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 PSMB5

Basic gene info.	Gene symbol	PSMB5
	Gene name	proteasome (prosome, macropain) subunit, beta type, 5
	Synonyms	LMPX\|MB1\|X
	Cytomap	UCSC genome browser: 14q11.2
	Genomic location	chr14 :23495059-23504429
	Type of gene	protein-coding
	RefGenes	NM_001130725.1, NM_001144932.2,NM_002797.4,
	Ensembl id	ENSG00000100804
	Description	PSX large multifunctional protease Xmacropain epsilon chainmulticatalytic endopeptidase complex epsilon chainproteasome beta 5 subunitproteasome catalytic subunit 3proteasome chain 6proteasome epsilon chainproteasome subunit MB1proteasome subunit
	Modification date	20141207
dbXrefs	MIM : 600306
	HGNC : HGNC
	Ensembl : ENSG00000100804
	HPRD : 02629
	Vega : OTTHUMG00000028713
Protein	UniProt: P28074 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMB5
	BioGPS: 5693
	Gene Expression Atlas: ENSG00000100804
	The Human Protein Atlas: ENSG00000100804
Pathway	NCI Pathway Interaction Database: PSMB5
	KEGG: PSMB5
	REACTOME: PSMB5
	ConsensusPathDB
	Pathway Commons: PSMB5
Metabolism	MetaCyc: PSMB5
	HUMANCyc: PSMB5
Regulation	Ensembl's Regulation: ENSG00000100804
	miRBase: chr14 :23,495,059-23,504,429
	TargetScan: NM_001130725
	cisRED: ENSG00000100804
Context	iHOP: PSMB5
	cancer metabolism search in PubMed: PSMB5
	UCL Cancer Institute: PSMB5
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PSMB5(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMB5
	Familial Cancer Database: PSMB5

* 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_AMINO_ACIDS_AND_DERIVATIVES REACTOME_METABOLISM_OF_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	600306; gene. 600306; gene.
Orphanet
Disease	KEGG Disease: PSMB5
	MedGen: PSMB5 (Human Medical Genetics with Condition)
	ClinVar: PSMB5
Phenotype	MGI: PSMB5 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMB5

Mutations for PSMB5

* 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

There's no structural variation information in COSMIC data for this gene.

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PSMB5 related fusion information.

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

BF761582

PSMB5

158

23495116

23495240

PSMB5

155

250

23495245

23495340

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=15)	Stat. for Synonymous SNVs (# total SNVs=6)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	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
chr14:23495299-23495299	p.264	2
chr14:23502856-23502856	p.D76H	1
chr14:23495517-23495517	p.S191S	1
chr14:23503893-23503893	p.K66N	1
chr14:23495561-23495561	p.G177W	1
chr14:23503928-23503928	p.E55Q	1
chr14:23502644-23502644	p.V146V	1
chr14:23503966-23503975	p.L39fs*31	1
chr14:23502692-23502692	p.K130K	1
chr14:23504006-23504006	p.D29N	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			4			2		2			1	1	1			1	1		5
# mutation	1			4			2		2			1	1	1			1	1		5
nonsynonymous SNV	1			2			2		1			1		1						4
synonymous SNV				2					1				1				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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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
chr14:23504085	p.L100L,PSMB5	1
chr14:23502760	p.I96I,PSMB5	1
chr14:23502761	p.Q88Q,PSMB5	1
chr14:23502782	p.D76H,PSMB5	1
chr14:23495350	p.D29N,PSMB5	1
chr14:23502794	p.V13L,PSMB5	1
chr14:23495375	p.L11Q,PSMB5	1
chr14:23502818	p.S144C,PSMB5	1
chr14:23495561	p.S5R,PSMB5	1
chr14:23502856	p.R136R,PSMB5	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 PSMB5 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 PSMB5

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


C14orf119,C6orf15,DAD1,EFS,EMC9,HAUS4,HSD17B10, IPO4,MRPL14,MRPL52,NEDD8,NGDN,OXA1L,PABPN1, PRMT5,PSMB5,PSMC3,PSME2,RABGGTA,RBM23,SNRPC	ANAPC11,ATP5I,BABAM1,LSM10,MRPL12,NDUFA13,NDUFA8, NDUFB2,NDUFS6,NDUFS8,PARK7,PRDX2,PSMB5,PSMB6, PSMC3,PSMD4,TACO1,TIMM8B,UQCR11,UQCRQ,WBSCR16

APEX1,C14orf119,SLIRP,C14orf166,C14orf2,CINP,DAD1, ERH,FKBP3,ISCA2,MRPL52,NDUFB1,NEDD8,OSGEP, PSMA3,PSMA6,PSMB5,PSMC1,PSMC6,SIVA1,TIMM9	C19orf10,CCT7,EIF2S2,EIF3I,EIF5AL1,H2AFZ,MRPL20, NPM3,PARK7,PPIB,PSMA3,PSMB5,PSMB6,PSMB7, PSMC2,PSMC3,PSMD14,RAN,RFC2,RPL26L1,SSBP1

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 PSMB5

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P28074; -.
Chemistry	ChEMBL	CHEMBL4662; -.
Chemistry	GuidetoPHARMACOLOGY	2406; -.
Chemistry	BindingDB	P28074; -.
Chemistry	ChEMBL	CHEMBL4662; -.
Chemistry	GuidetoPHARMACOLOGY	2406; -.
Organism-specific databases	PharmGKB	PA33887; -.
Organism-specific databases	PharmGKB	PA33887; -.
Organism-specific databases	CTD	5693; -.
Organism-specific databases	CTD	5693; -.

Drug-Gene Interaction Network

* Gene Centered Interaction Network.

* Drug Centered Interaction Network.

DrugBank ID	Target Name	Drug Groups	Generic Name	Drug Centered Network	Drug Structure
DB00188	proteasome (prosome, macropain) subunit, beta type, 5	approved; investigational	Bortezomib
DB07475	proteasome (prosome, macropain) subunit, beta type, 5	experimental	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB08515	proteasome (prosome, macropain) subunit, beta type, 5	experimental	(3AR,6R,6AS)-6-((S)-((S)-CYCLOHEX-2-ENYL)(HYDROXY)METHYL)-6A-METHYL-4-OXO-HEXAHYDRO-2H-FURO[3,2-C]PYRROLE-6-CARBALDEHYDE
DB00171	proteasome (prosome, macropain) subunit, beta type, 5	approved; nutraceutical	Adenosine triphosphate

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Cross referenced IDs for PSMB5

* 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