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 RPL5
Basic gene info.Gene symbolRPL5
Gene nameribosomal protein L5
SynonymsDBA6|L5|PPP1R135
CytomapUCSC genome browser: 1p22.1
Genomic locationchr1 :93297593-93307481
Type of geneprotein-coding
RefGenesNM_000969.3,
Ensembl idENSG00000122406
Description60S ribosomal protein L5protein phosphatase 1, regulatory subunit 135
Modification date20141222
dbXrefs MIM : 603634
HGNC : HGNC
Ensembl : ENSG00000122406
HPRD : 04699
Vega : OTTHUMG00000010899
ProteinUniProt: P46777
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL5
BioGPS: 6125
Gene Expression Atlas: ENSG00000122406
The Human Protein Atlas: ENSG00000122406
PathwayNCI Pathway Interaction Database: RPL5
KEGG: RPL5
REACTOME: RPL5
ConsensusPathDB
Pathway Commons: RPL5
MetabolismMetaCyc: RPL5
HUMANCyc: RPL5
RegulationEnsembl's Regulation: ENSG00000122406
miRBase: chr1 :93,297,593-93,307,481
TargetScan: NM_000969
cisRED: ENSG00000122406
ContextiHOP: RPL5
cancer metabolism search in PubMed: RPL5
UCL Cancer Institute: RPL5
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RPL5(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL5
Familial Cancer Database: RPL5
* 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 GBM 6,

Therapeutic Vulnerabilities in Cancer7

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,
6 http://www.sciencedirect.com/science/article/pii/S0092867413012087,
7Therapeutic 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 603634; gene.
612561; phenotype.
Orphanet 124; Blackfan-Diamond anemia.
DiseaseKEGG Disease: RPL5
MedGen: RPL5 (Human Medical Genetics with Condition)
ClinVar: RPL5
PhenotypeMGI: RPL5 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL5

Mutations for RPL5
* 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 RPL5 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI376067RPL5108019330740893307478WDR7672325154415833844158591
AI040133RPL5124419330611193307480MINK12353421747948104794917
EL584993FAM50A188212X153674180153674204RPL519464219329759493301795

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=34)
Stat. for Synonymous SNVs
(# total SNVs=3)
Stat. for Deletions
(# total SNVs=7)
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
chr1:93299194-93299197p.N57fs*123
chr1:93300390-93300390p.E82K2
chr1:93299188-93299188p.R54C2
chr1:93303161-93303161p.Y226H2
chr1:93301949-93301949p.S176fs*362
chr1:93298955-93298955p.K5*2
chr1:93301796-93301796p.V125A2
chr1:93298990-93298990p.Y16*2
chr1:93303104-93303104p.Y207H2
chr1:93306176-93306176p.K258N2

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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 42      12  141 8
# mutation 1 32      12  141 9
nonsynonymous SNV 1 32      12  131 7
synonymous SNV                1  2
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
chr1:93301796p.V125A2
chr1:93306176p.K258N2
chr1:93300451p.K164N1
chr1:93303108p.G169V1
chr1:93303111p.S176N1
chr1:93301883p.P181T1
chr1:93303151p.G182G1
chr1:93301914p.S185F1
chr1:93303161p.A205V1
chr1:93301928p.F3L1

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 RPL5 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 RPL5

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,EEF1G,RPL10A,RPL11,RPL17,RPL22,RPL27A,
RPL31,RPL32,RPL3,RPL4,RPL5,RPL6,RPS10,
RPS18,RPS25,RPS27A,RPS4X,RPS6,RPS7,RPS8
EEF1B2,GNB2L1,NACA,RPL10A,RPL12,RPL14,RPL22,
RPL24,RPL32,RPL35A,RPL37,RPL4,RPL5,RPL6,
RPS18,RPS27A,RPS3A,RPS4X,RPS6,RPS7,RPS8

DPH5,RPL10A,RPL12,RPL15,RPL24,RPL29,RPL32,
RPL36,RPL37A,RPL5,RPS10,RPS13,RPS14,RPS15A,
RPS18,RPS23,RPS29,RPS3,RPS6,RPS7,RPS8
BOD1,C12orf57,EEF1A1P9,MED28,PFDN5,RPL10A,RPL15,
RPL24,RPL35A,RPL41,RPL5,RPS11,RPS13,RPS3A,
RPS5,RPS6,RPS7,RPS8,RSL24D1,TIMM9,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 RPL5
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA34755; -.
Organism-specific databasesCTD 6125; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB03721ribosomal protein L5experimentalO-Sialic Acid
DB01033ribosomal protein L5approvedMercaptopurine
DB00563ribosomal protein L5approvedMethotrexate


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Cross referenced IDs for RPL5
* 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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