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 PSMA7

Basic gene info.	Gene symbol	PSMA7
	Gene name	proteasome (prosome, macropain) subunit, alpha type, 7
	Synonyms	C6\|HSPC\|RC6-1\|XAPC7
	Cytomap	UCSC genome browser: 20q13.33
	Genomic location	chr20 :60711790-60718474
	Type of gene	protein-coding
	RefGenes	NM_002792.3, NM_152255.1,
	Ensembl id	ENSG00000101182
	Description	proteasome subunit RC6-1proteasome subunit XAPC7proteasome subunit alpha 4proteasome subunit alpha type-7
	Modification date	20141207
dbXrefs	MIM : 606607
	HGNC : HGNC
	Ensembl : ENSG00000101182
	HPRD : 05967
	Vega : OTTHUMG00000032895
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMA7
	BioGPS: 5688
	Gene Expression Atlas: ENSG00000101182
	The Human Protein Atlas: ENSG00000101182
Pathway	NCI Pathway Interaction Database: PSMA7
	KEGG: PSMA7
	REACTOME: PSMA7
	ConsensusPathDB
	Pathway Commons: PSMA7
Metabolism	MetaCyc: PSMA7
	HUMANCyc: PSMA7
Regulation	Ensembl's Regulation: ENSG00000101182
	miRBase: chr20 :60,711,790-60,718,474
	TargetScan: NM_002792
	cisRED: ENSG00000101182
Context	iHOP: PSMA7
	cancer metabolism search in PubMed: PSMA7
	UCL Cancer Institute: PSMA7
Assigned class in ccmGDB	C

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Phenotypic Information for PSMA7(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMA7
	Familial Cancer Database: PSMA7

* 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: PSMA7
	MedGen: PSMA7 (Human Medical Genetics with Condition)
	ClinVar: PSMA7
Phenotype	MGI: PSMA7 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMA7

Mutations for PSMA7

* 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 PSMA7 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
EC492083	NCL	1	57	2	232325512	232325571	PSMA7	51	101	20	60713257	60713308
BQ685104	PSMA7	10	225	20	60714167	60714965	RBBP7	226	889	X	16870624	16876965
BG474310	TESC	2	275	12	117476879	117484452	PSMA7	274	669	20	60711994	60714913
AA581992	PSMA7	1	180	20	60711790	60711972	UBA52	167	528	19	18682669	18685899
CA312659	PSMA7	8	176	20	60711952	60713278	PSMA7	175	240	20	60713261	60713326
BF237904	PSMA7	16	127	20	60714185	60714879	PSMA7	125	434	20	60711952	60714202

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=9)	Stat. for Synonymous SNVs (# total SNVs=5)

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
chr20:60714232-60714232	p.R124C	2
chr20:60714888-60714888	p.E99E	2
chr20:60713265-60713265	p.D185Y	2
chr20:60713283-60713283	p.E179K	2
chr20:60714168-60714168	p.Y145C	1
chr20:60714221-60714221	p.F127F	1
chr20:60714246-60714246	p.T119M	1
chr20:60714841-60714841	p.K115T	1
chr20:60712432-60712432	p.D214D	1
chr20:60712444-60712444	p.V210V	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	1		2						1		2						5		3
# mutation	2	1		2						1		2						4		3
nonsynonymous SNV				1						1		1						4		2
synonymous SNV	2	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
chr20:60714232	p.D185Y	2
chr20:60713265	p.R124C	2
chr20:60714221	p.R95Q	1
chr20:60714246	p.I84I	1
chr20:60714841	p.V33V	1
chr20:60714888	p.R5R	1
chr20:60712432	p.D214D	1
chr20:60714901	p.V210V	1
chr20:60712444	p.E179K	1
chr20:60714933	p.Y145C	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 PSMA7 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 PSMA7

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


ADRM1,ARFGAP1,ARFRP1,ATP5E,GID8,MRGBP,C20orf24, DUS2,FAM96B,MTG2,LSM14B,OGFR,OSBPL2,PSMA7, RPS21,TAF4,NELFCD,ALYREF,TMEM208,TPD52L2,TUBA1C	ACADS,ARL2,ATP5I,BLOC1S1,BSG,ETFB,FPGS, MPST,MRPL41,MRPL46,MRPL53,MRPS11,MRPS15,NDUFA2, NDUFB8,POLR2E,PSMA7,PSMD8,SLC2A4RG,TALDO1,TMEM120A

ADRM1,AHCY,ATP5E,MRGBP,C20orf24,RTFDC1,COMMD7, DPM1,EIF2S2,EIF6,ERGIC3,PDRG1,PFDN4,PSMA7, RAE1,RALY,ROMO1,RPS21,NELFCD,TP53RK,TPD52L2	EMC7,MRPL20,MRPL52,MYEOV2,NEDD8,PHF5A,PSMA1, PSMA5,PSMA7,PSMB1,PSMD13,PSMD14,PSMD8,RBX1, SNRPG,SSBP1,STRA13,TCEB1,TIMM8B,TOMM5,UFD1L

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 PSMA7

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, 7	experimental	N-[(1R)-1-(DIHYDROXYBORYL)-3-METHYLBUTYL]-N-(PYRAZIN-2-YLCARBONYL)-L-PHENYLALANINAMIDE
DB07558	proteasome (prosome, macropain) subunit, alpha type, 7	experimental	2-ACETYLAMINO-4-METHYL-PENTANOIC ACID [1-(1-FORMYL-PENTYLCARBAMOYL)-3-METHYL-BUTYL]-AMIDE
DB08515	proteasome (prosome, macropain) subunit, alpha 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, alpha type, 7	approved; nutraceutical	Adenosine triphosphate

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Cross referenced IDs for PSMA7

* 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