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 UBA52
Basic gene info.Gene symbolUBA52
Gene nameubiquitin A-52 residue ribosomal protein fusion product 1
SynonymsCEP52|HUBCEP52|L40|RPL40
CytomapUCSC genome browser: 19p13.1-p12
Genomic locationchr19 :18682613-18688270
Type of geneprotein-coding
RefGenesNM_001033930.1,
NM_003333.3,
Ensembl idENSG00000221983
Description60S ribosomal protein L40ubiquitin carboxyl extension protein 52ubiquitin-52 amino acid fusion proteinubiquitin-60S ribosomal protein L40ubiquitin-CEP52
Modification date20141207
dbXrefs MIM : 191321
HGNC : HGNC
Ensembl : ENSG00000221983
HPRD : 08931
Vega : OTTHUMG00000183110
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_UBA52
BioGPS: 7311
Gene Expression Atlas: ENSG00000221983
The Human Protein Atlas: ENSG00000221983
PathwayNCI Pathway Interaction Database: UBA52
KEGG: UBA52
REACTOME: UBA52
ConsensusPathDB
Pathway Commons: UBA52
MetabolismMetaCyc: UBA52
HUMANCyc: UBA52
RegulationEnsembl's Regulation: ENSG00000221983
miRBase: chr19 :18,682,613-18,688,270
TargetScan: NM_001033930
cisRED: ENSG00000221983
ContextiHOP: UBA52
cancer metabolism search in PubMed: UBA52
UCL Cancer Institute: UBA52
Assigned class in ccmGDBC

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Phenotypic Information for UBA52(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: UBA52
Familial Cancer Database: UBA52
* 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: UBA52
MedGen: UBA52 (Human Medical Genetics with Condition)
ClinVar: UBA52
PhenotypeMGI: UBA52 (International Mouse Phenotyping Consortium)
PhenomicDB: UBA52

Mutations for UBA52
* 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
There's no inter-chromosomal structural variation.
- 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
ovaryUBA52chr191868412318684143ZNF653chr191160219911602219
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 UBA52 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=1

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=10)
Stat. for Synonymous SNVs
(# total SNVs=0)
There's no s-snv.
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
chr19:18684563-18684563p.?1
chr19:18685701-18685701p.L71S1
chr19:18685735-18685735p.L82L1
chr19:18685757-18685757p.N90Y1
chr19:18684123-18684123p.V5L1
chr19:18685770-18685770p.M94T1
chr19:18684132-18684132p.L8I1
chr19:18685883-18685883p.H104Y1
chr19:18684188-18684188p.V26V1
chr19:18685938-18685938p.R122H1

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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
# sample11132 1  1      11 1
# mutation11132 1  1      11 1
nonsynonymous SNV 1132 1  1       1 1
synonymous SNV1               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
chr19:18684538p.N90Y,UBA521
chr19:18685701p.M94T,UBA521
chr19:18685735p.H104Y,UBA521
chr19:18685757p.V5L,UBA521
chr19:18684123p.L8I,UBA521
chr19:18685770p.I13V,UBA521
chr19:18684132p.V26V,UBA521
chr19:18685883p.I30F,UBA521
chr19:18684147p.R42G,UBA521
chr19:18684188p.A46V,UBA521

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 UBA52 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 UBA52

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

C19orf43,KXD1,C19orf53,CCDC124,COPE,DDX49,FKBP8,
LSM4,NDUFB7,RFXANK,RPL13,RPL18A,RPL35,RPL36,
RPL37A,RPLP2,RPS10,RPS19,TMEM161A,UBA52,USE1
C17orf49,C19orf43,WDR83OS,CSNK2B,EIF3F,EXOSC1,GABARAP,
MRPL43,MRPS21,NENF,PSMB4,RPL30,RPL32,RPL38,
RPS11,RPS16,RPS20,SF3B5,SNRPA,UBA52,UXT

C19orf43,C19orf53,C19orf70,COPE,EIF3G,GADD45GIP1,NDUFA11,
NDUFA13,NDUFB7,RPL36,RPLP0,RPLP2,RPS10,RPS11,
RPS13,RPS14,RPS15,RPS16,RPS9,UBA52,UQCR11
C17orf49,EEF1G,RPL13,RPL18,RPL18A,RPL19,RPL23A,
RPL28,RPL30,RPL32,RPL36,RPL37,RPL37A,RPL38,
RPL7A,RPL8,RPS15,RPS16,RPS19,RPS9,UBA52
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 UBA52


There's no related Drug.
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Cross referenced IDs for UBA52
* 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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