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 RPL39
Basic gene info.Gene symbolRPL39
Gene nameribosomal protein L39
SynonymsL39|RPL39P42|RPL39_23_1806
CytomapUCSC genome browser: Xq24
Genomic locationchrX :118920468-118925606
Type of geneprotein-coding
RefGenesNM_001000.3,
Ensembl idENSG00000198918
Description60S ribosomal protein L39
Modification date20141222
dbXrefs MIM : 300899
HGNC : HGNC
Ensembl : ENSG00000198918
HPRD : 03546
Vega : OTTHUMG00000022278
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_RPL39
BioGPS: 6170
Gene Expression Atlas: ENSG00000198918
The Human Protein Atlas: ENSG00000198918
PathwayNCI Pathway Interaction Database: RPL39
KEGG: RPL39
REACTOME: RPL39
ConsensusPathDB
Pathway Commons: RPL39
MetabolismMetaCyc: RPL39
HUMANCyc: RPL39
RegulationEnsembl's Regulation: ENSG00000198918
miRBase: chrX :118,920,468-118,925,606
TargetScan: NM_001000
cisRED: ENSG00000198918
ContextiHOP: RPL39
cancer metabolism search in PubMed: RPL39
UCL Cancer Institute: RPL39
Assigned class in ccmGDBC

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Phenotypic Information for RPL39(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: RPL39
Familial Cancer Database: RPL39
* 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: RPL39
MedGen: RPL39 (Human Medical Genetics with Condition)
ClinVar: RPL39
PhenotypeMGI: RPL39 (International Mouse Phenotyping Consortium)
PhenomicDB: RPL39

Mutations for RPL39
* 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 RPL39 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BF848943FKTN53579108401945108402299RPL39350429X118920542118920621

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=6)
Stat. for Synonymous SNVs
(# total SNVs=3)
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
chr23:118923917-118923917p.R21C3
chr23:118923906-118923906p.P24P1
chr23:118923932-118923932p.K16E1
chr23:118923942-118923942p.F12F1
chr23:118923947-118923947p.R11R1
chr23:118920674-118920674p.H43Q1
chr23:118923897-118923897p.I27I1
chr23:118923899-118923899p.I27V1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample   4  1         2  6
# mutation   3  1         2  5
nonsynonymous SNV   2            1  3
synonymous SNV   1  1         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
chrX:118923917p.R21S4
chrX:118923897p.K16E1
chrX:118923899p.F12F1
chrX:118923906p.R11R1
chrX:118923932p.H43Q1
chrX:118923942p.R42R1
chrX:118923947p.M29I1
chrX:118920674p.I27I1
chrX:118920677p.I27V1
chrX:118923891p.P24P1

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 RPL39 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 RPL39

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

NDUFA1,RPL13,RPL14,RPL18,RPL24,RPL27A,RPL32,
RPL35,RPL35A,RPL37,RPL37A,RPL38,RPL39,RPLP1,
RPLP2,RPS11,RPS17,RPS18,RPS19,RPS2,RPS7
METTL23,C18orf21,CAMLG,COMMD6,DUT,EIF3M,EXOSC8,
LSM5,RPL15,RPL22L1,RPL23A,RPL30,RPL32,RPL34,
RPL39,RPS12,RPS13,RSL24D1,SNRPE,TIMM9,UXT

ATP5EP2,IGBP1P1,DUX4,HIST1H4K,LOC653544,FTX,PPIAL4G,
RPL13AP20,RPL13AP6,RPL21,RPL36A,RPL39,RPS26P11,RPSAP9,
TBC1D3P2,TPI1P3,Z
ACOT13,C2orf47,COX16,COX5A,DHRS7B,EAPP,H3F3A,
HSD17B8,MAT2B,RPL36,RPL37A,RPL39,RPLP2,RPS29,
SDHD,SFT2D1,TMEM179B,TMEM60,UQCRH,UQCRHL,UXT
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 RPL39


There's no related Drug.
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Cross referenced IDs for RPL39
* 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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