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 RPL34
Basic gene info.Gene symbolRPL34
Gene nameribosomal protein L34
SynonymsL34
CytomapUCSC genome browser: 4q25
Genomic locationchr4 :109541748-109551639
Type of geneprotein-coding
RefGenesNM_000995.3,
NM_033625.2,
Ensembl idENSG00000109475
Description60S ribosomal protein L34leukemia-associated protein
Modification date20141207
dbXrefs HGNC : HGNC
Ensembl : ENSG00000109475
HPRD : 17996
Vega : OTTHUMG00000131839
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL34
BioGPS: 6164
Gene Expression Atlas: ENSG00000109475
The Human Protein Atlas: ENSG00000109475
PathwayNCI Pathway Interaction Database: RPL34
KEGG: RPL34
REACTOME: RPL34
ConsensusPathDB
Pathway Commons: RPL34
MetabolismMetaCyc: RPL34
HUMANCyc: RPL34
RegulationEnsembl's Regulation: ENSG00000109475
miRBase: chr4 :109,541,748-109,551,639
TargetScan: NM_000995
cisRED: ENSG00000109475
ContextiHOP: RPL34
cancer metabolism search in PubMed: RPL34
UCL Cancer Institute: RPL34
Assigned class in ccmGDBC

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Phenotypic Information for RPL34(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL34
Familial Cancer Database: RPL34
* 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: RPL34
MedGen: RPL34 (Human Medical Genetics with Condition)
ClinVar: RPL34
PhenotypeMGI: RPL34 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL34

Mutations for RPL34
* 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

- Statistics for Tissue and Mutation typeTop
- For Inter-chromosomal Variations
* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.
- For Intra-chromosomal Variations
* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryRPL34chr4109548351109548371LOC285456chr4109535847109535867
pancreasRPL34chr4109544589109544609PKHD1L1chr8110515488110515508
cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows RPL34 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BM810873TP53INP210573203329711333298208RPL345696494109543688109543767
AA954224RPL3431614109543745109546412IQCJ1491683158826972158826991
BF697308INS-IGF214901121532792153766RPL344805364109546339109546396
AI624448RPL3411094109546303109546411NEK7934031198290707198291019
AU126976RPL3411664109541733109543328PCCB1665703135969191135975471

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=7)
Stat. for Synonymous SNVs
(# total SNVs=2)
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
chr4:109543718-109543718p.K71N1
chr4:109543723-109543723p.H73R1
chr4:109546291-109546291p.R93C1
chr4:109546299-109546299p.F95F1
chr4:109546339-109546339p.A109T1
chr4:109543139-109543139p.R8R1
chr4:109546364-109546364p.K117I1
chr4:109543317-109543317p.A41V1
chr4:109543328-109543328p.A45T1
chr4:109543342-109543342p.C49C1

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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
# sample   1    2   1   11 1
# mutation   1    2   1   11 1
nonsynonymous SNV   1    1        1 1
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
chr4:109546339p.A45T,RPL341
chr4:109543328p.C49C,RPL341
chr4:109543342p.G55G,RPL341
chr4:109543360p.H73R,RPL341
chr4:109543723p.R93C,RPL341
chr4:109546291p.F95F,RPL341
chr4:109546299p.A109T,RPL341

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 RPL34 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 RPL34

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

NACA,RPL11,RPL12,RPL14,RPL18,RPL24,RPL27A,
RPL29,RPL31,RPL32,RPL34,RPL37,RPL37A,RPL6,
RPLP2,RPS11,RPS14,RPS23,RPS4X,RPS8,RPS9
BTF3,CCT4,EIF3M,RPL15,RPL22,RPL23A,RPL24,
RPL30,RPL32,RPL34,RPL35A,RPL41,RPS13,RPS15A,
RPS27A,RPS29,RPS3A,RPS4X,RPS6,RPS7,UXT

RPL10A,RPL12,RPL14,RPL24,RPL29,RPL31,RPL32,
RPL34,RPL35A,RPL3,RPL36,RPL37,RPL37A,RPL5,
RPL7A,RPS11,RPS13,RPS23,RPS25,RPS2,RPS8
BOD1,DPH5,EEF1A1,EIF3E,RPL15,RPL24,RPL26,
RPL34,RPL35A,RPL5,RPS12,RPS13,RPS15A,RPS25,
RPS3A,RPS6,RPS8,TATDN1,TIMM9,TMEM182,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 RPL34


There's no related Drug.
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Cross referenced IDs for RPL34
* 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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