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 PSMC2

Basic gene info.	Gene symbol	PSMC2
	Gene name	proteasome (prosome, macropain) 26S subunit, ATPase, 2
	Synonyms	MSS1\|Nbla10058\|S7
	Cytomap	UCSC genome browser: 7q22.1-q22.3
	Genomic location	chr7 :102987970-103002914
	Type of gene	protein-coding
	RefGenes	NM_001204453.1, NM_002803.3,
	Ensembl id	ENSG00000161057
	Description	26S protease regulatory subunit 726S proteasome AAA-ATPase subunit RPT1mammalian suppressor of sgv-1 of yeastprotease 26S subunit 7proteasome 26S subunit ATPase 2proteasome 26S subunit, ATPase, 2putative protein product of Nbla10058
	Modification date	20141207
dbXrefs	MIM : 154365
	HGNC : HGNC
	Ensembl : ENSG00000161057
	HPRD : 01105
	Vega : OTTHUMG00000157206
Protein	UniProt: P35998 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSMC2
	BioGPS: 5701
	Gene Expression Atlas: ENSG00000161057
	The Human Protein Atlas: ENSG00000161057
Pathway	NCI Pathway Interaction Database: PSMC2
	KEGG: PSMC2
	REACTOME: PSMC2
	ConsensusPathDB
	Pathway Commons: PSMC2
Metabolism	MetaCyc: PSMC2
	HUMANCyc: PSMC2
Regulation	Ensembl's Regulation: ENSG00000161057
	miRBase: chr7 :102,987,970-103,002,914
	TargetScan: NM_001204453
	cisRED: ENSG00000161057
Context	iHOP: PSMC2
	cancer metabolism search in PubMed: PSMC2
	UCL Cancer Institute: PSMC2
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PSMC2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSMC2
	Familial Cancer Database: PSMC2

* 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	154365; gene.
Orphanet
Disease	KEGG Disease: PSMC2
	MedGen: PSMC2 (Human Medical Genetics with Condition)
	ClinVar: PSMC2
Phenotype	MGI: PSMC2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSMC2

Mutations for PSMC2

* 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 PSMC2 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
BM983260	PSMC2	18	75	7	103008545	103008602	PSMC2	73	229	7	103008158	103008401
DA326202	PSMC2	2	223	7	102988112	102995381	APC	218	549	5	112177806	112178137
BF985831	CGA	17	290	6	87795224	87795497	PSMC2	283	415	7	103008430	103008562
AU118024	GTF3C4	2	323	9	135559279	135559600	PSMC2	323	754	7	102988089	103002475
BQ315283	PSMC2	7	379	7	103004625	103008013	PTPRF	374	428	1	44010784	44010838

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=3

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=30)	Stat. for Synonymous SNVs (# total SNVs=13)

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
chr7:103003148-103003148	p.K146K	2
chr7:103004748-103004748	p.V250V	2
chr7:103003152-103003152	p.Q148E	2
chr7:102996218-102996218	p.E90*	2
chr7:103006538-103006538	p.R258C	2
chr7:102996237-102996237	p.A96V	2
chr7:103006556-103006556	p.A264P	2
chr7:103004631-103004631	p.G211G	2
chr7:103008218-103008218	p.R369K	2
chr7:103004703-103004703	p.A235A	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	5	1	2	5			4		4	1		2	4				2	7		4
# mutation	11	1	2	5			4		4	1		2	4				2	7		4
nonsynonymous SNV	8		1	3			3		2			2	4				2	5		3
synonymous SNV	3	1	1	2			1		2	1								2		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
chr7:103004703	p.G211G	2
chr7:103004631	p.A235A	2
chr7:103002424	p.P152S	1
chr7:103008365	p.G313A	1
chr7:103004686	p.V416V	1
chr7:103007958	p.T162A	1
chr7:103002469	p.I315V	1
chr7:103008390	p.P209H	1
chr7:103007988	p.D325N	1
chr7:103002482	p.I22I,PSMC2	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 PSMC2 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 PSMC2

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


ARMC10,ARPC1A,ATP5C1,ATP5J2,CMC2,CENPN,DBF4, DNAJC2,MGC72080,ORC5,PSMA2,PSMB2,PSMC2,PSMD14, RHEB,RINT1,SHFM1,SLC25A13,SNRPG,SSBP1,TUBA1C	PRADC1,C6orf106,FAM118B,FEZ2,FUNDC2,ICMT,LDHA, MAP4,NDUFB3,PGK1,PRKACA,PSMC2,PSMD14,PSMD1, PSMD2,PSMD7,SETD3,SGCG,SYNPO,UBE2D4,WSB2

AP4M1,ARMC10,ATP5J2,ATP6V1F,BUD31,MALSU1,CAPZA2, CDK5,CHCHD2,COPS6,DBF4,GTPBP10,ORC5,PMPCB, POP7,PSMA2,PSMC2,RHEB,RINT1,RPA3,SSBP1	CCDC167,COPS4,EIF2S2,HAT1,MORF4L2,MRPL20,PSMA1, PSMA2,PSMA3,PSMA7,PSMB1,PSMB5,PSMB6,PSMC2, PSMC3,PSMD14,PSMD6,PSMD7,RPL22L1,SSBP1,TCEB1

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 PSMC2

There's no related Drug.

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Cross referenced IDs for PSMC2

* 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