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 PSMD11

Basic gene info.	Gene symbol	PSMD11
	Gene name	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11
	Synonyms	Rpn6\|S9\|p44.5
	Cytomap	UCSC genome browser: 17q11.2
	Genomic location	chr17 :30771501-30808042
	Type of gene	protein-coding
	RefGenes	NM_001270482.1, NM_002815.3,
	Ensembl id	ENSG00000108671
	Description	26S proteasome non-ATPase regulatory subunit 1126S proteasome regulatory subunit 926S proteasome regulatory subunit RPN626S proteasome regulatory subunit S926S proteasome regulatory subunit p44.5
	Modification date	20141207
dbXrefs	MIM : 604449
	HGNC : HGNC
	Ensembl : ENSG00000108671
	HPRD : 05119
	Vega : OTTHUMG00000132811
Protein	UniProt: O00231 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMD11
	BioGPS: 5717
	Gene Expression Atlas: ENSG00000108671
	The Human Protein Atlas: ENSG00000108671
Pathway	NCI Pathway Interaction Database: PSMD11
	KEGG: PSMD11
	REACTOME: PSMD11
	ConsensusPathDB
	Pathway Commons: PSMD11
Metabolism	MetaCyc: PSMD11
	HUMANCyc: PSMD11
Regulation	Ensembl's Regulation: ENSG00000108671
	miRBase: chr17 :30,771,501-30,808,042
	TargetScan: NM_001270482
	cisRED: ENSG00000108671
Context	iHOP: PSMD11
	cancer metabolism search in PubMed: PSMD11
	UCL Cancer Institute: PSMD11
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PSMD11(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMD11
	Familial Cancer Database: PSMD11

* 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	604449; gene.
Orphanet
Disease	KEGG Disease: PSMD11
	MedGen: PSMD11 (Human Medical Genetics with Condition)
	ClinVar: PSMD11
Phenotype	MGI: PSMD11 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMD11

Mutations for PSMD11

* 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 PSMD11 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
AI291788	LINC00340	87	112	6	22054080	22054105	PSMD11	112	458	17	30800904	30806905
BF083127	PSMD11	6	62	17	30806292	30806348	PSMD11	55	222	17	30796104	30800878
AW835516	PSMD11	161	180	17	30777413	30777432	CTNND1	165	564	11	57536507	57537167

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=6

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=34)	Stat. for Synonymous SNVs (# total SNVs=8)

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
chr17:30791555-30791555	p.L136S	3
chr17:30774048-30774048	p.K59N	2
chr17:30791554-30791554	p.L136L	2
chr17:30806861-30806861	p.?	2
chr17:30807212-30807212	p.H375N	2
chr17:30804556-30804556	p.C289C	2
chr17:30804557-30804557	p.V290M	2
chr17:30791091-30791091	p.E115K	2
chr17:30791132-30791132	p.A128A	2
chr17:30796143-30796143	p.S192Y	2

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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	2	2		9			3		2			5	1	1			1	3		7
# mutation	2	2		6			3		2			5	1	1			1	3		7
nonsynonymous SNV	2	2		4			1		2			5	1					2		6
synonymous SNV				2			2							1			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
chr17:30791555	p.L136S,PSMD11	3
chr17:30804557	p.L136L,PSMD11	2
chr17:30791554	p.D161D,PSMD11	2
chr17:30796051	p.V290M,PSMD11	2
chr17:30781559	p.A128T,PSMD11	1
chr17:30800864	p.R337Q,PSMD11	1
chr17:30806902	p.S135Y,PSMD11	1
chr17:30781593	p.S357F,PSMD11	1
chr17:30800897	p.K358E,PSMD11	1
chr17:30807212	p.H375Y,PSMD11	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 PSMD11 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 PSMD11

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


TEFM,C17orf75,CDK5R1,CES1,CES1P1,CSHL1,DDX52, DUSP14,EME1,KPNA2,LIN28A,MYO1D,PSMD11,PSMD12, PSMD14,RAB11FIP4,RHOT1,SPAG5,SUZ12,UTP6,ZNF207	DNAJA4,DUSP3,EPM2A,FYCO1,IDE,KLHL31,KPNA1, KPNA3,MFN2,NDUFS1,NRD1,OGDH,PRKAR2A,PSMC2, PSMD11,PSMD2,PSMD7,SAR1B,SIX1,TACC2,UBE3C

ATAD5,BLMH,COPRS,EFTUD2,EIF4A3,EPR1,GOSR1, KPNB1,LIG3,NCAPH,NMT1,POLDIP2,PSMD11,PSME3, RAD51D,SPAG5,SUZ12,ALYREF,TUBG1,UTP18,UTP6	CAP1,CEACAM1,DHRS9,GDPD3,GHITM,GNAI3,HSPA4, KRT20,NAT1,NT5C3A,PLAC8,PSMD11,PSMD1,RALB, SEC61G,TPM3,TPMT,TTC39B,VDAC2,VPS26A,YWHAB

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 PSMD11

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA33902; -.
Organism-specific databases	CTD	5717; -.

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, 11	approved; nutraceutical	Adenosine triphosphate

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Cross referenced IDs for PSMD11

* 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