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 PSMD1

Basic gene info.	Gene symbol	PSMD1
	Gene name	proteasome (prosome, macropain) 26S subunit, non-ATPase, 1
	Synonyms	P112\|Rpn2\|S1
	Cytomap	UCSC genome browser: 2q37.1
	Genomic location	chr2 :231921577-232037540
	Type of gene	protein-coding
	RefGenes	NM_001191037.1, NM_002807.3,NR_034059.1,
	Ensembl id	ENSG00000173692
	Description	26S proteasome non-ATPase regulatory subunit 126S proteasome regulatory subunit RPN226S proteasome regulatory subunit S126S proteasome subunit p112
	Modification date	20141207
dbXrefs	HGNC : HGNC
	Ensembl : ENSG00000173692
	HPRD : 10169
	Vega : OTTHUMG00000133223
Protein	UniProt: Q99460 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMD1
	BioGPS: 5707
	Gene Expression Atlas: ENSG00000173692
	The Human Protein Atlas: ENSG00000173692
Pathway	NCI Pathway Interaction Database: PSMD1
	KEGG: PSMD1
	REACTOME: PSMD1
	ConsensusPathDB
	Pathway Commons: PSMD1
Metabolism	MetaCyc: PSMD1
	HUMANCyc: PSMD1
Regulation	Ensembl's Regulation: ENSG00000173692
	miRBase: chr2 :231,921,577-232,037,540
	TargetScan: NM_001191037
	cisRED: ENSG00000173692
Context	iHOP: PSMD1
	cancer metabolism search in PubMed: PSMD1
	UCL Cancer Institute: PSMD1
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PSMD1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMD1
	Familial Cancer Database: PSMD1

* 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: PSMD1
	MedGen: PSMD1 (Human Medical Genetics with Condition)
	ClinVar: PSMD1
Phenotype	MGI: PSMD1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMD1

Mutations for PSMD1

* 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

There's no inter-chromosomal structural variation.

- For Intra-chromosomal Variations

* Intra-chromosomal variantions includes 'intrachromosomal amplicon to amplicon', 'intrachromosomal amplicon to non-amplified dna', 'intrachromosomal deletion', 'intrachromosomal fold-back inversion', 'intrachromosomal inversion', 'intrachromosomal tandem duplication', 'Intrachromosomal unknown type', 'intrachromosomal with inverted orientation', 'intrachromosomal with non-inverted orientation'.

Sample	Symbol_a	Chr_a	Start_a	End_a	Symbol_b	Chr_b	Start_b	End_b
ovary	PSMD1	chr2	231931976	231931996	PSMD1	chr2	231953437	231953457
ovary	PSMD1	chr2	232030759	232030779	HTR2B	chr2	231973346	231973366
pancreas	PSMD1	chr2	231923765	231923785	PSMD1	chr2	231923823	231923843

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 PSMD1 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
BE769099	TRIM26	20	297	6	1445216	1445492	PSMD1	290	384	2	232035509	232035604
DA454373	PSMD1	1	322	2	232029976	232035428	PSMD1	319	572	2	231927240	231931723
BU730843	ATP2B3	18	272	X	152835166	152835420	PSMD1	270	755	2	232030589	232037436

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=2

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=60)	Stat. for Synonymous SNVs (# total SNVs=20)

Stat. for Deletions (# total SNVs=4)	Stat. for Insertions (# total SNVs=3)

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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
chr2:231937121-231937121	p.E291D	2
chr2:231943447-231943447	p.S382S	2
chr2:231927025-231927025	p.V42I	2
chr2:231949808-231949808	p.R600*	2
chr2:231931680-231931680	p.K124fs*11	2
chr2:232035319-232035319	p.E919K	2
chr2:231937097-231937097	p.N283N	2
chr2:232035369-232035369	p.I935I	2
chr2:231934886-231934886	p.?	2
chr2:231944984-231944984	p.I457V	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=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	3		13			2		4			3	6	1			6	4		8
# mutation	2	3		17			2		4			3	6	1			8	4		11
nonsynonymous SNV	2	3		13			1		1			3	4	1			5	4		9
synonymous SNV				4			1		3				2				3			2

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
chr2:232035369	p.R546C,PSMD1	2
chr2:231948391	p.I904I,PSMD1	2
chr2:231934768	p.N32S,PSMD1	1
chr2:231949777	p.E234D,PSMD1	1
chr2:231937111	p.Q421H,PSMD1	1
chr2:232035293	p.A726V,PSMD1	1
chr2:231927025	p.V42I,PSMD1	1
chr2:231947609	p.L242L,PSMD1	1
chr2:231934803	p.G476S,PSMD1	1
chr2:231951878	p.G729G,PSMD1	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 PSMD1 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 PSMD1

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


KNSTRN,MTFR2,FARSB,KCMF1,KPNA2,NCAPG,NOP58, OIP5,ORC6,PNO1,PSMA3,PSMA4,PSMB2,PSMC2, PSMD14,PSMD1,RRM2,SNRPG,SPC25,SSB,ZC3H15	ANXA7,ATG4A,BOLA3,C20orf24,FAM98A,GTF3A,GTF3C6, LDHA,MTCH2,PGK1,PRPS1,PSMA3,PSMC2,PSMD14, PSMD1,PSMD6,PSMD7,TIMM17A,TTC1,UBE2F,WSB2

CCT4,GLRX3,HSPE1,MEMO1,MRPL44,MRPS23,MYEOV2, NIF3L1,NME1,OLA1,ORC4,PNO1,PSMA1,PSMB1, PSMD14,SRSF3,SRSF7,SNRPG,SUMO1,WDR12,YWHAQ	EBNA1BP2,EIF5AL1,HAT1,HSPE1,MAGOHB,NME1,PPIL1, PSMA1,PSMA5,PSMA7,PSMC6,PSMD14,PSMD6,RAN, RPL26L1,SNRPD1,SNRPG,SSBP1,TCEB1,TOMM5,UBE2N

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 PSMD1

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA33899; -.
Organism-specific databases	PharmGKB	PA33899; -.
Organism-specific databases	CTD	5707; -.
Organism-specific databases	CTD	5707; -.

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, 1	approved; investigational	Bortezomib

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Cross referenced IDs for PSMD1

* 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