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 PSMD2

Basic gene info.	Gene symbol	PSMD2
	Gene name	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2
	Synonyms	P97\|RPN1\|S2\|TRAP2
	Cytomap	UCSC genome browser: 3q27.1
	Genomic location	chr3 :184017021-184026840
	Type of gene	protein-coding
	RefGenes	NM_001278708.1, NM_001278709.1,NM_002808.4,
	Ensembl id	ENSG00000175166
	Description	26S proteasome non-ATPase regulatory subunit 255.11 proteinTNFR-associated protein 2protein 55.11tumor necrosis factor type 1 receptor-associated protein 2
	Modification date	20141207
dbXrefs	MIM : 606223
	HGNC : HGNC
	Ensembl : ENSG00000175166
	HPRD : 05870
	Vega : OTTHUMG00000156796
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMD2
	BioGPS: 5708
	Gene Expression Atlas: ENSG00000175166
	The Human Protein Atlas: ENSG00000175166
Pathway	NCI Pathway Interaction Database: PSMD2
	KEGG: PSMD2
	REACTOME: PSMD2
	ConsensusPathDB
	Pathway Commons: PSMD2
Metabolism	MetaCyc: PSMD2
	HUMANCyc: PSMD2
Regulation	Ensembl's Regulation: ENSG00000175166
	miRBase: chr3 :184,017,021-184,026,840
	TargetScan: NM_001278708
	cisRED: ENSG00000175166
Context	iHOP: PSMD2
	cancer metabolism search in PubMed: PSMD2
	UCL Cancer Institute: PSMD2
Assigned class in ccmGDB	C

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Phenotypic Information for PSMD2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMD2
	Familial Cancer Database: PSMD2

* 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: PSMD2
	MedGen: PSMD2 (Human Medical Genetics with Condition)
	ClinVar: PSMD2
Phenotype	MGI: PSMD2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMD2

Mutations for PSMD2

* 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 PSMD2 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
CA336957	PSMD2	37	273	3	184017116	184018173	HDAC10	271	358	22	50683616	50683703
CA336827	PSMD2	37	273	3	184017116	184018173	HDAC10	271	362	22	50683612	50683703
CA336584	PSMD2	1	155	3	184017035	184017189	YBX2	156	215	17	7191584	7191643
DA541950	DHFR	1	107	5	79947318	79947424	PSMD2	108	556	3	184019408	184020492
BE002761	PSMD2	5	158	3	184018072	184018227	TTC39C	141	514	18	21619719	21620092
BF081412	DST	10	355	6	56371298	56373505	PSMD2	343	570	3	184023571	184023926
BE720207	PSMD2	6	279	3	184021161	184021806	INPP1	260	458	2	191236012	191236210
AI201767	SYS1	1	221	20	43996535	43996755	PSMD2	216	332	3	184019372	184019676
AF075367	SERPINA1	1	439	14	94849170	94854926	PSMD2	429	683	3	184026505	184026757
CO245088	PSMD2	18	73	3	184023562	184023617	PSMD2	72	751	3	184017638	184020284
AI110868	SERPINA1	1	439	14	94849170	94854926	PSMD2	429	683	3	184026505	184026757
BE720196	PSMD2	2	285	3	184021161	184021818	INPP1	266	464	2	191236012	191236210
BE003023	PSMD2	15	119	3	184018072	184018176	PSMD2	112	312	3	184018205	184019685

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=40)	Stat. for Synonymous SNVs (# total SNVs=18)

Stat. for Deletions (# total SNVs=2)	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
chr3:184020156-184020156	p.?	3
chr3:184024196-184024196	p.D621E	2
chr3:184017699-184017699	p.?	2
chr3:184025278-184025278	p.Y723C	2
chr3:184025435-184025435	p.R746H	2
chr3:184021749-184021749	p.L446L	2
chr3:184018174-184018174	p.R100H	2
chr3:184019697-184019697	p.R181Q	2
chr3:184026538-184026538	p.T863A	1
chr3:184019718-184019718	p.V188A	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	8	1		7		2			6	4			1	7	15		12
# mutation		2	1	8	1		7		2			7	4			1	7	18		12
nonsynonymous SNV		2	1	5			3		2			4	2			1	2	14		9
synonymous SNV				3	1		4					3	2				5	4		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
chr3:184019697	p.L758F,PSMD2	2
chr3:184026613	p.R100H	2
chr3:184018174	p.R616H,PSMD2	2
chr3:184025435	p.R51Q,PSMD2	2
chr3:184025484	p.R557Q,PSMD2	1
chr3:184020522	p.T733A,PSMD2	1
chr3:184026546	p.C121C,PSMD2	1
chr3:184022099	p.G356G,PSMD2	1
chr3:184024268	p.N575N,PSMD2	1
chr3:184025708	p.F735F,PSMD2	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 PSMD2 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 PSMD2

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


ABCF3,ACTL6A,ALG3,AP2M1,DCUN1D1,DNAJB11,DVL3, ECE2,EIF4G1,FBXO45,FXR1,GMPS,LSG1,PCYT1A, PLK1,PSMD2,RFC4,SENP5,TBCCD1,WDR53,YEATS2	PRADC1,C6orf106,CDK16,HAGH,KIF1C,MAP4,NDUFA8, NFE2L1,OGDH,PGK1,PINK1,PRKACA,PSMC2,PSMD2, PSMD7,RNF10,SDHA,SNTA1,VCP,WBSCR16,ZFAND3

ABCF3,CCNF,CLSPN,COPB2,DNMT1,DTX3L,EIF4G1, INCENP,EMC1,KIAA1524,KLHL18,KPNA1,MCM2,NAA50, NUP210,PCYT1A,PLK1,PSMD1,PSMD2,RNF168,SHCBP1	ACTR3,ADRM1,CALR,CAP1,CARS,CEACAM6,ENO1, OR52I1,PCBP1,PGAM1,PLIN3,PSMB2,PSMC3,PSMC4, PSMD1,PSMD2,PSMD3,RALB,SNORA45B,TARS,TFG

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 PSMD2

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
DB00188	proteasome (prosome, macropain) 26S subunit, non-ATPase, 2	approved; investigational	Bortezomib

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Cross referenced IDs for PSMD2

* 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