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 RPS24
Basic gene info.Gene symbolRPS24
Gene nameribosomal protein S24
SynonymsDBA3|S24
CytomapUCSC genome browser: 10q22
Genomic locationchr10 :79793517-79816571
Type of geneprotein-coding
RefGenesNM_001026.4,
NM_001142282.1,NM_001142283.1,NM_001142284.1,NM_001142285.1,
NM_033022.3,
Ensembl idENSG00000138326
Description40S ribosomal protein S24
Modification date20141219
dbXrefs MIM : 602412
HGNC : HGNC
Ensembl : ENSG00000138326
HPRD : 03877
Vega : OTTHUMG00000018549
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS24
BioGPS: 6229
Gene Expression Atlas: ENSG00000138326
The Human Protein Atlas: ENSG00000138326
PathwayNCI Pathway Interaction Database: RPS24
KEGG: RPS24
REACTOME: RPS24
ConsensusPathDB
Pathway Commons: RPS24
MetabolismMetaCyc: RPS24
HUMANCyc: RPS24
RegulationEnsembl's Regulation: ENSG00000138326
miRBase: chr10 :79,793,517-79,816,571
TargetScan: NM_001026
cisRED: ENSG00000138326
ContextiHOP: RPS24
cancer metabolism search in PubMed: RPS24
UCL Cancer Institute: RPS24
Assigned class in ccmGDBC

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Phenotypic Information for RPS24(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS24
Familial Cancer Database: RPS24
* 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: RPS24
MedGen: RPS24 (Human Medical Genetics with Condition)
ClinVar: RPS24
PhenotypeMGI: RPS24 (International Mouse Phenotyping Consortium)
PhenomicDB: RPS24

Mutations for RPS24
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
There's no inter-chromosomal structural variation.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasRPS24chr107980167279801692chr108361887883618898
pancreasRPS24chr107981614279816162RPS24chr107981619279816212
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPS24 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
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample1         1      
GAIN (# sample)          1      
LOSS (# sample)1                
cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=13)
Stat. for Synonymous SNVs
(# total SNVs=1)
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
chr10:79797001-79797001p.R110H3
chr10:79795125-79795125p.I7V2
chr10:79795362-79795362p.I55L1
chr10:79795386-79795386p.H63Y1
chr10:79795387-79795387p.H63R1
chr10:79795448-79795448p.K83K1
chr10:79796969-79796969p.K99K1
chr10:79793660-79793660p.M1L1
chr10:79796974-79796974p.K101R1
chr10:79795119-79795119p.V5I1

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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
# sample   1     1   1  12 3
# mutation   1     1   1  12 2
nonsynonymous SNV   1     1   1  11 2
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
chr10:79797001p.R110H,RPS242
chr10:79797042p.N124D,RPS241
chr10:79814360p.K154N1
chr10:79795119p.V5I,RPS241
chr10:79795304p.V35V,RPS241
chr10:79795312p.T38R,RPS241
chr10:79795386p.H63Y,RPS241
chr10:79796974p.K101R,RPS241

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 RPS24 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 RPS24

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

NACA,RPL11,RPL12,RPL24,RPL27A,RPL29,RPL31,
RPL32,RPL35A,RPL37,RPL38,RPL39,RPL6,RPL7A,
RPS11,RPS18,RPS19,RPS24,RPS2,RPS7,RPS8
BTF3,RPL12,RPL22,RPL24,RPL26,RPL27A,RPL30,
RPL32,RPL35A,RPL38,RPL41,RPL5,RPL6,RPS11,
RPS15A,RPS24,RPS25,RPS29,RPS3A,RPS4X,RPS7

NACA,RPL11,RPL12,RPL14,RPL26,RPL29,RPL31,
RPL32,RPL34,RPL35A,RPL37,RPL37A,RPL6,RPL7A,
RPS13,RPS18,RPS23,RPS24,RPS25,RPS27A,RPS6
C12orf57,EEF1A1P9,HSCB,MED28,RPL12,RPL15,RPL19,
RPL24,RPL32,RPL35A,RPL41,RPL5,RPL6,RPL7,
RPL7A,RPS11,RPS13,RPS24,RPS25,RPS6,ZNF22
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 RPS24


There's no related Drug.
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Cross referenced IDs for RPS24
* 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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