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 PSMD13

Basic gene info.	Gene symbol	PSMD13
	Gene name	proteasome (prosome, macropain) 26S subunit, non-ATPase, 13
	Synonyms	HSPC027\|Rpn9\|S11\|p40.5
	Cytomap	UCSC genome browser: 11p15.5
	Genomic location	chr11 :236807-252984
	Type of gene	protein-coding
	RefGenes	NM_002817.3, NM_175932.2,
	Ensembl id	ENSG00000185627
	Description	26S proteasome non-ATPase regulatory subunit 1326S proteasome regulatory subunit RPN926S proteasome regulatory subunit S1126S proteasome regulatory subunit p40.526S proteasome subunit p40.5
	Modification date	20141207
dbXrefs	MIM : 603481
	HGNC : HGNC
	Ensembl : ENSG00000185627
	HPRD : 04595
	Vega : OTTHUMG00000119072
Protein	UniProt: Q9UNM6 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMD13
	BioGPS: 5719
	Gene Expression Atlas: ENSG00000185627
	The Human Protein Atlas: ENSG00000185627
Pathway	NCI Pathway Interaction Database: PSMD13
	KEGG: PSMD13
	REACTOME: PSMD13
	ConsensusPathDB
	Pathway Commons: PSMD13
Metabolism	MetaCyc: PSMD13
	HUMANCyc: PSMD13
Regulation	Ensembl's Regulation: ENSG00000185627
	miRBase: chr11 :236,807-252,984
	TargetScan: NM_002817
	cisRED: ENSG00000185627
Context	iHOP: PSMD13
	cancer metabolism search in PubMed: PSMD13
	UCL Cancer Institute: PSMD13
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PSMD13(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMD13
	Familial Cancer Database: PSMD13

* 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	603481; gene.
Orphanet
Disease	KEGG Disease: PSMD13
	MedGen: PSMD13 (Human Medical Genetics with Condition)
	ClinVar: PSMD13
Phenotype	MGI: PSMD13 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMD13

Mutations for PSMD13

* 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

* Inter-chromosomal variantions includes 'interchromosomal amplicon to amplicon', 'interchromosomal amplicon to non-amplified dna', 'interchromosomal insertion', 'Interchromosomal unknown type'.

- For Intra-chromosomal Variations

There's no intra-chromosomal structural variation.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	PSMD13	chr11	237770	237790		chr16	21518285	21518305

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 PSMD13 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
BX103504	PSMD13	1	401	11	237045	244761	FAM157B	400	493	9	141131447	141131540
BF768948	EIF3D	2	312	22	36914891	36916733	PSMD13	303	404	11	252820	252921

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=5

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=19)	Stat. for Synonymous SNVs (# total SNVs=14)

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
chr11:244167-244167	p.N72N	5
chr11:237087-237087	p.N13S	4
chr11:247370-247370	p.Q164K	3
chr11:247372-247372	p.Q164Q	2
chr11:244171-244171	p.L74L	2
chr11:244428-244428	p.P90S	2
chr11:250827-250827	p.Q267*	2
chr11:251591-251591	p.E295Q	1
chr11:248825-248825	p.L206L	1
chr11:251630-251630	p.?	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		1	1	9					2			3	1	1			3	2		1
# mutation		1	1	8					2			4	1	1			2	2		2
nonsynonymous SNV				6								3	1	1			2	2		1
synonymous SNV		1	1	2					2			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
chr11:247370	p.Q166K,PSMD13	3
chr11:247372	p.N74N,PSMD13	2
chr11:244167	p.P92S,PSMD13	2
chr11:244428	p.Q166Q,PSMD13	2
chr11:244466	p.Q269H,PSMD13	1
chr11:251895	p.E281E,PSMD13	1
chr11:244732	p.A316T,PSMD13	1
chr11:251916	p.T30S,PSMD13	1
chr11:252523	p.A316V,PSMD13	1
chr11:252542	p.T38A	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 PSMD13 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 PSMD13

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


LBHD1___C11orf98,HRAS,MOB2,MRPL17,MRPL23,NDUFA11,NDUFS3, PEX16,PKP3,PRDX5,PSMB6,PSMC3,PSMD13,PTDSS2, RHOG,RPL27A,RPLP2,SURF2,TAF10,TALDO1,TSSC4	ASNA1,ELP6,CHMP2A,FAM58A,MRPL28,MRPL51,MRPS34, NUDC,PFDN6,PMF1,PMVK,POLR2F,POP7,PPP1CA, PSMC5,PSMD13,RAB1B,RNF187,SNRNP35,UBE2J2,WBSCR22

ATP5L,BANF1,EMG1,GADD45GIP1,LSM4,MRPL11,MRPL17, MRPL23,NDUFS3,PSMA1,PSMB1,PSMB3,PSMB4,PSMC3, PSMD13,PTPMT1,RNF181,SDHAF2,MSRB1,TALDO1,PAM16	SLIRP,EMC7,DAD1,LSM1,MRPL20,PGK1,POMP, PSMA1,PSMA2,PSMA5,PSMA6,PSMA7,PSMB1,PSMB4, PSMC6,PSMD13,PSMD8,PTS,RBX1,STRA13,UFD1L

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 PSMD13

There's no related Drug.

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Cross referenced IDs for PSMD13

* 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