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 PSMA4

Basic gene info.	Gene symbol	PSMA4
	Gene name	proteasome (prosome, macropain) subunit, alpha type, 4
	Synonyms	HC9\|HsT17706\|PSC9
	Cytomap	UCSC genome browser: 15q25.1
	Genomic location	chr15 :78832746-78841563
	Type of gene	protein-coding
	RefGenes	NM_001102667.1, NM_001102668.1,NM_002789.4,
	Ensembl id	ENSG00000041357
	Description	macropain subunit C9multicatalytic endopeptidase complex subunit C9proteasome component C9proteasome subunit HC9proteasome subunit Lproteasome subunit alpha type-4
	Modification date	20141207
dbXrefs	MIM : 176846
	HGNC : HGNC
	Ensembl : ENSG00000041357
	HPRD : 10168
	Vega : OTTHUMG00000143859
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMA4
	BioGPS: 5685
	Gene Expression Atlas: ENSG00000041357
	The Human Protein Atlas: ENSG00000041357
Pathway	NCI Pathway Interaction Database: PSMA4
	KEGG: PSMA4
	REACTOME: PSMA4
	ConsensusPathDB
	Pathway Commons: PSMA4
Metabolism	MetaCyc: PSMA4
	HUMANCyc: PSMA4
Regulation	Ensembl's Regulation: ENSG00000041357
	miRBase: chr15 :78,832,746-78,841,563
	TargetScan: NM_001102667
	cisRED: ENSG00000041357
Context	iHOP: PSMA4
	cancer metabolism search in PubMed: PSMA4
	UCL Cancer Institute: PSMA4
Assigned class in ccmGDB	C

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Phenotypic Information for PSMA4(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMA4
	Familial Cancer Database: PSMA4

* 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: PSMA4
	MedGen: PSMA4 (Human Medical Genetics with Condition)
	ClinVar: PSMA4
Phenotype	MGI: PSMA4 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMA4

Mutations for PSMA4

* 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 PSMA4 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
BU190440	PSMA4	2	311	15	78841212	78841523	PSAP	304	820	10	73578373	73579633
AW149658	RAB31	2	276	18	9862275	9862549	PSMA4	267	622	15	78841164	78841518

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=15)	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
chr15:78834927-78834927	p.R50H	2
chr15:78834948-78834948	p.D57A	1
chr15:78837982-78837982	p.R128H	1
chr15:78841258-78841258	p.E253G	1
chr15:78834954-78834954	p.V59A	1
chr15:78837990-78837990	p.G131C	1
chr15:78834977-78834977	p.K67E	1
chr15:78838104-78838104	p.A169S	1
chr15:78834992-78834992	p.?	1
chr15:78838948-78838950	p.E181delE	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				2					2			2	1	1				2		2
# mutation				2					2			2	1	1				3		2
nonsynonymous SNV				1					2			2	1	1				3		2
synonymous SNV				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
chr15:78836557	p.I34M,PSMA4	1
chr15:78837238	p.A42V,PSMA4	1
chr15:78837261	p.G60C,PSMA4	1
chr15:78837990	p.A98S,PSMA4	1
chr15:78838104	p.I123S,PSMA4	1
chr15:78838990	p.V132V,PSMA4	1
chr15:78839018	p.K158E,PSMA4	1
chr15:78834894	p.R178C,PSMA4	1
chr15:78841185	p.R178H,PSMA4	1
chr15:78834926	p.A39V,PSMA4	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 PSMA4 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 PSMA4

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


HYKK,BOLA3,COX5A,FAM103A1,FBXO22,FBXO22-AS1,IDH3A, IMP3,MORF4L1,MRPS11,MTHFS,PSMA3,PSMA4,PSMA5, PSMD14,RCN2,SNRPA1,SNRPG,SNUPN,TIPIN,WDR61	ARPC2,CMC2,C20orf24,CCDC53,CDC123,EIF2S2,GTF3C6, LSM3,MRPL47,NOP10,POMP,PSMA1,PSMA3,PSMA4, PSMA5,PSMA6,RBX1,SNRPG,TOMM5,TTC1,ZBTB8OS

EMC7,CCNB2,DUT,ERH,FAM96A,FBXO22,KIAA0101, MRPL46,MRPS11,MTHFS,NOP10,OIP5,PSMA3,PSMA4, PSMA5,PSMA6,RAB11A,SEC11A,SRSF3,TIPIN,WDR61	C1GALT1C1,DYNLT1,EIF5A,EIF5AL1,ERH,GOLT1B,NMI, POMP,PPA1,PSMA1,PSMA2,PSMA3,PSMA4,PSMA5, PSMA6,PSMA7,PSMB1,PSMB4,RASL11A,SARNP,TMSB10

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 PSMA4

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, 4	experimental	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB08515	proteasome (prosome, macropain) subunit, alpha type, 4	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, 4	approved; nutraceutical	Adenosine triphosphate

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Cross referenced IDs for PSMA4

* 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