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 RPL27
Basic gene info.Gene symbolRPL27
Gene nameribosomal protein L27
SynonymsL27
CytomapUCSC genome browser: 17q21
Genomic locationchr17 :41150445-41154971
Type of geneprotein-coding
RefGenesNM_000988.3,
Ensembl idENSG00000131469
Description60S ribosomal protein L27
Modification date20141207
dbXrefs MIM : 607526
HGNC : HGNC
Ensembl : ENSG00000131469
HPRD : 09602
Vega : OTTHUMG00000180660
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL27
BioGPS: 6155
Gene Expression Atlas: ENSG00000131469
The Human Protein Atlas: ENSG00000131469
PathwayNCI Pathway Interaction Database: RPL27
KEGG: RPL27
REACTOME: RPL27
ConsensusPathDB
Pathway Commons: RPL27
MetabolismMetaCyc: RPL27
HUMANCyc: RPL27
RegulationEnsembl's Regulation: ENSG00000131469
miRBase: chr17 :41,150,445-41,154,971
TargetScan: NM_000988
cisRED: ENSG00000131469
ContextiHOP: RPL27
cancer metabolism search in PubMed: RPL27
UCL Cancer Institute: RPL27
Assigned class in ccmGDBC

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Phenotypic Information for RPL27(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL27
Familial Cancer Database: RPL27
* 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: RPL27
MedGen: RPL27 (Human Medical Genetics with Condition)
ClinVar: RPL27
PhenotypeMGI: RPL27 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL27

Mutations for RPL27
* 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 RPL27 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
EC440105RPL27148174115080141150848NME24496174924560849245660
EC572330RPL27551174115080241150848NME24799174924560849245660
DB013482RPL271450174115045241154938KRT13451576173966173939661864
EC578828RPL27149174115080041150848CASP12375811104761981104762002
BU674462RPL278456174115076941154976C1orf21045364014374791243748098
AA503644OXA1L1273142324071423240992RPL27272485174115076041152074
CV327307RPL271339174115076041154769RASIP1334401194922815249228219
CV327308RPL271339174115076041154769RASIP1334401194922815249228219
BC021886RPL27170174115490641154975RPL2766482174115080141154976
CV327306RPL271339174115076041154769RASIP1334542194922815249230303
BU685466RPL27169174115491341155331RPL2765393174115194841154934
T59674RPS6115091937625319376507RPL27150432174115047241152121
FJ655906RPL2711345174115076041154765NME2345395174924888249248932

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=8)
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
chr17:41152038-41152038p.M57K2
chr17:41152077-41152077p.S70F1
chr17:41152095-41152095p.N76S1
chr17:41154694-41154694p.S86T1
chr17:41154751-41154751p.A105S1
chr17:41154776-41154776p.E113G1
chr17:41151963-41151963p.G32D1
chr17:41154798-41154798p.E120D1
chr17:41151974-41151974p.R36C1
chr17:41151975-41151975p.R36H1

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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  11    2       3  2
# mutation  11    2       3  2
nonsynonymous SNV  11    2       3  2
synonymous SNV                    
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
chr17:41152038p.M57T2
chr17:41154694p.E120D1
chr17:41154751p.R36C1
chr17:41154776p.R36H1
chr17:41154798p.S70F1
chr17:41151974p.S86T1
chr17:41151975p.A105S1
chr17:41152077p.E113G1

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 RPL27 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 RPL27

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

EIF3F,RPL11,RPL13,RPL14,RPL18,RPL24,RPL27A,
RPL31,RPL32,RPL36,RPL37,RPL37A,RPLP2,RPS10,
RPS11,RPS13,RPS18,RPS19,RPS2,RPS8,RPS9
NME2,PFDN5,RPL10,RPL11,RPL12,RPL13,RPL18,
RPL24,RPL27A,RPL36,RPL38,RPL7A,RPL8,RPLP1,
RPS11,RPS14,RPS24,RPS3,RPS8,SNRPD2,SNRPF

AKIP1,LCN15,RPL14,RPL24,RPL27A,RPL29,RPL32,
RPL35A,RPL7A,RPS11,RPS13,RPS14,RPS15A,RPS18,
RPS25,RPS3,RPS9,RPSA,RPSAP58,TMEM9B,TSSC4
TMEM261,DPY30,EEF1B2,HSCB,LSM2,RPL24,RPL27A,
RPL35,RPL35A,RPL41,RPS10,RPS11,RPS13,RPS14,
RPS18,RPS3A,RPS5,RPS6,RPS7,RPS8,SNRPD2
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 RPL27


There's no related Drug.
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Cross referenced IDs for RPL27
* 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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