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 RPS21
Basic gene info.Gene symbolRPS21
Gene nameribosomal protein S21
SynonymsHLDF|S21
CytomapUCSC genome browser: 20q13.3
Genomic locationchr20 :60962120-60963576
Type of geneprotein-coding
RefGenesNM_001024.3,
Ensembl idENSG00000171858
Description40S ribosomal protein S218.2 kDa differentiation factorhuman leukemia differentiation factor
Modification date20141207
dbXrefs MIM : 180477
HGNC : HGNC
Ensembl : ENSG00000171858
HPRD : 01605
Vega : OTTHUMG00000032915
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS21
BioGPS: 6227
Gene Expression Atlas: ENSG00000171858
The Human Protein Atlas: ENSG00000171858
PathwayNCI Pathway Interaction Database: RPS21
KEGG: RPS21
REACTOME: RPS21
ConsensusPathDB
Pathway Commons: RPS21
MetabolismMetaCyc: RPS21
HUMANCyc: RPS21
RegulationEnsembl's Regulation: ENSG00000171858
miRBase: chr20 :60,962,120-60,963,576
TargetScan: NM_001024
cisRED: ENSG00000171858
ContextiHOP: RPS21
cancer metabolism search in PubMed: RPS21
UCL Cancer Institute: RPS21
Assigned class in ccmGDBC

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Phenotypic Information for RPS21(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS21
Familial Cancer Database: RPS21
* 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: RPS21
MedGen: RPS21 (Human Medical Genetics with Condition)
ClinVar: RPS21
PhenotypeMGI: RPS21 (International Mouse Phenotyping Consortium)
PhenomicDB: RPS21

Mutations for RPS21
* 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 RPS21 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AV751221RPS2117276206096266660963578XIST275412X7306952673069668
BC036946ANKRD52123464125663548956646649RPS2134563777206096237960963576
BP251502RPS211399206096211560963573LRBA3824034151616176151616197
AI275065RPS21397206096348260963576PIAS3933451145578462145578714

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    1      
GAIN (# sample)1         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=2

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=4)
Stat. for Synonymous SNVs
(# total SNVs=4)
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
chr20:60963374-60963374p.D66H1
chr20:60963378-60963395p.D67_L72delDSILRL1
chr20:60963388-60963388p.L70L1
chr20:60963410-60963410p.I78F1
chr20:60963412-60963412p.I78I1
chr20:60963413-60963413p.V79F1
chr20:60962424-60962424p.D10D1
chr20:60962678-60962678p.N21S1
chr20:60962688-60962688p.I24I1
chr20:60962906-60962906p.K41T1

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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     1      2
# mutation 1  1 1     1      2
nonsynonymous SNV    1 1     1      1
synonymous SNV 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
chr20:60963412p.K41T1
chr20:60962906p.D66H1
chr20:60963374p.L70L1
chr20:60963388p.D76N1
chr20:60963404p.I78F1
chr20:60963410p.I78I1

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 RPS21 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 RPS21

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

ADRM1,UQCC3,LSM7,MRPS26,NDUFA11,NDUFB7,POLR2I,
RPL13,RPL18A,RPL27A,RPL28,RPL35,RPL36,RPL37A,
RPLP2,RPS10,RPS19,RPS21,RPS9,SNRPD2,UBA52
RPL10,RPL13,RPL13A,RPL14,RPL18,RPL18A,RPL19,
RPL28,RPL29,RPL32,RPL35,RPL36,RPL37,RPS10,
RPS14,RPS16,RPS19,RPS21,RPS2,RPS8,RPSAP58

AHCY,ATP5E,ATP5J2,C11orf31,C8orf59,CHCHD2,COMMD7,
EEF1B2,MYEOV2,PDRG1,PFDN4,PSMA7,ROMO1,RPS10,
RPS14,RPS15A,RPS18,RPS21,RPS3,RPS7,UBL5
ABT1,EEF1B2,MRPL54,PHB2,RPL18A,RPL32,RPL35,
RPLP1,RPS10,RPS11,RPS13,RPS14,RPS18,RPS21,
RPS3,RPS3A,RPS5,RPS6,RPS8,SNRPD2,UXT
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 RPS21


There's no related Drug.
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Cross referenced IDs for RPS21
* 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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