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 PPP2CB

Basic gene info.	Gene symbol	PPP2CB
	Gene name	protein phosphatase 2, catalytic subunit, beta isozyme
	Synonyms	PP2Abeta\|PP2CB
	Cytomap	UCSC genome browser: 8p12
	Genomic location	chr8 :30643125-30670352
	Type of gene	protein-coding
	RefGenes	NM_001009552.1, NM_004156.2,
	Ensembl id	ENSG00000104695
	Description	PP2A-betaprotein phosphatase 2 (formerly 2A), catalytic subunit, beta isoformprotein phosphatase 2, catalytic subunit, beta isoformprotein phosphatase 2A catalytic subunit, beta isoformprotein phosphatase type 2A catalytic subunitserine/threonine pro
	Modification date	20141207
dbXrefs	MIM : 176916
	HGNC : HGNC
	Ensembl : ENSG00000104695
	HPRD : 01487
	Vega : OTTHUMG00000163949
Protein	UniProt: P62714 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PPP2CB
	BioGPS: 5516
	Gene Expression Atlas: ENSG00000104695
	The Human Protein Atlas: ENSG00000104695
Pathway	NCI Pathway Interaction Database: PPP2CB
	KEGG: PPP2CB
	REACTOME: PPP2CB
	ConsensusPathDB
	Pathway Commons: PPP2CB
Metabolism	MetaCyc: PPP2CB
	HUMANCyc: PPP2CB
Regulation	Ensembl's Regulation: ENSG00000104695
	miRBase: chr8 :30,643,125-30,670,352
	TargetScan: NM_001009552
	cisRED: ENSG00000104695
Context	iHOP: PPP2CB
	cancer metabolism search in PubMed: PPP2CB
	UCL Cancer Institute: PPP2CB
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PPP2CB in cancer cell metabolism	1. Loo LW, Tiirikainen M, Cheng I, Lum‐Jones A, Seifried A, et al. (2013) Integrated analysis of genome‐wide copy number alterations and gene expression in microsatellite stable, CpG island methylator phenotype‐negative colon cancer. Genes, Chromosomes and Cancer 52: 450-466. go to article

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Phenotypic Information for PPP2CB(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PPP2CB
	Familial Cancer Database: PPP2CB

* 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_INTEGRATION_OF_ENERGY_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM	176916; gene.
Orphanet
Disease	KEGG Disease: PPP2CB
	MedGen: PPP2CB (Human Medical Genetics with Condition)
	ClinVar: PPP2CB
Phenotype	MGI: PPP2CB (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PPP2CB

Mutations for PPP2CB

* 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	PPP2CB	chr8	30648151	30648171	STK31	chr7	23816445	23816465
ovary	PPP2CB	chr8	30648191	30648211	GPR124	chr8	37699627	37699647
ovary	PPP2CB	chr8	30662623	30662643		chr8	30637631	30637651
pancreas	PPP2CB	chr8	30649235	30649255	RBPMS	chr8	30381730	30381750

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 PPP2CB related fusion information.

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

BF809982

PPP2CB

213

30643738

30648832

COL1A2

204

288

94045799

94047103

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=22)	Stat. for Synonymous SNVs (# total SNVs=3)

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
chr8:30643831-30643831	p.?	2
chr8:30651555-30651555	p.R206C	2
chr8:30651800-30651800	p.?	1
chr8:30657186-30657186	p.H63R	1
chr8:30651447-30651447	p.Q242E	1
chr8:30655114-30655114	p.A157T	1
chr8:30643751-30643751	p.*310Y	1
chr8:30657228-30657228	p.R49H	1
chr8:30651484-30651484	p.N229N	1
chr8:30655116-30655116	p.T156I	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		3	1	3					1			4					2	3		3
# mutation		3	1	4					1			4					2	3		4
nonsynonymous SNV		3		4								3					2	3		3
synonymous SNV			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
chr8:30651555	p.R206C	2
chr8:30657228	p.H118H	1
chr8:30655114	p.P108T	1
chr8:30669865	p.R106C	1
chr8:30643766	p.P305P	1
chr8:30655116	p.K104N	1
chr8:30648767	p.R268H	1
chr8:30655186	p.E95D	1
chr8:30648809	p.R254L	1
chr8:30655229	p.D77Y	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 PPP2CB 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 PPP2CB

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,CNOT7,DCTN6,ELP3,GSR,GTF2E2, INTS9,LEPROTL1,MCPH1,MTMR9,PPP2CB,PPP2R2A,RPL23AP53, SARAF,TNKS,TRIM35,UBXN8,VPS37A,WRN,ZNF395	ARL2BP,ARPP19,BNIP2,C4orf3,CLIC4,GNG12,GOLT1B, MBNL2,MMGT1,NDFIP1,OSTM1,PLEKHA3,PPP2CB,PRKRIR, RAP1B,RNF11,RRAS2,SEPT7,TMEM126B,VAMP7,VPS26A

ASAH1,TTI2,CCDC25,CHMP7,CNOT7,DCTN6,ENTPD4, ERI1,FUT10,GSR,GTF2E2,KCTD9,KIF13B,LEPROTL1, PPP2CB,PPP2R2A,SH2D4A,SARAF,TNFRSF10A,TNFRSF10B,VPS37A	CAB39,CCDC68,CDKN1A,CHMP2B,CHMP4B,GCNT3,KRT20, LHFPL2,MAPK6,PLS1,PPP2CB,PRR13,PTPRH,RAB5A, RIOK3,SHOC2,SLC2A13,TUBAL3,VAPA,VDAC2,WSB2

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 PPP2CB

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA33664; -.
Organism-specific databases	CTD	5516; -.

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
DB00163	protein phosphatase 2, catalytic subunit, beta isozyme	approved; nutraceutical	Vitamin E

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Cross referenced IDs for PPP2CB

* 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