Cancer Cell Metabolism Database ~~ Bioinformatics and Systems Medicine Laboratory ~~

Cancer Cell Metabolism Gene Database

Cancer Cell Metabolism Gene DB

Home

	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 PSMC5

Basic gene info.	Gene symbol	PSMC5
	Gene name	proteasome (prosome, macropain) 26S subunit, ATPase, 5
	Synonyms	S8\|SUG-1\|SUG1\|TBP10\|TRIP1\|p45\|p45/SUG
	Cytomap	UCSC genome browser: 17q23.3
	Genomic location	chr17 :61904769-61909387
	Type of gene	protein-coding
	RefGenes	NM_001199163.1, NM_002805.5,
	Ensembl id	ENSG00000087191
	Description	26S protease regulatory subunit 826S proteasome AAA-ATPase subunit RPT6MSUG1 proteinTat-binding protein homolog 10proteasome 26S ATPase subunit 5proteasome 26S subunit ATPase 5proteasome subunit p45thyroid hormone receptor-interacting protein 1thy
	Modification date	20141207
dbXrefs	MIM : 601681
	HGNC : HGNC
	Ensembl : ENSG00000087191
	HPRD : 03400
	Vega : OTTHUMG00000179013
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMC5
	BioGPS: 5705
	Gene Expression Atlas: ENSG00000087191
	The Human Protein Atlas: ENSG00000087191
Pathway	NCI Pathway Interaction Database: PSMC5
	KEGG: PSMC5
	REACTOME: PSMC5
	ConsensusPathDB
	Pathway Commons: PSMC5
Metabolism	MetaCyc: PSMC5
	HUMANCyc: PSMC5
Regulation	Ensembl's Regulation: ENSG00000087191
	miRBase: chr17 :61,904,769-61,909,387
	TargetScan: NM_001199163
	cisRED: ENSG00000087191
Context	iHOP: PSMC5
	cancer metabolism search in PubMed: PSMC5
	UCL Cancer Institute: PSMC5
Assigned class in ccmGDB	C

Top

Phenotypic Information for PSMC5(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMC5
	Familial Cancer Database: PSMC5

* 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: PSMC5
	MedGen: PSMC5 (Human Medical Genetics with Condition)
	ClinVar: PSMC5
Phenotype	MGI: PSMC5 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMC5

Mutations for PSMC5

* 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 PSMC5 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
CV422250	PSMC5	6	199	17	61908210	61908502	PSMC5	193	347	17	61908522	61908776
BF948995	PSMC5	2	110	17	61908718	61908827	PER1	95	186	17	8043855	8043945
CN413033	PSMC5	21	359	17	61905495	61907669	SLC4A5	355	551	2	74588368	74588563
AU143199	PSMC5	1	210	17	61908875	61909296	ATP5A1	210	695	18	43669875	43678287
CK725100	PSMC5	17	161	17	61909127	61909376	PSD3	156	687	8	18725438	18729525
BI002868	PSMC5	9	124	17	61908916	61909140	PSMC5	110	160	17	61909289	61909339
DB320226	PSMC5	1	181	17	61909094	61909379	ALDH4A1	174	510	1	19198500	19198836
AB209036	PSMC5	1	1056	17	61905185	61908877	PNPO	1052	5749	17	46026318	46031022

Other DBs for Structural Variants

Structural Variants in Ensembl: go to Ensembl Structural variation

Structural Variants in dbVar: go to dbVar

Top

Copy Number Variations in COSMIC : go to COSMIC mutation CNV/Expr

There's no copy number variation information in COSMIC data for this gene.

Top

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=4

Top

Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=29)	Stat. for Synonymous SNVs (# total SNVs=16)

Stat. for Deletions (# total SNVs=1)	Stat. for Insertions (# total SNVs=0)
	There's no inserted snv.

Top

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
chr17:61907831-61907831	p.L174L	4
chr17:61906877-61906877	p.Q40Q	3
chr17:61907804-61907804	p.I165I	2
chr17:61908745-61908745	p.R310H	2
chr17:61907214-61907214	p.R57C	2
chr17:61907764-61907764	p.G152V	2
chr17:61907223-61907223	p.R60W	2
chr17:61907224-61907224	p.R60L	2
chr17:61907257-61907258	p.S71L	1
chr17:61908556-61908556	p.L280L	1

Top

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				9	1		1		2				3	2			4	4		8
# mutation				11	1		1		1				3	2			4	5		9
nonsynonymous SNV				9			1						3	1			1	4		6
synonymous SNV				2	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])

Top

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
chr17:61906877	p.Q32Q,PSMC5	3
chr17:61907804	p.I157I,PSMC5	2
chr17:61907214	p.R49C,PSMC5	2
chr17:61907223	p.R52W,PSMC5	2
chr17:61907224	p.R52L,PSMC5	2
chr17:61907721	p.V156V,PSMC5	1
chr17:61908237	p.N270T,PSMC5	1
chr17:61908745	p.L293M,PSMC5	1
chr17:61907723	p.E158K,PSMC5	1
chr17:61908429	p.S295L,PSMC5	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 PSMC5 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]

Top

Gene Expression for PSMC5

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))

Top

CNV vs Gene Expression Plot

* This plots show the correlation between CNV and gene expression.

: Open all plots for all cancer types

Top

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


AMZ2,AMZ2P1,CEP95,CCDC47,CYB561,DDX42,DDX5, EMC9,FTSJ3,HRAS,MAP3K3,METTL2A,MRPL38,POLG2, PSMC5,PTRH2,SMARCD2,STRADA,TACO1,TEX2,TLK2	ARL6IP4,AURKAIP1,HYPK,TSR3,C19orf70,CDC37,CHMP2A, COPS6,CUEDC2,FIS1,GADD45GIP1,MRPL28,NAA10,NDUFA13, NDUFS6,PDAP1,PSMC3,PSMC5,SNF8,STUB1,UBXN6

AARSD1,ARHGDIA,ATP5H,CCDC137,DDX42,DNAJC7,FTSJ3, GPS1,H3F3B,HGS,PSMC5,PTRH2,SAP30BP,SIRT7, SLC25A19,SMARCD2,SNF8,STRADA,TACO1,TAF15,UBE2O	ADCYAP1,APLN,KIAA1549L,CMSS1,CCDC124,ENO1,HARS, IFITM2,LEPREL1,NUDC,PDAP1,PFDN2,PGAM1,PSMB2, PSMB6,PSMC3,PSMC5,S100A11,STOM,TUBG1,U2AF1

Co-Expressed gene's Protein-protein interaction Network Plot

: Open all plots for all cancer types

Top

Interacting Genes (from Pathway Commons)

: Open all interacting genes' information including KEGG pathway for all interacting genes from DAVID

Top

Pharmacological Information for PSMC5

There's no related Drug.

Top

Cross referenced IDs for PSMC5

* 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