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 PSME1

Basic gene info.	Gene symbol	PSME1
	Gene name	proteasome (prosome, macropain) activator subunit 1 (PA28 alpha)
	Synonyms	IFI5111\|PA28A\|PA28alpha\|REGalpha
	Cytomap	UCSC genome browser: 14q11.2
	Genomic location	chr14 :24605377-24608176
	Type of gene	protein-coding
	RefGenes	NM_001281528.1, NM_001281529.1,NM_006263.3,NM_176783.2,
	Ensembl id	ENSG00000092010
	Description	11S regulator complex subunit alpha29-kD MCP activator subunitIGUP I-5111activator of multicatalytic protease subunit 1interferon gamma up-regulated I-5111 proteininterferon-gamma IEF SSP 5111interferon-gamma-inducible protein 5111proteasome activa
	Modification date	20141207
dbXrefs	MIM : 600654
	HGNC : HGNC
	Ensembl : ENSG00000092010
	HPRD : 02803
	Vega : OTTHUMG00000028795
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSME1
	BioGPS: 5720
	Gene Expression Atlas: ENSG00000092010
	The Human Protein Atlas: ENSG00000092010
Pathway	NCI Pathway Interaction Database: PSME1
	KEGG: PSME1
	REACTOME: PSME1
	ConsensusPathDB
	Pathway Commons: PSME1
Metabolism	MetaCyc: PSME1
	HUMANCyc: PSME1
Regulation	Ensembl's Regulation: ENSG00000092010
	miRBase: chr14 :24,605,377-24,608,176
	TargetScan: NM_001281528
	cisRED: ENSG00000092010
Context	iHOP: PSME1
	cancer metabolism search in PubMed: PSME1
	UCL Cancer Institute: PSME1
Assigned class in ccmGDB	C

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Phenotypic Information for PSME1(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSME1
	Familial Cancer Database: PSME1

* 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: PSME1
	MedGen: PSME1 (Human Medical Genetics with Condition)
	ClinVar: PSME1
Phenotype	MGI: PSME1 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSME1

Mutations for PSME1

* 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 PSME1 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
BI048257	KCNE3	74	94	11	74176021	74176041	PSME1	81	339	14	24606001	24606259
BG979539	MYH9	30	174	22	36681947	36682855	PSME1	173	293	14	24606350	24606585
BM990679	PSME1	19	455	14	24607403	24608168	IQCE	447	506	7	2647130	2647189

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=7)	Stat. for Synonymous SNVs (# total SNVs=4)

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
chr14:24607306-24607306	p.N147D	2
chr14:24606616-24606616	p.K74K	1
chr14:24607315-24607315	p.V150L	1
chr14:24606744-24606744	p.E88*	1
chr14:24607316-24607316	p.V150A	1
chr14:24606746-24606746	p.E88E	1
chr14:24607332-24607332	p.?	1
chr14:24606928-24606928	p.V104V	1
chr14:24607399-24607399	p.?	1
chr14:24606933-24606933	p.C106Y	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=1

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		2			2		1			1		1				1		1
# mutation	2	1		2			2		1			1		1				1		1
nonsynonymous SNV	1			1			1					1		1				1		1
synonymous SNV	1	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
chr14:24606936	p.V150A,PSME1	1
chr14:24606965	p.M160I,PSME1	1
chr14:24606976	p.G169G,PSME1	1
chr14:24607315	p.R198W,PSME1	1
chr14:24607316	p.A10A,PSME1	1
chr14:24607425	p.K74K,PSME1	1
chr14:24607452	p.E88E,PSME1	1
chr14:24605501	p.K90N,PSME1	1
chr14:24607692	p.N107S,PSME1	1
chr14:24606616	p.L117V,PSME1	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 PSME1 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 PSME1

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


BST2,IFT43,CHMP4A,EMC9,GMPR2,IFI35,IRF9, MDP1,NEDD8,NRL,PSMB10,PSMB8,PSME1,PSME2, RABGGTA,RARRES3,RNF181,RNF31,RPL36AL,TM9SF1,UBE2L6	ARPC4,C17orf49,EIF6,GSTP1,IMP3,LSM2,LY6E, MANF,PRELID1,PSMB10,PSMB8,PSME1,PSME2,PSMG3, PYCARD,RAB34,RANBP1,RARRES3,SDF2,SNRPF,WDR54

EIF5A,ETV7,FBXO6,IFI27,IRF1,NAA38,MRPL52, NMI,PSMA3,PSMA6,PSMB10,PSMB8,PSMB9,PSMD9, PSME1,PSME2,RARRES3,RPL36AL,SCO2,TAP1,UBE2L6	C5orf15,CARD16,CASP1,EPSTI1,ETV7,FAM26F,GBP4, IFI30,IFI35,IRF1,NMI,PSMB10,PSMB8,PSMB9, PSME1,PSME2,RARRES3,STAT1,TAP1,TRIM21,UBE2L6

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 PSME1

There's no related Drug.

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Cross referenced IDs for PSME1

* 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