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 PPP2R2A

Basic gene info.	Gene symbol	PPP2R2A
	Gene name	protein phosphatase 2, regulatory subunit B, alpha
	Synonyms	B55A\|B55ALPHA\|PR52A\|PR55A
	Cytomap	UCSC genome browser: 8p21.2
	Genomic location	chr8 :26150731-26230195
	Type of gene	protein-coding
	RefGenes	NM_001177591.1, NM_002717.3,
	Ensembl id	ENSG00000221914
	Description	protein phosphatase 2 (formerly 2A), regulatory subunit B (PR52), alpha isoformserine/threonine protein phosphatase 2A, 55 KDA regulatory subunit B, alpha isoformserine/threonine-protein phosphatase 2A 55 kDa regulatory subunit B alpha isoform
	Modification date	20141207
dbXrefs	MIM : 604941
	HGNC : HGNC
	Ensembl : ENSG00000221914
	HPRD : 09223
	Vega : OTTHUMG00000163850
Protein	UniProt: P63151 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PPP2R2A
	BioGPS: 5520
	Gene Expression Atlas: ENSG00000221914
	The Human Protein Atlas: ENSG00000221914
Pathway	NCI Pathway Interaction Database: PPP2R2A
	KEGG: PPP2R2A
	REACTOME: PPP2R2A
	ConsensusPathDB
	Pathway Commons: PPP2R2A
Metabolism	MetaCyc: PPP2R2A
	HUMANCyc: PPP2R2A
Regulation	Ensembl's Regulation: ENSG00000221914
	miRBase: chr8 :26,150,731-26,230,195
	TargetScan: NM_001177591
	cisRED: ENSG00000221914
Context	iHOP: PPP2R2A
	cancer metabolism search in PubMed: PPP2R2A
	UCL Cancer Institute: PPP2R2A
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PPP2R2A in cancer cell metabolism	1. Zhao X-J, Zhuo H (2014) ECR-MAPK Regulation in Liver Early Development. BioMed research international. go to article

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Phenotypic Information for PPP2R2A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PPP2R2A
	Familial Cancer Database: PPP2R2A

* 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_MRNA REACTOME_METABOLISM_OF_RNA

Others
OMIM	604941; gene.
Orphanet
Disease	KEGG Disease: PPP2R2A
	MedGen: PPP2R2A (Human Medical Genetics with Condition)
	ClinVar: PPP2R2A
Phenotype	MGI: PPP2R2A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PPP2R2A

Mutations for PPP2R2A

* 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

* 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	PPP2R2A	chr8	26157693	26157713	PPP2R2A	chr8	26217091	26217111
ovary	PPP2R2A	chr8	26158489	26158509	PPP2R2A	chr8	26161740	26161760
ovary	PPP2R2A	chr8	26159717	26159737	PPP2R2A	chr8	26161690	26161710
ovary	PPP2R2A	chr8	26166708	26166728	PPP2R2A	chr8	26185253	26185273
ovary	PPP2R2A	chr8	26170011	26170031	PPP2R2A	chr8	26173426	26173446
ovary	PPP2R2A	chr8	26175240	26175260		chr12	34086235	34086255
prostate	PPP2R2A	chr8	26191039	26193039		chr20	46625222	46627222

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 PPP2R2A 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
BM014893	PPP2R2A	1	209	8	26227651	26227860	SH3KBP1	203	794	X	19553732	19554335
CB988238	PPP2R2A	28	300	8	26149147	26151258	PCMTD1	297	786	8	52733190	52758325
CF994096	PPP2R2A	28	300	8	26149147	26151258	PCMTD1	297	699	8	52744004	52758325
AF130091	ARL15	133	1533	5	53345654	53347054	PPP2R2A	1529	1939	8	25285773	25286183
AW879061	PPP2R2A	1	84	8	26228134	26228218	PPP2R2A	77	182	8	26228002	26228107
AW879127	PPP2R2A	5	89	8	26228132	26228218	PPP2R2A	82	187	8	26228002	26228107
BF771688	PPP2R2A	24	104	8	26227958	26228038	GEMIN2	96	306	14	39597484	39602895
CF994079	PPP2R2A	28	300	8	26149147	26151258	PCMTD1	297	696	8	52744004	52758325
AL050206	PPP2R2A	1	94	8	26228891	26228984	PPP2R2A	86	844	8	26228929	26229687
AW170574	TSEN15	100	154	1	184014902	184190216	PPP2R2A	155	579	8	26164337	26164761
AL041184	PPP2R2A	22	228	8	25282476	25282682	PPP2R2A	222	636	8	25282102	25282518

