25A6,UXT
EEF1G,EIF1AX,EIF3H,GNB2L1,MACROD1,JPX,PNPLA4,
RPL10,RPL13,RPL13A,RPL14,RPL18,RPL30,RPL32,
RPL3,RPL36,RPL37A,RPL38,RPL7A,RPS12,RPS4X
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 RPS4X


There's no related Drug.
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Cross referenced IDs for RPS4X
* 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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