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 PSMA5

Basic gene info.	Gene symbol	PSMA5
	Gene name	proteasome (prosome, macropain) subunit, alpha type, 5
	Synonyms	PSC5\|ZETA
	Cytomap	UCSC genome browser: 1p13
	Genomic location	chr1 :109941652-109969108
	Type of gene	protein-coding
	RefGenes	NM_001199772.1, NM_001199773.1,NM_001199774.1,NM_002790.3,
	Ensembl id	ENSG00000143106
	Description	macropain subunit zetamacropain zeta chainmulticatalytic endopeptidase complex zeta chainproteasome alpha 5 subunitproteasome component 5proteasome subunit alpha type-5proteasome subunit zetaproteasome zeta chain
	Modification date	20141207
dbXrefs	MIM : 176844
	HGNC : HGNC
	Ensembl : ENSG00000143106
	HPRD : 01464
	Vega : OTTHUMG00000012001
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMA5
	BioGPS: 5686
	Gene Expression Atlas: ENSG00000143106
	The Human Protein Atlas: ENSG00000143106
Pathway	NCI Pathway Interaction Database: PSMA5
	KEGG: PSMA5
	REACTOME: PSMA5
	ConsensusPathDB
	Pathway Commons: PSMA5
Metabolism	MetaCyc: PSMA5
	HUMANCyc: PSMA5
Regulation	Ensembl's Regulation: ENSG00000143106
	miRBase: chr1 :109,941,652-109,969,108
	TargetScan: NM_001199772
	cisRED: ENSG00000143106
Context	iHOP: PSMA5
	cancer metabolism search in PubMed: PSMA5
	UCL Cancer Institute: PSMA5
Assigned class in ccmGDB	C

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Phenotypic Information for PSMA5(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMA5
	Familial Cancer Database: PSMA5

* 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: PSMA5
	MedGen: PSMA5 (Human Medical Genetics with Condition)
	ClinVar: PSMA5
Phenotype	MGI: PSMA5 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMA5

Mutations for PSMA5

* 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	PSMA5	chr1	109961538	109961538	PSMA5	chr1	109964437	109964437
ovary	PSMA5	chr1	109944206	109944226	ZC3H18	chr16	88683329	88683349
ovary	PSMA5	chr1	109946699	109946719	SORT1	chr1	109925311	109925331

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 PSMA5 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

BP284679

PSMA5

442

109954767

109969062

USF1

432

588

161012649

161015686

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=11)	Stat. for Synonymous SNVs (# total SNVs=5)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=1)

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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
chr1:109957929-109957929	p.E51E	2
chr1:109952632-109952632	p.M189R	1
chr1:109955744-109955744	p.S79S	1
chr1:109952635-109952635	p.S188Y	1
chr1:109957887-109957887	p.E65E	1
chr1:109953641-109953642	p.V184_Y185insN	1
chr1:109953687-109953687	p.A169A	1
chr1:109957934-109957934	p.V50L	1
chr1:109953692-109953692	p.R168*	1
chr1:109957948-109957948	p.G45D	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	2		5	1								1				3	1		1
# mutation	1	2		4	1								1				3	1		1
nonsynonymous SNV	1	1		3	1								1				2	1		1
synonymous SNV		1		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
chr1:109955744	p.S21S,PSMA5	2
chr1:109954795	p.E7D,PSMA5	1
chr1:109955694	p.E51E	1
chr1:109957887	p.V50L	1
chr1:109957929	p.G45D	1
chr1:109957934	p.G19R	1
chr1:109957948	p.P17S	1
chr1:109944647	p.S6F	1
chr1:109964523	p.I180M,PSMA5	1
chr1:109952611	p.K138T,PSMA5	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 PSMA5 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 PSMA5

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


ALG3,ATP5F1,BOLA3,C20orf24,LAMTOR5,MRPS15,PSMA2, PSMA4,PSMA5,PSMB2,PSMC1,PSMD14,PSME2,PSRC1, PTTG1,SARS,SNRPC,SNRPG,TALDO1,TUBA1C,WDR77	CDC123,CHCHD1,CIAPIN1,DYNLT1,ERH,H2AFZ,HN1, JTB,MAD2L1BP,MRPL17,MRPS23,NUTF2,PSMA4,PSMA5, RBX1,SLC35B1,SNRPG,SSBP1,TMEM147,TXNDC17,UCHL3

AK2,ATP5F1,BCAS2,COX7A2,EBNA1BP2,EIF3I,LAMTOR5, LSM2,MRPL22,MRPS15,MRPS18C,PHF5A,PPIH,PSMA4, PSMA5,PSMA6,RAN,TIMM8B,TOMM22,UQCRQ,VPS29	EMC7,CKS1B,MRPL52,PGK1,POMP,PSMA1,PSMA2, PSMA3,PSMA4,PSMA5,PSMA6,PSMA7,PSMB1,PSMD13, PSMD14,RBX1,RPL26L1,SNRPG,STRA13,TMSB10,TOMM5

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 PSMA5

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, alpha type, 5	experimental	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB08515	proteasome (prosome, macropain) subunit, alpha 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, alpha type, 5	approved; nutraceutical	Adenosine triphosphate

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Cross referenced IDs for PSMA5

* 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