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 PSMC3

Basic gene info.	Gene symbol	PSMC3
	Gene name	proteasome (prosome, macropain) 26S subunit, ATPase, 3
	Synonyms	TBP1
	Cytomap	UCSC genome browser: 11p11.2
	Genomic location	chr11 :47440319-47448024
	Type of gene	protein-coding
	RefGenes	NM_002804.4,
	Ensembl id	ENSG00000165916
	Description	26S protease regulatory subunit 6A26S proteasome AAA-ATPase subunit RPT5TBP-1Tat-binding protein 1human immunodeficiency virus tat transactivator binding protein-1proteasome 26S subunit ATPase 3proteasome subunit P50
	Modification date	20141207
dbXrefs	MIM : 186852
	HGNC : HGNC
	Ensembl : ENSG00000165916
	HPRD : 01733
	Vega : OTTHUMG00000167692
Protein	UniProt: P17980 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMC3
	BioGPS: 5702
	Gene Expression Atlas: ENSG00000165916
	The Human Protein Atlas: ENSG00000165916
Pathway	NCI Pathway Interaction Database: PSMC3
	KEGG: PSMC3
	REACTOME: PSMC3
	ConsensusPathDB
	Pathway Commons: PSMC3
Metabolism	MetaCyc: PSMC3
	HUMANCyc: PSMC3
Regulation	Ensembl's Regulation: ENSG00000165916
	miRBase: chr11 :47,440,319-47,448,024
	TargetScan: NM_002804
	cisRED: ENSG00000165916
Context	iHOP: PSMC3
	cancer metabolism search in PubMed: PSMC3
	UCL Cancer Institute: PSMC3
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PSMC3(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMC3
	Familial Cancer Database: PSMC3

* 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	186852; gene.
Orphanet
Disease	KEGG Disease: PSMC3
	MedGen: PSMC3 (Human Medical Genetics with Condition)
	ClinVar: PSMC3
Phenotype	MGI: PSMC3 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMC3

Mutations for PSMC3

* 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 PSMC3 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
BG248359	PSMC3	2	186	11	47446742	47447800	AKIRIN1	184	738	1	39463845	39469930
BU183660	PSMC3	1	420	11	47440326	47442202	POLR2D	421	487	2	128605647	128605713
BM843762	PSMC3	12	101	11	47447447	47447790	DAP	98	518	5	10680762	10681182

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=30)	Stat. for Synonymous SNVs (# total SNVs=9)

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
chr11:47444157-47444157	p.F284L	2
chr11:47445638-47445638	p.Q184*	2
chr11:47446256-47446256	p.D98H	2
chr11:47447465-47447465	p.T38S	2
chr11:47444417-47444417	p.K233N	2
chr11:47446696-47446696	p.P87P	2
chr11:47444496-47444496	p.N207S	2
chr11:47440504-47440504	p.?	2
chr11:47444520-47444520	p.V199G	1
chr11:47440687-47440687	p.K397Q	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=3

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	11			1					1	3	2			7	7		4
# mutation	2		1	10			1					1	3	2			7	7		4
nonsynonymous SNV	2		1	9			1						2	2			4	6		1
synonymous SNV				1								1	1				3	1		3

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
chr11:47444496	p.D98N	2
chr11:47446256	p.N207S	2
chr11:47444453	p.G292G	1
chr11:47446173	p.P135S	1
chr11:47441884	p.E287Q	1
chr11:47446202	p.F133F	1
chr11:47444133	p.A279E	1
chr11:47444497	p.Q130P	1
chr11:47446219	p.G264C	1
chr11:47444150	p.S127F	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 PSMC3 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 PSMC3

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


ARL6IP4,CCDC124,COPE,FAM50A,GADD45GIP1,LSM7,MRPL23, NDUFA11,NDUFB7,NDUFS3,NDUFS6,PACSIN3,PEX16,PRDX5, PSMB6,PSMC3,PSMD13,RALY,NELFE,SART1,ZNF408	ADRM1,ANAPC11,TSR3,BABAM1,C19orf70,CDC37,CLTB, CUEDC2,FIS1,GADD45GIP1,MAF1,NDUFA13,NDUFB7,NDUFS6, NOSIP,PDAP1,PSMB6,PSMC3,PSMC5,PSMD4,STUB1

ARFIP2,BRMS1,LBHD1___C11orf98,UQCC3,CCDC124,GADD45GIP1,HMBS, HRAS,MRPL17,MRPL23,MRPL28,NDUFS3,POLR2L,PSMA1, PSMB6,PSMC1,PSMC3,PSMD13,PTPMT1,SSSCA1,TALDO1	CCDC167,RRP36,CCT7,EIF2S2,EIF3I,EIF5AL1,ENSA, MED27,MRPL20,PARK7,PGAM1,POLR2L,PSMA3,PSMA7, PSMB5,PSMB6,PSMC2,PSMC3,PSMD13,PSMD4,PSMD7

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 PSMC3

There's no related Drug.

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Cross referenced IDs for PSMC3

* 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