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 RPL8
Basic gene info.Gene symbolRPL8
Gene nameribosomal protein L8
SynonymsL8
CytomapUCSC genome browser: 8q24.3
Genomic locationchr8 :146015153-146017729
Type of geneprotein-coding
RefGenesNM_000973.3,
NM_033301.1,
Ensembl idENSG00000161016
Description60S ribosomal protein L8
Modification date20141207
dbXrefs MIM : 604177
HGNC : HGNC
Ensembl : ENSG00000161016
HPRD : 16044
Vega : OTTHUMG00000165249
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL8
BioGPS: 6132
Gene Expression Atlas: ENSG00000161016
The Human Protein Atlas: ENSG00000161016
PathwayNCI Pathway Interaction Database: RPL8
KEGG: RPL8
REACTOME: RPL8
ConsensusPathDB
Pathway Commons: RPL8
MetabolismMetaCyc: RPL8
HUMANCyc: RPL8
RegulationEnsembl's Regulation: ENSG00000161016
miRBase: chr8 :146,015,153-146,017,729
TargetScan: NM_000973
cisRED: ENSG00000161016
ContextiHOP: RPL8
cancer metabolism search in PubMed: RPL8
UCL Cancer Institute: RPL8
Assigned class in ccmGDBC

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Phenotypic Information for RPL8(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL8
Familial Cancer Database: RPL8
* 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: RPL8
MedGen: RPL8 (Human Medical Genetics with Condition)
ClinVar: RPL8
PhenotypeMGI: RPL8 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL8

Mutations for RPL8
* 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 RPL8 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
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=12

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=25)
Stat. for Synonymous SNVs
(# total SNVs=6)
Stat. for Deletions
(# total SNVs=0)
Stat. for Insertions
(# total SNVs=1)
There's no deleted 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
chr8:146016704-146016704p.G153S12
chr8:146015195-146015195p.E256D2
chr8:146016869-146016869p.I98V2
chr8:146015839-146015839p.G172G1
chr8:146017171-146017171p.Y89Y1
chr8:146015848-146015848p.V169V1
chr8:146017173-146017173p.Y89H1
chr8:146015194-146015194p.N257D1
chr8:146015856-146015856p.?1
chr8:146017189-146017189p.H83H1

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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  11 1 261 133 2
# mutation   2  11 1 261 144 2
nonsynonymous SNV   2   1 1 131 1 2 2
synonymous SNV      1    13   42  
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
chr8:146015195p.E256D,RPL82
chr8:146015800p.A185A,RPL81
chr8:146017270p.D176G,RPL81
chr8:146015828p.V169V,RPL81
chr8:146017419p.N162S,RPL81
chr8:146015194p.G131G,RPL81
chr8:146015848p.I112I,RPL81
chr8:146017431p.I98L,RPL81
chr8:146016676p.N257D,RPL81
chr8:146017507p.Y89H,RPL81

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 RPL8 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 RPL8

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

COMMD5,CYC1,CYHR1,EEF1D,EXOSC4,GLI4,HSF1,
MAF1,C8orf82,PUF60,PYCRL,RPL30,RPL36,RPL37A,
RPL8,RPS20,SHARPIN,SLC39A4,TIGD5,TOP1MT,VPS28
VPS51___IFT46,EEF1D,EIF3G,EXOSC5,FAU,GLTSCR2,RPL13,
RPL13A,RPL18,RPL19,RPL35,RPL3,RPL36,RPL7A,
RPL8,RPS15,RPS16,RPS3,RPS8,RPS9,SNRPD2

NDUFAF6,C8orf59,COMMD5,COPS5,CYC1,EEF1D,EIF3E,
EIF3H,MAF1,MED30,MRPS28,NDUFB9,PUF60,RPL30,
RPL35,RPL8,RPS20,TATDN1,WDYHV1,ZFAND1,ZNF16
PHB2,RPL18,RPL18A,RPL19,RPL29,RPL32,RPL35,
RPL7A,RPL8,RPLP0,RPLP1,RPS10,RPS11,RPS14,
RPS21,RPS3,RPS5,RPS6,RPS8,RPS9,RPSAP58
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 RPL8
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02494ribosomal protein L8experimentalAlpha-Hydroxy-Beta-Phenyl-Propionic Acid
DB07374ribosomal protein L8experimentalANISOMYCIN
DB08437ribosomal protein L8experimentalPUROMYCIN


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Cross referenced IDs for RPL8
* 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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