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 PSMD4

Basic gene info.	Gene symbol	PSMD4
	Gene name	proteasome (prosome, macropain) 26S subunit, non-ATPase, 4
	Synonyms	AF\|AF-1\|ASF\|MCB1\|Rpn10\|S5A\|pUB-R5
	Cytomap	UCSC genome browser: 1q21.3
	Genomic location	chr1 :151227196-151239954
	Type of gene	protein-coding
	RefGenes	NM_002810.2, NM_153822.2,
	Ensembl id	ENSG00000159352
	Description	26S proteasome non-ATPase regulatory subunit 426S proteasome regulatory subunit S5AS5a/antisecretory factor proteinangiocidinantisecretory factor 1multiubiquitin chain-binding protein
	Modification date	20141207
dbXrefs	MIM : 601648
	HGNC : HGNC
	Ensembl : ENSG00000159352
	HPRD : 03386
	Vega : OTTHUMG00000012349
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMD4
	BioGPS: 5710
	Gene Expression Atlas: ENSG00000159352
	The Human Protein Atlas: ENSG00000159352
Pathway	NCI Pathway Interaction Database: PSMD4
	KEGG: PSMD4
	REACTOME: PSMD4
	ConsensusPathDB
	Pathway Commons: PSMD4
Metabolism	MetaCyc: PSMD4
	HUMANCyc: PSMD4
Regulation	Ensembl's Regulation: ENSG00000159352
	miRBase: chr1 :151,227,196-151,239,954
	TargetScan: NM_002810
	cisRED: ENSG00000159352
Context	iHOP: PSMD4
	cancer metabolism search in PubMed: PSMD4
	UCL Cancer Institute: PSMD4
Assigned class in ccmGDB	C

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Phenotypic Information for PSMD4(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMD4
	Familial Cancer Database: PSMD4

* 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: PSMD4
	MedGen: PSMD4 (Human Medical Genetics with Condition)
	ClinVar: PSMD4
Phenotype	MGI: PSMD4 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMD4

Mutations for PSMD4

* 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

- Statistics for Tissue and Mutation type

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- For Inter-chromosomal Variations

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
pancreas	PSMD4	chr1	151236464	151236484	PI4KB	chr1	151295275	151295295

cf) Tissue number; Tissue name (1;Breast, 2;Central_nervous_system, 3;Haematopoietic_and_lymphoid_tissue, 4;Large_intestine, 5;Liver, 6;Lung, 7;Ovary, 8;Pancreas, 9;Prostate, 10;Skin, 11;Soft_tissue, 12;Upper_aerodigestive_tract)

Related fusion transcripts : go to Chitars2.0

* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PSMD4 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
BU590293	RPS9	1	325	19	54705447	54711372	PSMD4	312	506	1	151239761	151239955
BU538390	C20orf27	1	335	20	3734588	3735159	PSMD4	335	670	1	151237348	151238086
U51007	IQGAP1	7	128	15	91045344	91045467	PSMD4	119	1323	1	151227233	151239865

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=24)	Stat. for Synonymous SNVs (# total SNVs=4)

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
chr1:151234659-151234659	p.R17W	2
chr1:151234661-151234661	p.R17R	1
chr1:151237918-151237918	p.K163E	1
chr1:151238873-151238873	p.E285K	1
chr1:151234711-151234711	p.N34S	1
chr1:151237936-151237936	p.H169Y	1
chr1:151238994-151238994	p.?	1
chr1:151236442-151236442	p.K74E	1
chr1:151237951-151237951	p.P174S	1
chr1:151239035-151239035	p.S312*	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	1	2		3	1		3		2			5	1				2	2		3
# mutation	1	2		4	1		3		2			5	1				2	2		4
nonsynonymous SNV	1	2		2	1		1		2			1	1				2	1		4
synonymous SNV				2			2					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
chr1:151234661	p.R17R	2
chr1:151237936	p.T88M	1
chr1:151239749	p.E283Q	1
chr1:151234711	p.R91R	1
chr1:151237951	p.D309Y	1
chr1:151239784	p.R108C	1
chr1:151236485	p.P332P	1
chr1:151237991	p.R130C	1
chr1:151236495	p.P347P	1
chr1:151238020	p.L131L	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 PSMD4 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 PSMD4

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


BOLA1,C1orf35,CRTC2,DPM3,HAX1,JTB,MRPL24, MRPL55,MRPL9,MRPS21,MTX1,PFDN2,PIPSL,PMF1, PSMB4,PSMD4,RAB13,LAMTOR2,SCNM1,SF3B4,VPS72	AKT1S1,BLOC1S1,BABAM1,RTFDC1,COPS6,FIS1,GRHPR, MAF1,MRPL16,MRPL24,MRPL2,MRPS11,NDUFA13,NDUFB7, NDUFS6,PARK7,PPP1R7,PSMB6,PSMC3,PSMD4,STUB1

C1orf35,CCT3,DAP3,HAX1,JTB,KRTCAP2,MRPL24, MRPL55,MRPL9,MTX1,PFDN2,PMVK,PPOX,PSMB4, PSMD4,PYCR2,LAMTOR2,SCAMP3,SCNM1,SNRPE,VPS72	C11orf73,COPRS,BRK1,COPS6,CREB3,DPCD,DRAP1, MANBAL,MEA1,MPV17,NUBP1,PARK7,PFDN1,PSMB6, PSMC3,PSMD4,RANGRF,SNAPIN,SSSCA1,TRMT112,UROD

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 PSMD4

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
DB00171	proteasome (prosome, macropain) 26S subunit, non-ATPase, 4	approved; nutraceutical	Adenosine triphosphate

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Cross referenced IDs for PSMD4

* 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