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

Mutation type/ Tissue ID

brca

cns

cerv

endome

haematopo

kidn

Lintest

liver

lung

ovary

pancre

prost

skin

stoma

thyro

urina

Total # sample

GAIN (# sample)

LOSS (# sample)

cf) Tissue ID; Tissue type (1; Breast, 2; Central_nervous_system, 3; Cervix, 4; Endometrium, 5; Haematopoietic_and_lymphoid_tissue, 6; Kidney, 7; Large_intestine, 8; Liver, 9; Lung, 10; NS, 11; Ovary, 12; Pancreas, 13; Prostate, 14; Skin, 15; Stomach, 16; Thyroid, 17; Urinary_tract)

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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=1

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=3)	Stat. for Synonymous SNVs (# total SNVs=1)

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
chr8:26227751-26227751	p.R389H	1
chr8:26227853-26227853	p.A423V	1
chr8:26220313-26220313	p.I251V	1
chr8:26227731-26227731	p.S382S	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	2		5					1			4	1	2			2	5		9
# mutation	1	2		9					1			4	1	2			2	6		11
nonsynonymous SNV		1		4					1			4	1	2			1	4		9
synonymous SNV	1	1		5													1	2		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
chr8:26227731	p.S392S,PPP2R2A	2
chr8:26218532	p.R262Q,PPP2R2A	1
chr8:26221281	p.R399R,PPP2R2A	1
chr8:26227751	p.F87L,PPP2R2A	1
chr8:26196503	p.M266I,PPP2R2A	1
chr8:26218536	p.F425F,PPP2R2A	1
chr8:26221289	p.S89G,PPP2R2A	1
chr8:26227752	p.C272G,PPP2R2A	1
chr8:26212032	p.K427T,PPP2R2A	1
chr8:26218603	p.P92P,PPP2R2A	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 PPP2R2A 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 PPP2R2A

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


BNIP3L,CCDC25,CHMP7,CNOT7,ELP3,ENTPD4,HMBOX1, INTS9,CCAR2,LONRF1,MCPH1,MTMR9,PCM1,PPP2R2A, RPL23AP53,TNKS,TRIM35,VPS37A,WRN,XPO7,ZNF395	ANKRD28,ARIH1,TRAPPC11,C5orf22,CUL3,DHX29,DHX36, FASTKD2,MAP2K4,NAA15,NOC3L,PATL1,PLAA,PPP2R2A, RBM18,RINT1,UCHL5,USP15,UTP15,ZNF460,ZW10

BIN3,TTI2,CCDC25,CHMP7,CNOT7,DCTN6,ELP3, ERI1,ESCO2,FUT10,INTS10,KCTD9,MCPH1,PBK, PPP2R2A,R3HCC1,SH2D4A,TNFRSF10A,TNFRSF10B,VPS37A,XPO7	ATG4A,BZW1,CAPZA1,CHUK,DERL2,ERP44,GDI2, LYSMD3,PI4K2B,PPP2CA,PPP2R2A,PSMD12,RAB11A,RAB1A, RBM7,SEC61G,TMED10,TSPAN8,TWF1,VPS26A,ZBTB8OS

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 PPP2R2A

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P63151; -.
Chemistry	ChEMBL	CHEMBL4284; -.
Organism-specific databases	PharmGKB	PA33668; -.
Organism-specific databases	CTD	5520; -.

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
DB02506	protein phosphatase 2, regulatory subunit B, alpha	experimental	2,6,8-Trimethyl-3-Amino-9-Benzyl-9-Methoxynonanoic Acid

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Cross referenced IDs for PPP2R2A

* 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