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 RPL21
Basic gene info.Gene symbolRPL21
Gene nameribosomal protein L21
SynonymsHYPT12|L21
CytomapUCSC genome browser: 13q12.2
Genomic locationchr13 :27825691-27830702
Type of geneprotein-coding
RefGenesNM_000982.3,
Ensembl idENSG00000122026
Description60S ribosomal protein L21
Modification date20141207
dbXrefs MIM : 603636
HGNC : HGNC
Ensembl : ENSG00000122026
HPRD : 04700
Vega : OTTHUMG00000016630
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL21
BioGPS: 6144
Gene Expression Atlas: ENSG00000122026
The Human Protein Atlas: ENSG00000122026
PathwayNCI Pathway Interaction Database: RPL21
KEGG: RPL21
REACTOME: RPL21
ConsensusPathDB
Pathway Commons: RPL21
MetabolismMetaCyc: RPL21
HUMANCyc: RPL21
RegulationEnsembl's Regulation: ENSG00000122026
miRBase: chr13 :27,825,691-27,830,702
TargetScan: NM_000982
cisRED: ENSG00000122026
ContextiHOP: RPL21
cancer metabolism search in PubMed: RPL21
UCL Cancer Institute: RPL21
Assigned class in ccmGDBC

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Phenotypic Information for RPL21(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL21
Familial Cancer Database: RPL21
* 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: RPL21
MedGen: RPL21 (Human Medical Genetics with Condition)
ClinVar: RPL21
PhenotypeMGI: RPL21 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL21

Mutations for RPL21
* 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 RPL21 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DA999428RPL21161132782920927829269ELF3625381201979753201981308
AW084964RPL21187132783061427830700AHNAK76531116229344562293899

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=10)
Stat. for Synonymous SNVs
(# total SNVs=6)
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
chr13:27830400-27830400p.R108S2
chr13:27828382-27828382p.M31I2
chr13:27828396-27828396p.K36T1
chr13:27830610-27830610p.N144T1
chr13:27829397-27829397p.K50Q1
chr13:27829453-27829453p.T68T1
chr13:27829489-27829489p.V80V1
chr13:27827946-27827946p.T11T1
chr13:27830354-27830354p.R92R1
chr13:27827958-27827958p.F15L1

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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   2    1       11 4
# mutation   2    1       11 4
nonsynonymous SNV   1    1       1  3
synonymous SNV   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
chr13:27830372p.H98H2
chr13:27830610p.F15L1
chr13:27827958p.V25A1
chr13:27828363p.Y30F1
chr13:27828378p.K50Q1
chr13:27829397p.R92R1
chr13:27830354p.R130C1
chr13:27830466p.N144T1

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 RPL21 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 RPL21

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

ATP5D,COMMD6,GLTSCR2,RPL11,RPL13,RPL13AP6,RPL18,
RPL21,RPL32,RPL35,RPL36,RPL37A,RPLP1,RPLP2,
RPS10,RPS15,RPS17,RPS19,RPS29,RPS9,RPSAP9
BTF3,ZFAS1,EPB41L4A-AS1,NME2P1,NOL7,RPL15,RPL19P12,
RPL21,RPL22,RPL23A,RPL24,RPL26,RPL30,RPL34,
RPL35A,RPL38,RPL41,RPS15A,RPS27A,RPS29,SLC35D2

ACTR3BP2,HSFX1,LCE2B,LOC728410,OR6N2,OR8B3,PPIAL4B,
PRAMEF17,PRAMEF3,RBMY1B,RPL21,RPS26P11,SNORA38,SNORD104,
SNORD16,SNORD35B,SNORD58C,SNORD62A,SNORD76,SNORD88B,SNORD88C
ANKRD19P,ANXA2P1,BCAS4,IGBP1P1,HMGN2P46,EDARADD,LOC100130331,
LOC100133957,LOC407835,LOC649330,LYPLA2P1,NACA2,NME2P1,PGAM4,
PIN1P1,POTEF,RPL13AP6,RPL19P12,RPL21,RPL31P11,UBE2NL
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 RPL21


There's no related Drug.
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Cross referenced IDs for RPL21
* 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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