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 PSME2

Basic gene info.	Gene symbol	PSME2
	Gene name	proteasome (prosome, macropain) activator subunit 2 (PA28 beta)
	Synonyms	PA28B\|PA28beta\|REGbeta
	Cytomap	UCSC genome browser: 14q11.2
	Genomic location	chr14 :24612573-24615855
	Type of gene	protein-coding
	RefGenes	NM_002818.2,
	Ensembl id	ENSG00000100911
	Description	11S regulator complex beta subunit11S regulator complex subunit betaMCP activator, 31-kD subunitREG-betaactivator of multicatalytic protease subunit 2cell migration-inducing protein 22proteasome activator 28 subunit betaproteasome activator 28-beta
	Modification date	20141207
dbXrefs	MIM : 602161
	HGNC : HGNC
	Ensembl : ENSG00000100911
	HPRD : 03697
	Vega : OTTHUMG00000028797
Protein	UniProt: go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PSME2
	BioGPS: 5721
	Gene Expression Atlas: ENSG00000100911
	The Human Protein Atlas: ENSG00000100911
Pathway	NCI Pathway Interaction Database: PSME2
	KEGG: PSME2
	REACTOME: PSME2
	ConsensusPathDB
	Pathway Commons: PSME2
Metabolism	MetaCyc: PSME2
	HUMANCyc: PSME2
Regulation	Ensembl's Regulation: ENSG00000100911
	miRBase: chr14 :24,612,573-24,615,855
	TargetScan: NM_002818
	cisRED: ENSG00000100911
Context	iHOP: PSME2
	cancer metabolism search in PubMed: PSME2
	UCL Cancer Institute: PSME2
Assigned class in ccmGDB	C

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Phenotypic Information for PSME2(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PSME2
	Familial Cancer Database: PSME2

* 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: PSME2
	MedGen: PSME2 (Human Medical Genetics with Condition)
	ClinVar: PSME2
Phenotype	MGI: PSME2 (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PSME2

Mutations for PSME2

* 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	PSME2	chr14	24612887	24612907		chr14	24637616	24637636

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 PSME2 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
AV646791	PSME2	2	109	14	24614462	24614674	ANKRD46	103	367	8	101534603	101534921
AV651403	PSME2	2	109	14	24614462	24614674	ANKRD46	103	363	8	101534607	101534921
AV652105	PSME2	2	109	14	24614462	24614674	ANKRD46	103	606	8	101534418	101534921
AV651374	PSME2	2	109	14	24614462	24614674	ANKRD46	103	368	8	101534602	101534921
BF205135	PSME2	125	198	14	24615741	24615814	RPS20	199	691	8	56985619	56987051
BF884903	PSME2	1	112	14	24614339	24614642	SNAP91	104	123	6	84312558	84312577
AW997232	PSME2	3	236	14	24614613	24615821	RAB10	233	383	2	26298749	26298901
BG999584	TGOLN2	26	302	2	85548105	85548383	PSME2	301	556	14	24613284	24613539

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=8

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=12)	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
chr14:24615447-24615447	p.V17V	8
chr14:24612871-24612871	p.R188W	2
chr14:24612869-24612869	p.R188R	1
chr14:24613646-24613646	p.K131R	1
chr14:24614958-24614958	p.F35L	1
chr14:24613650-24613650	p.P130S	1
chr14:24614962-24614962	p.R34I	1
chr14:24613196-24613196	p.K180N	1
chr14:24614267-24614267	p.L120L	1
chr14:24615432-24615432	p.Q22Q	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		2	2			1	4	2		5
# mutation							1			1		2	2			1	4	2		5
nonsynonymous SNV							1			1		1	1				4	2		3
synonymous SNV												1	1			1				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
chr14:24612869	p.R188W	1
chr14:24614473	p.S179F	1
chr14:24612871	p.E170E	1
chr14:24614958	p.K156R	1
chr14:24613200	p.V153V	1
chr14:24614962	p.Q143K	1
chr14:24613226	p.K131R	1
chr14:24615432	p.P130S	1
chr14:24613431	p.P109S	1
chr14:24615758	p.Q83E	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 PSME2 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 PSME2

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


APOL1,APOL2,EMC9,HLA-B,IFI35,IRF1,IRF9, MRPL52,NEDD8,PSMA3,PSMB10,PSMB8,PSMB9,PSMC1, PSME1,PSME2,RNF181,RNF31,RPL36AL,TRIM21,UBE2L6	LY6E,MANF,NANS,NFKBIE,PPIB,PRELID1,PSMB10, PSMB8,PSME1,PSME2,RAB34,RANBP1,RARRES3,RNASEH2A, RUVBL1,SDF2L1,SNRPF,SSR4,TAPBP,TOR3A,UBE2L6

APOL2,BAK1,BATF2,BST2,EIF5A,ETV7,FBXO6, HLA-DMA,IRF1,NMI,PSMA3,PSMA6,PSMB10,PSMB8, PSMB9,PSME1,PSME2,RARRES3,RPL36AL,TAP1,UBE2L6	APOL1,ASS1,CASP1,CXCL9,ETV7,FAM26F,GBP1, GBP4,GBP7,GZMB,HRASLS2,IFI35,IFITM1,LAP3, PARP9,PSMB10,PSMB9,PSME1,PSME2,STAT1,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 PSME2

There's no related Drug.

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Cross referenced IDs for PSME2

* 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