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 PSMB6

Basic gene info.	Gene symbol	PSMB6
	Gene name	proteasome (prosome, macropain) subunit, beta type, 6
	Synonyms	DELTA\|LMPY\|Y
	Cytomap	UCSC genome browser: 17p13
	Genomic location	chr17 :4699456-4701790
	Type of gene	protein-coding
	RefGenes	NM_001270481.1, NM_002798.2,
	Ensembl id	ENSG00000142507
	Description	PSY large multifunctional protease Ymacropain delta chainmulticatalytic endopeptidase complex delta chainproteasome catalytic subunit 1proteasome delta chainproteasome subunit Yproteasome subunit beta type-6proteasome subunit delta
	Modification date	20141207
dbXrefs	MIM : 600307
	HGNC : HGNC
	Ensembl : ENSG00000142507
	HPRD : 02630
	Vega : OTTHUMG00000090777
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMB6
	BioGPS: 5694
	Gene Expression Atlas: ENSG00000142507
	The Human Protein Atlas: ENSG00000142507
Pathway	NCI Pathway Interaction Database: PSMB6
	KEGG: PSMB6
	REACTOME: PSMB6
	ConsensusPathDB
	Pathway Commons: PSMB6
Metabolism	MetaCyc: PSMB6
	HUMANCyc: PSMB6
Regulation	Ensembl's Regulation: ENSG00000142507
	miRBase: chr17 :4,699,456-4,701,790
	TargetScan: NM_001270481
	cisRED: ENSG00000142507
Context	iHOP: PSMB6
	cancer metabolism search in PubMed: PSMB6
	UCL Cancer Institute: PSMB6
Assigned class in ccmGDB	C

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Phenotypic Information for PSMB6(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMB6
	Familial Cancer Database: PSMB6

* 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
Orphanet
Disease	KEGG Disease: PSMB6
	MedGen: PSMB6 (Human Medical Genetics with Condition)
	ClinVar: PSMB6
Phenotype	MGI: PSMB6 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMB6

Mutations for PSMB6

* 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 PSMB6 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

CN430188

PSMB6

499

4699474

4701354

ANKRD27

495

646

33095169

33095320

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=12)	Stat. for Synonymous SNVs (# total SNVs=8)

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
chr17:4700797-4700797	p.R79C	1
chr17:4701345-4701345	p.S158S	1
chr17:4699490-4699490	p.M1V	1
chr17:4700837-4700837	p.A92V	1
chr17:4701402-4701402	p.Y177Y	1
chr17:4699552-4699552	p.A21A	1
chr17:4700982-4700982	p.E103G	1
chr17:4701416-4701416	p.T182N	1
chr17:4700075-4700075	p.S52F	1
chr17:4700983-4700983	p.E103E	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=2

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	2	1	5			1					1	1	2	1		1	2		5
# mutation	1	2	1	4			1					1	1	2	1		1	2		5
nonsynonymous SNV	1	2		2			1					1	1	1	1		1	1		3
synonymous SNV			1	2										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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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
chr17:4700837	p.A92V,PSMB6	2
chr17:4701048	p.V40M,PSMB6	1
chr17:4701657	p.G165G,PSMB6	1
chr17:4700038	p.S52F,PSMB6	1
chr17:4701064	p.T182N,PSMB6	1
chr17:4700075	p.Y59H,PSMB6	1
chr17:4701076	p.G207R,PSMB6	1
chr17:4700737	p.N62K,PSMB6	1
chr17:4701090	p.L210L	1
chr17:4700748	p.R63Q,PSMB6	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 PSMB6 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 PSMB6

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


C17orf49,EIF5A,GADD45GIP1,GPS2,NAA38,MED11,NDUFA13, NDUFB8,OVCA2,PELP1,PFN1,PSMB6,RNASEK,RNMTL1, SLC25A11,SPAG7,TIMM22,EMC6,TRAPPC1,TXNDC17,WRAP53	AKT1S1,ANAPC11,BABAM1,C19orf70,COPS6,FAM89B,FIS1, GPS1,LSM10,MRPL2,NDUFA13,NDUFB7,NDUFS6,NDUFS8, NOSIP,PARK7,PSMB5,PSMB6,PSMC3,PSMD4,STUB1

ATPAF2,ELP5,DERL2,CTDNEP1,EIF4A1,EIF5A,EIF5AL1, ELAC2,NAA38,MED11,MPDU1,OVCA2,PFN1,PSMB6, RNASEK,RNMTL1,SLC25A11,TIMM22,EMC6,TXNDC17,WRAP53	DPCD,ENSA,LSM3,NEDD8,NUBP1,PARK7,PGAM1, POLR2L,PSMA3,PSMA7,PSMB1,PSMB4,PSMB5,PSMB6, PSMB7,PSMC2,PSMC3,PSMD13,PSMD4,PSMD7,SSSCA1

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 PSMB6

Cross-referenced pharmacological DB IDs from Uniprot

DB Category

DB Name

DB's ID and Url link

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
DB07475	proteasome (prosome, macropain) subunit, beta type, 6	experimental	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB08515	proteasome (prosome, macropain) subunit, beta type, 6	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, 6	approved; nutraceutical	Adenosine triphosphate

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Cross referenced IDs for PSMB6

* 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