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 RPL4
Basic gene info.Gene symbolRPL4
Gene nameribosomal protein L4
SynonymsL4
CytomapUCSC genome browser: 15q22
Genomic locationchr15 :66791652-66797193
Type of geneprotein-coding
RefGenesNM_000968.3,
Ensembl idENSG00000174444
Description60S ribosomal protein L160S ribosomal protein L4
Modification date20141207
dbXrefs MIM : 180479
HGNC : HGNC
HPRD : 01607
ProteinUniProt: P36578
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL4
BioGPS: 6124
Gene Expression Atlas: ENSG00000174444
The Human Protein Atlas: ENSG00000174444
PathwayNCI Pathway Interaction Database: RPL4
KEGG: RPL4
REACTOME: RPL4
ConsensusPathDB
Pathway Commons: RPL4
MetabolismMetaCyc: RPL4
HUMANCyc: RPL4
RegulationEnsembl's Regulation: ENSG00000174444
miRBase: chr15 :66,791,652-66,797,193
TargetScan: NM_000968
cisRED: ENSG00000174444
ContextiHOP: RPL4
cancer metabolism search in PubMed: RPL4
UCL Cancer Institute: RPL4
Assigned class in ccmGDBB - This gene belongs to cancer gene.

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Phenotypic Information for RPL4(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL4
Familial Cancer Database: RPL4
* 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 180479; gene.
Orphanet
DiseaseKEGG Disease: RPL4
MedGen: RPL4 (Human Medical Genetics with Condition)
ClinVar: RPL4
PhenotypeMGI: RPL4 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL4

Mutations for RPL4
* 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 RPL4 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BU540332TMSB10416428513277885133222RPL4156284156679165866791786
DN601711RPL41366156679497166795836ACTN1363748146934517769347620
DA300676RPL4183156679516366795245LOC653739845797134832839134849481
DA783707RPL4197156679514966795245HS6ST397594139748748897487986
BG910912RPL41313156679539666797157OGFOD231482712123462872123463558
DB504144RPL42360156679539666797205LOC10050576136148010104215798104215917
DB575395RPL41222156679539666795810LOC10050576122347410104215798104216049
BU932269SPCS1312135274013552740253RPL4115652156679377266795784
AK290436TMTC312907128853607388589368RPL429003004156679166166791765
BC001010CDK4681772125814502958145120RPL47732172156679166666797165
AV754796RPL42799156679435266794428KRT22284284173881187038812069

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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=20)
Stat. for Synonymous SNVs
(# total SNVs=7)
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
chr15:66795439-66795439p.R80Q2
chr15:66794245-66794245p.R143C2
chr15:66795078-66795078p.G98E2
chr15:66791967-66791967p.A354A1
chr15:66795411-66795411p.Q89H1
chr15:66792697-66792697p.M284T1
chr15:66794220-66794220p.P151H1
chr15:66795413-66795413p.Q89E1
chr15:66792408-66792408p.R342C1
chr15:66793328-66793328p.Y264Y1

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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
# sample22 5  2 2 153   4215
# mutation22 5  2 2 153   4216
nonsynonymous SNV21 4  1 2 151   3 14
synonymous SNV 1 1  1     2   12 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
chr15:66791860p.R342C1
chr15:66793360p.K163N1
chr15:66795005p.R336C1
chr15:66792408p.P148S1
chr15:66793735p.P330Q1
chr15:66795006p.R143H1
chr15:66792426p.L322L1
chr15:66793741p.R143C1
chr15:66795050p.H310R1
chr15:66792443p.A135P1

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 RPL4 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 RPL4

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

ATP5G2,NACA,PFDN5,RPL10,RPL10A,RPL11,RPL13A,
RPL29,RPL31,RPL34,RPL36,RPL37A,RPL41,RPL7A,
RPLP0,RPS14,RPS23,RPS26,RPS29,RPS4X,RPS9
BTF3,CCT4,RPL14,RPL15,RPL23A,RPL24,RPL30,
RPL32,RPL35A,RPL37,RPL38,RPL41,RPL6,RPS11,
RPS15A,RPS24,RPS2,RPS29,RPS3A,RPS4X,RPS7

EEF1A1,EEF1A1P9,LRRC75A-AS1,PFDN5,RPL10A,RPL13A,RPL18A,
RPL36,RPL41,RPLP0,RPS11,RPS14,RPS16,RPS29,
RPS3,RPS3A,RPS5,RPS8,RPS9,RPSA,RPSAP58
C12orf57,DPY30,FAU,PFDN5,RPL15,RPL24,RPL27A,
RPL35,RPL35A,RPL41,RPL5,RPS11,RPS13,RPS18,
RPS3A,RPS5,RPS6,RPS7,RPSAP58,SNRPD2,SSR2
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 RPL4


There's no related Drug.
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Cross referenced IDs for RPL4
* 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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