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 PSMB1

Basic gene info.	Gene symbol	PSMB1
	Gene name	proteasome (prosome, macropain) subunit, beta type, 1
	Synonyms	HC5\|PMSB1\|PSC5
	Cytomap	UCSC genome browser: 6q27
	Genomic location	chr6 :170844203-170862417
	Type of gene	protein-coding
	RefGenes	NM_002793.3,
	Ensembl id	ENSG00000008018
	Description	macropain subunit C5multicatalytic endopeptidase complex subunit C5proteasome beta 1 subunitproteasome component C5proteasome gamma chainproteasome subunit HC5proteasome subunit beta type-1
	Modification date	20141207
dbXrefs	MIM : 602017
	HGNC : HGNC
	Ensembl : ENSG00000008018
	HPRD : 03603
	Vega : OTTHUMG00000016087
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMB1
	BioGPS: 5689
	Gene Expression Atlas: ENSG00000008018
	The Human Protein Atlas: ENSG00000008018
Pathway	NCI Pathway Interaction Database: PSMB1
	KEGG: PSMB1
	REACTOME: PSMB1
	ConsensusPathDB
	Pathway Commons: PSMB1
Metabolism	MetaCyc: PSMB1
	HUMANCyc: PSMB1
Regulation	Ensembl's Regulation: ENSG00000008018
	miRBase: chr6 :170,844,203-170,862,417
	TargetScan: NM_002793
	cisRED: ENSG00000008018
Context	iHOP: PSMB1
	cancer metabolism search in PubMed: PSMB1
	UCL Cancer Institute: PSMB1
Assigned class in ccmGDB	C

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Phenotypic Information for PSMB1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMB1
	Familial Cancer Database: PSMB1

* 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: PSMB1
	MedGen: PSMB1 (Human Medical Genetics with Condition)
	ClinVar: PSMB1
Phenotype	MGI: PSMB1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMB1

Mutations for PSMB1

* 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 PSMB1 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
CB122525	ZFAND6	1	115	15	80352037	80352151	PSMB1	113	593	6	170844443	170858204
DA076564	CDYL2	1	139	16	80837674	80837812	PSMB1	137	566	6	170846322	170858204
DB153796	BCLAF1	1	134	6	136610851	136610984	PSMB1	131	577	6	170854940	170858205
BG978110	GSTP1	27	204	11	67352170	67352713	PSMB1	205	459	6	170855254	170862345
BG272210	PSMB1	7	234	6	170844210	170844437	GPBP1	231	407	5	56545371	56546923
BE122757	CSDA	1	179	12	10856655	10862592	PSMB1	176	393	6	170844386	170846431

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=11)	Stat. for Synonymous SNVs (# total SNVs=4)

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
chr6:170844433-170844433	p.R201W	3
chr6:170862300-170862300	p.P11A	3
chr6:170844377-170844377	p.D219D	1
chr6:170855238-170855238	p.H86Y	1
chr6:170855244-170855244	p.G84S	1
chr6:170844489-170844489	p.G182D	1
chr6:170858099-170858099	p.Y72*	1
chr6:170844498-170844498	p.?	1
chr6:170858120-170858120	p.T65T	1
chr6:170846342-170846342	p.Q174E	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	2			2						1		4		1			3	2		3
# mutation	2			2						1		4		1			3	2		3
nonsynonymous SNV	2									1		2		1			1			2
synonymous SNV				2								2					2	2		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
chr6:170844370	p.R222R	1
chr6:170858120	p.L2L	1
chr6:170844377	p.D219D	1
chr6:170858188	p.R201W	1
chr6:170844433	p.Q174E	1
chr6:170862291	p.G166G	1
chr6:170846342	p.G166A	1
chr6:170862293	p.S162S	1
chr6:170846364	p.I138I	1
chr6:170862307	p.N107T	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 PSMB1 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 PSMB1

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


CCM2,COX4I1,CYBA,EFHD2,FLT3LG,GUK1,HCST, IRF3,LIME1,LOC606724,LST1,PSMB10,PSMB8,PSMB9, PSME2,RHOG,RNF166,IGFLR1,TRADD,TYMP,VAMP5	BAX,COPE,CYBA,GALK1,IFI27L2,MBD3,NPDC1, PLSCR3,PSMB10,PYCARD,RALY,RBM42,RGS19,SCO2, SHKBP1,SIPA1,SIRT6,SNAPC2,SSBP4,TBCB,ZDHHC12

APOL2,BAK1,BATF2,ETV7,FBXO6,HLA-DMA,IFI35, IL15RA,IL32,IRF1,NMI,ODF3B,PSMB10,PSMB8, PSMB9,PSME1,PSME2,RARRES3,SCO2,TAP1,UBE2L6	BATF2,CARD16,EPSTI1,ETV7,FAM26F,GZMB,IFI30, IFI35,IRF1,PARP9,PSMB10,PSMB8,PSMB9,PSME1, PSME2,RARRES3,STAT1,TAP1,TRIM21,TYMP,UBE2L6

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 PSMB1

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
DB00188	proteasome (prosome, macropain) subunit, beta type, 1	approved; investigational	Bortezomib
DB07475	proteasome (prosome, macropain) subunit, beta type, 1	experimental	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB08515	proteasome (prosome, macropain) subunit, beta type, 1	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, 1	approved; nutraceutical	Adenosine triphosphate

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Cross referenced IDs for PSMB1

* 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