Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

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	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 symbol	UBA52
	Gene name	ubiquitin A-52 residue ribosomal protein fusion product 1
	Synonyms	CEP52\|HUBCEP52\|L40\|RPL40
	Cytomap	UCSC genome browser: 19p13.1-p12
	Genomic location	chr19 :18682613-18688270
	Type of gene	protein-coding
	RefGenes	NM_001033930.1, NM_003333.3,
	Ensembl id	ENSG00000221983
	Description	60S ribosomal protein L40ubiquitin carboxyl extension protein 52ubiquitin-52 amino acid fusion proteinubiquitin-60S ribosomal protein L40ubiquitin-CEP52
	Modification date	20141207
dbXrefs	MIM : 191321
	HGNC : HGNC
	Ensembl : ENSG00000221983
	HPRD : 08931
	Vega : OTTHUMG00000183110
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_UBA52
	BioGPS: 7311
	Gene Expression Atlas: ENSG00000221983
	The Human Protein Atlas: ENSG00000221983
Pathway	NCI Pathway Interaction Database: UBA52
	KEGG: UBA52
	REACTOME: UBA52
	ConsensusPathDB
	Pathway Commons: UBA52
Metabolism	MetaCyc: UBA52
	HUMANCyc: UBA52
Regulation	Ensembl's Regulation: ENSG00000221983
	miRBase: chr19 :18,682,613-18,688,270
	TargetScan: NM_001033930
	cisRED: ENSG00000221983
Context	iHOP: UBA52
	cancer metabolism search in PubMed: UBA52
	UCL Cancer Institute: UBA52
Assigned class in ccmGDB	C

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Phenotypic Information for UBA52(metabolism pathway, cancer, disease, phenome)

Cancer 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/

Metabolic Pathway Description
REACTOME_METABOLISM_OF_PROTEINS REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM
Orphanet
Disease	KEGG Disease: UBA52
	MedGen: UBA52 (Human Medical Genetics with Condition)
	ClinVar: UBA52
Phenotype	MGI: UBA52 (International Mouse Phenotyping Consortium)
Phenotype	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.

Structural Variants in COSMIC : go to COSMIC mutation histogram

- Statistics for Tissue and Mutation type

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- 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'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	UBA52	chr19	18684123	18684143	ZNF653	chr19	11602199	11602219

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)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows UBA52 related fusion information.

ID	Head Gene						Tail Gene
Accession	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a	Gene_a	qStart_a	qEnd_a	Chromosome_a	tStart_a	tEnd_a
BE070452	UBA52	11	113	19	18684189	18684552	TM4SF1	105	409	3	149093262	149095258
CD250077	UBA52	23	400	19	18682671	18685916	LOC100129620	386	587	1	99473907	99474110
AA581992	PSMA7	1	180	20	60711790	60711972	UBA52	167	528	19	18682669	18685899
AA165052	RAPGEF5	1	30	7	22291385	22291414	UBA52	21	371	19	18684485	18686040
AA304512	UBA52	1	193	19	18684108	18684558	UBC	175	206	17	21731098	21731129
CD579874	UBA52	13	155	19	18685909	18686051	SMARCC1	153	229	3	47737252	47738023
AA329258	UBA52	1	378	19	18684206	18686037	DZIP1L	360	383	3	137795036	137795142
AA368309	UBA52	6	138	19	18682671	18684186	CSH1	138	260	17	61972973	61973188
N85706	UBA52	2	233	19	18682661	18684558	UBC	215	249	12	125397428	125397462
BQ016698	UBA52	19	334	19	18684523	18686042	NDE1	331	703	16	15797350	15797723
BF082819	UBA52	3	82	19	18685867	18685946	SPTAN1	67	478	9	131353865	131370253
BP212026	UBA52	30	409	19	18684102	18685944	SUGP2	407	583	19	19103413	19103589
BG482364	UBA52	4	122	19	18685733	18685935	VPS28	116	483	8	145649000	145649367
BC019044	UBA52	44	732	19	18684102	18686253	ACTG1	732	2486	17	79476997	79479810
AW270263	UBA52	6	76	19	18685884	18685954	UBA52	74	174	19	18685951	18686051

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

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Copy 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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SNV 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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Somatic 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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Top 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 position	Mutation(aa)	Unique sampleID count
chr19:18684529-18684529	p.R54H	1
chr19:18684563-18684563	p.?	1
chr19:18685701-18685701	p.L71S	1
chr19:18685735-18685735	p.L82L	1
chr19:18685757-18685757	p.N90Y	1
chr19:18684123-18684123	p.V5L	1
chr19:18685770-18685770	p.M94T	1
chr19:18684132-18684132	p.L8I	1
chr19:18685883-18685883	p.H104Y	1
chr19:18684188-18684188	p.V26V	1

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SNV 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 ID	1	2	3	4	5	6	7	8	9	10	11	12	13	14	15	16	17	18	19	20
# sample	1	1	1	3	2		1			1							1	1		1
# mutation	1	1	1	3	2		1			1							1	1		1
nonsynonymous SNV		1	1	3	2		1			1								1		1
synonymous SNV	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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Top 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 Position	Mutation(aa)	Unique sampleID count
chr19:18684505	p.L82L,UBA52	1
chr19:18684538	p.N90Y,UBA52	1
chr19:18685701	p.M94T,UBA52	1
chr19:18685735	p.H104Y,UBA52	1
chr19:18685757	p.V5L,UBA52	1
chr19:18684123	p.L8I,UBA52	1
chr19:18685770	p.I13V,UBA52	1
chr19:18684132	p.V26V,UBA52	1
chr19:18685883	p.I30F,UBA52	1
chr19:18684147	p.R42G,UBA52	1

Other 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

Copy 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

Gene 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.

Differential 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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CNV 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

Co-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

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

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Interacting 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