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 PSMB2

Basic gene info.	Gene symbol	PSMB2
	Gene name	proteasome (prosome, macropain) subunit, beta type, 2
	Synonyms	HC7-I
	Cytomap	UCSC genome browser: 1p34.2
	Genomic location	chr1 :36065142-36097138
	Type of gene	protein-coding
	RefGenes	NM_001199779.1, NM_001199780.1,NM_002794.4,
	Ensembl id	ENSG00000126067
	Description	macropain subunit C7-Imulticatalytic endopeptidase complex subunit C7-1multicatalytic endopeptidase complex subunit C7-Iproteasome beta 2 subunitproteasome component C7-Iproteasome subunit beta type-2proteasome subunit, beta type, 2
	Modification date	20141207
dbXrefs	MIM : 602175
	HGNC : HGNC
	Ensembl : ENSG00000126067
	HPRD : 03708
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMB2
	BioGPS: 5690
	Gene Expression Atlas: ENSG00000126067
	The Human Protein Atlas: ENSG00000126067
Pathway	NCI Pathway Interaction Database: PSMB2
	KEGG: PSMB2
	REACTOME: PSMB2
	ConsensusPathDB
	Pathway Commons: PSMB2
Metabolism	MetaCyc: PSMB2
	HUMANCyc: PSMB2
Regulation	Ensembl's Regulation: ENSG00000126067
	miRBase: chr1 :36,065,142-36,097,138
	TargetScan: NM_001199779
	cisRED: ENSG00000126067
Context	iHOP: PSMB2
	cancer metabolism search in PubMed: PSMB2
	UCL Cancer Institute: PSMB2
Assigned class in ccmGDB	C

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Phenotypic Information for PSMB2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMB2
	Familial Cancer Database: PSMB2

* 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: PSMB2
	MedGen: PSMB2 (Human Medical Genetics with Condition)
	ClinVar: PSMB2
Phenotype	MGI: PSMB2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMB2

Mutations for PSMB2

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- 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
breast	PSMB2	chr1	36085155	36085155		chr10	15216835	15216835
ovary	PSMB2	chr1	36091530	36091550	DLGAP3	chr1	35335849	35335869

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 PSMB2 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
BE908471	SRC	1	221	20	36031753	36031973	PSMB2	208	478	1	36068745	36070873
AA393815	PSMB2	1	238	1	36068559	36068796	PSMB2	234	518	1	36101927	36107120
CB156087	PSMB2	1	472	1	36067669	36068140	SLC25A35	467	660	17	8193447	8193640
AA393918	PSMB2	1	350	1	36096896	36107120	PSMB2	346	430	1	36068559	36068643

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=9)	Stat. for Synonymous SNVs (# total SNVs=1)

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
chr1:36101971-36101971	p.D52H	2
chr1:36074989-36074989	p.L102L	1
chr1:36096876-36096876	p.R95L	1
chr1:36101916-36101916	p.R70Q	1
chr1:36101917-36101917	p.R70*	1
chr1:36070882-36070882	p.T150T	1
chr1:36074873-36074873	p.S141T	1
chr1:36102023-36102023	p.K34N	1
chr1:36074881-36074891	p.G135fs*16	1
chr1:36107026-36107026	p.Y3C	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				4			1										2	3		1
# mutation				3			1										2	3		1
nonsynonymous SNV				2			1										2	2		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
chr1:36074882	p.L21P,PSMB2	2
chr1:36096876	p.Y3S,PSMB2	1
chr1:36096883	p.S62T,PSMB2	1
chr1:36102014	p.T60I,PSMB2	1
chr1:36107026	p.T33T,PSMB2	1
chr1:36068938	p.S24T,PSMB2	1
chr1:36068944	p.A6T,PSMB2	1
chr1:36070882	p.A89A,PSMB2	1
chr1:36074873	p.R70L,PSMB2	1
chr1:36074928	p.R68W,PSMB2	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 PSMB2 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 PSMB2

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


ADPRHL2,AK2,AUNIP,CDC20,CDCA8,EIF2B3,ERI3, GNL2,KIF2C,MAGOH,MED8,MRPL37,PSMB2,PSMG1, PTTG1,TRAPPC3,TUBA1C,UQCRH,UQCRHL,UTP11L,YARS	CDC123,COX16,DYNLT1,GNG5,MRPL47,MYL12B,NOP10, NUTF2,PSMA1,PSMA3,PSMA4,PSMA5,PSMB2,RBX1, RRAGA,SDHAF2,SLC35B1,SNRPG,TOMM5,TOMM6,UCHL3

ACOT7,ADPRHL2,AK2,SMIM12,CDC20,EBNA1BP2,EIF3I, HDAC1,MRPL20,MRPL37,MRPS15,NOC2L,NUDC,PEF1, PRDX1,PSMA5,PSMB2,TRAPPC3,TUBA1C,UTP11L,YARS	ACTR3,ASS1,CALR,CRELD2,DDX39A,DNAJB11,EIF5AL1, ENO1,H2AFZ,MANF,NOS2,PDIA6,PPIB,PSMA3, PSMB2,PSMB5,PSMC4,RPN1,SDF2L1,SEC61B,SNRPF

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 PSMB2

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

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Cross referenced IDs for PSMB2

* 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