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 RPS27A
Basic gene info.Gene symbolRPS27A
Gene nameribosomal protein S27a
SynonymsCEP80|HEL112|S27A|UBA80|UBC|UBCEP1|UBCEP80
CytomapUCSC genome browser: 2p16
Genomic locationchr2 :55459813-55462989
Type of geneprotein-coding
RefGenesNM_001135592.2,
NM_001177413.1,NM_002954.5,
Ensembl idENSG00000143947
Description40S ribosomal protein S27aepididymis luminal protein 112ubiquitin Cubiquitin and ribosomal protein S27aubiquitin carboxyl extension protein 80ubiquitin-40S ribosomal protein S27aubiquitin-CEP80
Modification date20141207
dbXrefs MIM : 191343
HGNC : HGNC
Ensembl : ENSG00000143947
HPRD : 01878
Vega : OTTHUMG00000151919
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPS27A
BioGPS: 6233
Gene Expression Atlas: ENSG00000143947
The Human Protein Atlas: ENSG00000143947
PathwayNCI Pathway Interaction Database: RPS27A
KEGG: RPS27A
REACTOME: RPS27A
ConsensusPathDB
Pathway Commons: RPS27A
MetabolismMetaCyc: RPS27A
HUMANCyc: RPS27A
RegulationEnsembl's Regulation: ENSG00000143947
miRBase: chr2 :55,459,813-55,462,989
TargetScan: NM_001135592
cisRED: ENSG00000143947
ContextiHOP: RPS27A
cancer metabolism search in PubMed: RPS27A
UCL Cancer Institute: RPS27A
Assigned class in ccmGDBC

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Phenotypic Information for RPS27A(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPS27A
Familial Cancer Database: RPS27A
* 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: RPS27A
MedGen: RPS27A (Human Medical Genetics with Condition)
ClinVar: RPS27A
PhenotypeMGI: RPS27A (International Mouse Phenotyping Consortium)
PhenomicDB: RPS27A

Mutations for RPS27A
* 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 RPS27A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF375146RPS27A917525546199855462629LIPH1684993185232431185232763
DA583490TOX41103142194636321946465RPS27A10054525546097355461418
BM312306RPS27A2419325546257455462743UBE3C1893587156985035156985204

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 # sample        1        
GAIN (# sample)        1        
LOSS (# sample)                 
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=7)
Stat. for Synonymous SNVs
(# total SNVs=3)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=1)

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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
chr2:55459972-55459972p.F4F1
chr2:55462079-55462079p.A101D1
chr2:55459989-55459989p.G10E1
chr2:55462090-55462090p.Y105H1
chr2:55460516-55460516p.T22T1
chr2:55462091-55462091p.Y105F1
chr2:55461266-55461267p.P38_D39insG1
chr2:55462094-55462094p.Y106C1
chr2:55461267-55461268p.D39>ES1
chr2:55462554-55462554p.?1

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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
# sample1 1   2 1    11 11 3
# mutation1 1   2 1    11 11 4
nonsynonymous SNV1     1 1    11 11 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
chr2:55459972p.G10E,RPS27A1
chr2:55462091p.S20W,RPS27A1
chr2:55459989p.T22T,RPS27A1
chr2:55462577p.A46V,RPS27A1
chr2:55460509p.Y59C,RPS27A1
chr2:55460516p.L67V,RPS27A1
chr2:55461288p.K94K,RPS27A1
chr2:55461327p.K97N,RPS27A1
chr2:55461976p.L103M,RPS27A1
chr2:55462059p.Y105H,RPS27A1

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 RPS27A 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 RPS27A

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

EEF1B2,RPL10A,RPL11,RPL17,RPL27A,RPL31,RPL35A,
RPL36,RPL37,RPL37A,RPL5,RPLP2,RPS10,RPS13,
RPS17,RPS18,RPS19,RPS27A,RPS7,RPS8,RPSAP58
BTF3,RPL10,RPL14,RPL15,RPL22,RPL23A,RPL24,
RPL31,RPL32,RPL34,RPL35A,RPL37,RPL5,RPL6,
RPS12,RPS23,RPS27A,RPS3A,RPS4X,RPS6,RPS7

EEF1B2,OLA1,RPL10A,RPL12,RPL14,RPL31,RPL35A,
RPL37,RPL37A,RPL6,RPL7A,RPS12,RPS13,RPS17,
RPS18,RPS23,RPS24,RPS25,RPS27A,RPS6,RPS7
ALKBH2,EEF1A1,FAU,PFDN5,RPL15,RPL17,RPL24,
RPL27,RPL31,RPL34,RPL35A,RPL38,RPL41,RPL5,
RPS13,RPS20,RPS23,RPS24,RPS25,RPS27A,ZFAND1
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 RPS27A


There's no related Drug.
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Cross referenced IDs for RPS27A
* 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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