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 PSMB7

Basic gene info.	Gene symbol	PSMB7
	Gene name	proteasome (prosome, macropain) subunit, beta type, 7
	Synonyms	Z
	Cytomap	UCSC genome browser: 9q34.11-q34.12
	Genomic location	chr9 :127115743-127177721
	Type of gene	protein-coding
	RefGenes	NM_002799.3,
	Ensembl id	ENSG00000136930
	Description	macropain chain Zmulticatalytic endopeptidase complex chain Zproteasome catalytic subunit 2proteasome subunit Zproteasome subunit alphaproteasome subunit beta type-7
	Modification date	20141207
dbXrefs	MIM : 604030
	HGNC : HGNC
	Ensembl : ENSG00000136930
	HPRD : 04940
	Vega : OTTHUMG00000021042
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMB7
	BioGPS: 5695
	Gene Expression Atlas: ENSG00000136930
	The Human Protein Atlas: ENSG00000136930
Pathway	NCI Pathway Interaction Database: PSMB7
	KEGG: PSMB7
	REACTOME: PSMB7
	ConsensusPathDB
	Pathway Commons: PSMB7
Metabolism	MetaCyc: PSMB7
	HUMANCyc: PSMB7
Regulation	Ensembl's Regulation: ENSG00000136930
	miRBase: chr9 :127,115,743-127,177,721
	TargetScan: NM_002799
	cisRED: ENSG00000136930
Context	iHOP: PSMB7
	cancer metabolism search in PubMed: PSMB7
	UCL Cancer Institute: PSMB7
Assigned class in ccmGDB	C

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Phenotypic Information for PSMB7(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMB7
	Familial Cancer Database: PSMB7

* 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: PSMB7
	MedGen: PSMB7 (Human Medical Genetics with Condition)
	ClinVar: PSMB7
Phenotype	MGI: PSMB7 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMB7

Mutations for PSMB7

* 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
skin	PSMB7	chr9	127118224	127118224		chr9	128022004	128022004

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 PSMB7 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
BQ925563	PSMB7	1	607	9	127119210	127119816	EEF1D	608	855	8	144668389	144679566
DA677584	PSMB7	4	412	9	127174629	127177716	SMEK1	409	549	14	91951992	91957148
W23061	PSMB7	13	365	9	127174680	127177711	PSMB7	358	517	9	127167596	127174681
AA488934	KDM5C	1	159	X	53221378	53221536	PSMB7	155	370	9	127115749	127115964
AI638157	SMYD5	1	190	2	73454162	73454351	PSMB7	187	516	9	127150948	127151277
AW449088	FUS	15	306	16	31202347	31202926	PSMB7	304	414	9	127116963	127117073
BQ424626	PSMB7	16	264	9	127176187	127177699	PSMB7	264	693	9	127119052	127174738
BF831316	DCTN4	7	96	5	150112318	150112409	PSMB7	81	371	9	127120646	127120937
BM990034	PSMB7	18	224	9	127115749	127115955	ZFP36	222	621	19	39899603	39900002
BF969613	PSMB7	122	480	9	127115746	127119158	MARCH1	468	492	4	164585083	164585107
DW438983	PSMB7	17	187	9	127171672	127171842	PDS5B	187	243	13	33214285	33214341

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=7)	Stat. for Synonymous SNVs (# total SNVs=2)

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
chr9:127115882-127115882	p.S277fs?	1
chr9:127177168-127177168	p.P37T	1
chr9:127115901-127115901	p.T270T	1
chr9:127177641-127177641	p.?	1
chr9:127115981-127115981	p.R244W	1
chr9:127177673-127177673	p.V11D	1
chr9:127115993-127115993	p.?	1
chr9:127177679-127177679	p.P9L	1
chr9:127119142-127119142	p.N208S	1
chr9:127177691-127177691	p.S5*	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	1				1	1	1	2
# mutation							1		1			1	1				1	1	1	2
nonsynonymous SNV							1		1								1		1	1
synonymous SNV												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
chr9:127115901	p.G12E	1
chr9:127119142	p.V11D	1
chr9:127167675	p.P9L	1
chr9:127176280	p.S5S	1
chr9:127177648	p.T270T	1
chr9:127177670	p.N208S	1
chr9:127177673	p.G144G	1
chr9:127177679	p.G54V	1
chr9:127177690	p.C19C	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 PSMB7 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 PSMB7

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


ARPC5L,COX6B1,DPM2,EDF1,LSM4,MED27,NTMT1, NDUFA8,PSMB7,PSMC1,PTGES2,RABEPK,RPL35,SEC61B, SNRPF,SSNA1,SURF2,TXN,WDR34,ZDHHC12,ZMYND19	CCT7,CHCHD2,COPS6,COX4I1,DCTN3,EIF3I,EIF3K, GRHPR,LOC440957,MRPL11,MRPL20,MRPL43,MRPL51,MRPS18A, NDUFA11,PARK7,POLR2I,PSMB7,STOML2,TXN2,ZNF511

ARPC5L,CKS2,DPM2,EDF1,MED27,NTMT1,MRPS2, NDUFA8,PMPCA,PSMB1,PSMB7,PTTG1,RPL35,RPL7A, SEC61B,SSNA1,TMEM203,TRUB2,TXN,URM1,ZMYND19	TMEM258,EMC7,DAD1,LSM3,MRPL52,NDUFA7,NDUFB4, NEDD8,OSGEP,POLR2L,PSMA1,PSMA2,PSMA5,PSMA7, PSMB1,PSMB3,PSMB4,PSMB7,PSMD13,PSMD8,RBX1

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 PSMB7

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, 7	experimental	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB08515	proteasome (prosome, macropain) subunit, beta type, 7	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, 7	approved; nutraceutical	Adenosine triphosphate

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Cross referenced IDs for PSMB7

* 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