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 PSMD12

Basic gene info.	Gene symbol	PSMD12
	Gene name	proteasome (prosome, macropain) 26S subunit, non-ATPase, 12
	Synonyms	Rpn5\|p55
	Cytomap	UCSC genome browser: 17q24.2
	Genomic location	chr17 :65336618-65362721
	Type of gene	protein-coding
	RefGenes	NM_002816.3, NM_174871.2,
	Ensembl id	ENSG00000197170
	Description	26S proteasome non-ATPase regulatory subunit 1226S proteasome regulatory subunit RPN526S proteasome regulatory subunit p55
	Modification date	20141207
dbXrefs	MIM : 604450
	HGNC : HGNC
	HPRD : 05120
Protein	UniProt: O00232 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMD12
	BioGPS: 5718
	Gene Expression Atlas: ENSG00000197170
	The Human Protein Atlas: ENSG00000197170
Pathway	NCI Pathway Interaction Database: PSMD12
	KEGG: PSMD12
	REACTOME: PSMD12
	ConsensusPathDB
	Pathway Commons: PSMD12
Metabolism	MetaCyc: PSMD12
	HUMANCyc: PSMD12
Regulation	Ensembl's Regulation: ENSG00000197170
	miRBase: chr17 :65,336,618-65,362,721
	TargetScan: NM_002816
	cisRED: ENSG00000197170
Context	iHOP: PSMD12
	cancer metabolism search in PubMed: PSMD12
	UCL Cancer Institute: PSMD12
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PSMD12(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMD12
	Familial Cancer Database: PSMD12

* 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	604450; gene.
Orphanet
Disease	KEGG Disease: PSMD12
	MedGen: PSMD12 (Human Medical Genetics with Condition)
	ClinVar: PSMD12
Phenotype	MGI: PSMD12 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMD12

Mutations for PSMD12

* 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 PSMD12 related fusion information.

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

BF064196

ABAT

354

392

8865884

8865922

PSMD12

389

490

65351510

65351611

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=25)	Stat. for Synonymous SNVs (# total SNVs=11)

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
chr17:65362552-65362552	p.L28L	4
chr17:65344748-65344748	p.A143V	2
chr17:65353701-65353701	p.?	2
chr17:65346383-65346383	p.R123*	2
chr17:65343510-65343510	p.R201Q	2
chr17:65340752-65340752	p.W351C	2
chr17:65340841-65340841	p.E322*	1
chr17:65344684-65344684	p.S164S	1
chr17:65337018-65337018	p.L438V	1
chr17:65353488-65353488	p.E76E	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		4								5	2				1	2		5
# mutation	2	1		3								5	2				1	2		6
nonsynonymous SNV	1	1		3								5	1				1	2		3
synonymous SNV	1												1							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
chr17:65343510	p.R181Q,PSMD12	2
chr17:65341972	p.M416I,PSMD12	1
chr17:65362551	p.E113K,PSMD12	1
chr17:65337022	p.L404V,PSMD12	1
chr17:65362568	p.E94D,PSMD12	1
chr17:65337060	p.R388I,PSMD12	1
chr17:65344684	p.E56E,PSMD12	1
chr17:65337107	p.S374L,PSMD12	1
chr17:65344689	p.R45S,PSMD12	1
chr17:65337149	p.S369S,PSMD12	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 PSMD12 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 PSMD12

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


AMZ2,BPTF,SMG8,CLTC,COIL,CYB561,GNA13, HELZ,KPNA2,LOC651250,MED13,METTL2A,MRPS23,NOL11, PPM1D,PRKAR1A,PSMD12,SKA2,SMURF2,TLK2,TRIM37	BTBD1,CUL2,EIF2S1,FYTTD1,GFM1,KCMF1,KIAA1279, KPNA1,KPNA4,MAPK9,MRPS10,NAA50,PLAA,PPM1B, PSMC6,PSMD12,SLC16A1,SPPL2A,STAU2,TIMM17A,USP14

AMZ2,BOLA3,C17orf58,CCDC137,CCDC47,DCUN1D5,GPS1, KPNA2,METTL2A,MRPL12,NOL11,PIGW,PSMC5,PSMD11, PSMD12,PTRH2,RPS6KB1,TACO1,ALYREF,VMP1,TOMM40	ACTR3,ARPC5L,BZW1,CHUK,DNAJB11,DNAJC3,ETF1, GNAI3,MAP2K4,NAMPT,PNP,PPP2CA,PPP2R2A,PSMB2, PSMC4,PSMD12,PSME3,RAB1A,SEC61G,SSR1,UBQLN1

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 PSMD12

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA33903; -.
Organism-specific databases	CTD	5718; -.

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, 12	approved; nutraceutical	Adenosine triphosphate

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Cross referenced IDs for PSMD12

* 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