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 PSMD6

Basic gene info.	Gene symbol	PSMD6
	Gene name	proteasome (prosome, macropain) 26S subunit, non-ATPase, 6
	Synonyms	Rpn7\|S10\|SGA-113M\|p42A\|p44S10
	Cytomap	UCSC genome browser: 3p14.1
	Genomic location	chr3 :63996230-64009120
	Type of gene	protein-coding
	RefGenes	NM_001271779.1, NM_001271780.1,NM_001271781.1,NM_014814.2,
	Ensembl id	ENSG00000163636
	Description	26S proteasome non-ATPase regulatory subunit 6breast cancer-associated protein SGA-113Mphosphonoformate immuno-associated protein 4proteasome regulatory particle subunit p44S10
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000163636
	HPRD : 18370
	Vega : OTTHUMG00000158765
Protein	UniProt: Q15008 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMD6
	BioGPS: 9861
	Gene Expression Atlas: ENSG00000163636
	The Human Protein Atlas: ENSG00000163636
Pathway	NCI Pathway Interaction Database: PSMD6
	KEGG: PSMD6
	REACTOME: PSMD6
	ConsensusPathDB
	Pathway Commons: PSMD6
Metabolism	MetaCyc: PSMD6
	HUMANCyc: PSMD6
Regulation	Ensembl's Regulation: ENSG00000163636
	miRBase: chr3 :63,996,230-64,009,120
	TargetScan: NM_001271779
	cisRED: ENSG00000163636
Context	iHOP: PSMD6
	cancer metabolism search in PubMed: PSMD6
	UCL Cancer Institute: PSMD6
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PSMD6(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMD6
	Familial Cancer Database: PSMD6

* 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: PSMD6
	MedGen: PSMD6 (Human Medical Genetics with Condition)
	ClinVar: PSMD6
Phenotype	MGI: PSMD6 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMD6

Mutations for PSMD6

* 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 PSMD6 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
DA942713	PSMD6	1	281	3	64008050	64009080	EIF3A	273	582	10	120802239	120809487
CD626170	PSMD6	3	471	3	64005007	64009108	ZNF646	471	693	16	31088783	31089005
CD626167	ZNF646	13	240	16	31088783	31089010	PSMD6	240	541	3	64008056	64009108
CD626168	PSMD6	3	472	3	64005007	64009108	ZNF646	472	680	16	31088783	31088997
CD626169	ZNF646	13	240	16	31088783	31089010	PSMD6	240	699	3	64005019	64009108
CD626166	PSMD6	15	484	3	64005007	64009108	ZNF646	484	670	16	31088783	31088971

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=29)	Stat. for Synonymous SNVs (# total SNVs=5)

Stat. for Deletions (# total SNVs=0)	Stat. for Insertions (# total SNVs=0)
There's no deleted snv.	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
chr3:64008049-64008049	p.E99G	4
chr3:64004505-64004505	p.L236F	2
chr3:64004514-64004514	p.R233G	2
chr3:64008050-64008050	p.E99K	2
chr3:64004282-64004282	p.Q273H	2
chr3:63996436-63996436	p.D360N	2
chr3:64005033-64005033	p.R146R	2
chr3:64009039-64009039	p.I19M	2
chr3:63999137-63999137	p.V325F	1
chr3:64007994-64007994	p.K117N	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		2		12					1			2	1			1	1	3		3
# mutation		2		7					1			2	1			1	1	3		3
nonsynonymous SNV		2		5					1			2				1		2		3
synonymous SNV				3									1				1	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
chr3:64008049	p.E61G,PSMD6	4
chr3:64004505	p.L198F,PSMD6	3
chr3:64008051	p.S60R,PSMD6	2
chr3:64004302	p.K55N,PSMD6	1
chr3:64008044	p.S231F,PSMD6	1
chr3:64004323	p.L43S,PSMD6	1
chr3:64004350	p.R229R,PSMD6	1
chr3:64008066	p.R229C,PSMD6	1
chr3:64004611	p.L222L,PSMD6	1
chr3:64008103	p.H213Y,PSMD6	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 PSMD6 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 PSMD6

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


ANO10,APEH,ARF4,C3orf14,CMC1,GNL3,NDUFV2, NPRL2,PDE12,PDHB,PSMD6,RFT1,RHOA,RPP14, SELK,SHQ1,SPCS1,THOC7,TUSC2,UBA3,UQCRC1	ATP5C1,ATP5F1,BOLA3,SLIRP,CMC2,COPS4,COX7B, EIF2S2,GLRX5,LAMTOR5,MRPL47,NDUFAB1,NDUFB1,NDUFB4, NDUFB6,NDUFV2,PSMA3,PSMA6,PSMD14,PSMD6,TCEB1

BRIX1,CCDC58,TMA7,CCNB1,DYNC1LI1,GNL3,KCTD6, LSM3,MRPL47,PDCD10,PDHB,PSMA1,PSMD14,PSMD6, SRSF3,SPCS1,TAF9,TBCA,THOC7,UBA3,UBE2N	MCMBP,COPS4,EIF2B3,EIF2S1,HAT1,MAGOHB,MORF4L2, MRPS10,PPIL1,PSMC2,PSMD14,PSMD6,PSMD7,RAN, SNRPB2,SSBP1,TCEB1,TIMM17A,TOMM5,UBE2N,VBP1

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 PSMD6

There's no related Drug.

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Cross referenced IDs for PSMD6

* 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