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 PSMC4

Basic gene info.	Gene symbol	PSMC4
	Gene name	proteasome (prosome, macropain) 26S subunit, ATPase, 4
	Synonyms	MIP224\|RPT3\|S6\|TBP-7\|TBP7
	Cytomap	UCSC genome browser: 19q13.11-q13.13
	Genomic location	chr19 :40477072-40487353
	Type of gene	protein-coding
	RefGenes	NM_006503.3, NM_153001.2,
	Ensembl id	ENSG00000013275
	Description	26S protease regulatory subunit 6B26S proteasome AAA-ATPase subunit RPT3MB67-interacting proteinTat-binding protein 7protease 26S subunit 6
	Modification date	20141207
dbXrefs	MIM : 602707
	HGNC : HGNC
	Ensembl : ENSG00000013275
	HPRD : 04085
	Vega : OTTHUMG00000182577
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMC4
	BioGPS: 5704
	Gene Expression Atlas: ENSG00000013275
	The Human Protein Atlas: ENSG00000013275
Pathway	NCI Pathway Interaction Database: PSMC4
	KEGG: PSMC4
	REACTOME: PSMC4
	ConsensusPathDB
	Pathway Commons: PSMC4
Metabolism	MetaCyc: PSMC4
	HUMANCyc: PSMC4
Regulation	Ensembl's Regulation: ENSG00000013275
	miRBase: chr19 :40,477,072-40,487,353
	TargetScan: NM_006503
	cisRED: ENSG00000013275
Context	iHOP: PSMC4
	cancer metabolism search in PubMed: PSMC4
	UCL Cancer Institute: PSMC4
Assigned class in ccmGDB	C

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Phenotypic Information for PSMC4(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMC4
	Familial Cancer Database: PSMC4

* 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: PSMC4
	MedGen: PSMC4 (Human Medical Genetics with Condition)
	ClinVar: PSMC4
Phenotype	MGI: PSMC4 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMC4

Mutations for PSMC4

* 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 PSMC4 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
BP432759	MXD4	9	87	4	2259708	2263498	PSMC4	87	369	19	40485976	40486604
BQ219974	ELL3	1	479	15	44084544	44086239	PSMC4	479	557	19	40480336	40480497
AI143487	PSMC4	10	124	19	40487233	40487348	WNT7B	121	186	22	46316306	46316371
BU674697	PSMC4	17	138	19	40487233	40487353	PSMC4	138	339	19	40486343	40487225
BU608468	PSMC4	17	126	19	40487235	40487344	PSMC4	121	265	19	40487098	40487242
CV361424	PSMC4	1	134	19	40485834	40486052	PSMC4	131	476	19	40477072	40478447

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=4

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=39)	Stat. for Synonymous SNVs (# total SNVs=15)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=2)

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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
chr19:40485861-40485861	p.A271T	4
chr19:40478338-40478338	p.K66N	3
chr19:40487161-40487161	p.A402A	2
chr19:40487178-40487178	p.K408T	2
chr19:40480235-40480235	p.I119I	2
chr19:40477113-40477113	p.E2K	2
chr19:40480653-40480654	p.R200fs*43	2
chr19:40480659-40480659	p.P199P	2
chr19:40485749-40485749	p.S233S	2
chr19:40478056-40478056	p.E14K	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=4

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	3		4			1			2		7	2	1		1	5	6		11
# mutation	1	3		4			1			2		7	2	1		1	4	6		10
nonsynonymous SNV		3		3			1					4	2				1	2		9
synonymous SNV	1			1						2		3		1		1	3	4		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
chr19:40478338	p.K66N	3
chr19:40485861	p.I119I,PSMC4	2
chr19:40480235	p.A271T,PSMC4	2
chr19:40478337	p.L68L	1
chr19:40486259	p.H221H,PSMC4	1
chr19:40480516	p.S355S,PSMC4	1
chr19:40485749	p.T100I,PSMC4	1
chr19:40486287	p.R229Q,PSMC4	1
chr19:40480518	p.K369N,PSMC4	1
chr19:40485783	p.T107T,PSMC4	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 PSMC4 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 PSMC4

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


AKT2,C19orf47,COX6B1,EID2,EIF3K,FBL,LRFN1, MAP3K10,MRPS12,NFKBIB,PAF1,PSMC4,PSMD8,RPS16, SARS2,SHKBP1,SIRT2,SPINT2,SUPT5H,TIMM50,YIF1B	ADRM1,ASNA1,ATP6V0D1,COPE,FAM58A,LSM4,NAA38, MRPL28,PPP1CA,PPP1R14B,PSMB6,PSMC4,ROMO1,SEC13, SLC39A3,TBCB,TSPAN17,TUBB4B,USP5,YIF1A,YIF1B

ALKBH6,AP2S1,BCL2L12,C19orf47,COX6B1,EGLN2,EID2, LIN37,MRPS12,NFKBIB,PDCD2L,PDCD5,POLR2I,PRMT1, PSENEN,PSMC4,PSMD8,RBM42,RUVBL2,TIMM50,YIF1B	ACTR3,ADRM1,ASS1,CALR,CASP5,CRELD2,DNAJB11, PDIA6,PGK1,POMP,PSMA1,PSMA3,PSMB2,PSMB3, PSMC4,PSMD13,PSMD2,RPN1,SDF2L1,SEC61B,TMED9

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 PSMC4

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
DB00877	proteasome (prosome, macropain) 26S subunit, ATPase, 4	approved; investigational	Sirolimus

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Cross referenced IDs for PSMC4

* 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