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 PPP2CA

Basic gene info.	Gene symbol	PPP2CA
	Gene name	protein phosphatase 2, catalytic subunit, alpha isozyme
	Synonyms	PP2Ac\|PP2CA\|PP2Calpha\|RP-C
	Cytomap	UCSC genome browser: 5q31.1
	Genomic location	chr5 :133532147-133561950
	Type of gene	protein-coding
	RefGenes	NM_002715.2,
	Ensembl id	ENSG00000113575
	Description	PP2A-alphaprotein phosphatase 2 (formerly 2A), catalytic subunit, alpha isoformprotein phosphatase 2A catalytic subunit, alpha isoformreplication protein Cserine/threonine protein phosphatase 2A, catalytic subunit, alpha isoformserine/threonine-prote
	Modification date	20141222
dbXrefs	MIM : 176915
	HGNC : HGNC
	HPRD : 08912
Protein	UniProt: P67775 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PPP2CA
	BioGPS: 5515
	Gene Expression Atlas: ENSG00000113575
	The Human Protein Atlas: ENSG00000113575
Pathway	NCI Pathway Interaction Database: PPP2CA
	KEGG: PPP2CA
	REACTOME: PPP2CA
	ConsensusPathDB
	Pathway Commons: PPP2CA
Metabolism	MetaCyc: PPP2CA
	HUMANCyc: PPP2CA
Regulation	Ensembl's Regulation: ENSG00000113575
	miRBase: chr5 :133,532,147-133,561,950
	TargetScan: NM_002715
	cisRED: ENSG00000113575
Context	iHOP: PPP2CA
	cancer metabolism search in PubMed: PPP2CA
	UCL Cancer Institute: PPP2CA
Assigned class in ccmGDB	B - This gene belongs to cancer gene.

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Phenotypic Information for PPP2CA(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PPP2CA
	Familial Cancer Database: PPP2CA

* 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_MRNA REACTOME_METABOLISM_OF_RNA REACTOME_METABOLISM_OF_CARBOHYDRATES REACTOME_GLUCOSE_METABOLISM

Others
OMIM	176915; gene.
Orphanet
Disease	KEGG Disease: PPP2CA
	MedGen: PPP2CA (Human Medical Genetics with Condition)
	ClinVar: PPP2CA
Phenotype	MGI: PPP2CA (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PPP2CA

Mutations for PPP2CA

* 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
breast	PPP2CA	chr5	133538588	133538588		chr5	133576604	133576604
breast	PPP2CA	chr5	133538588	133538588		chr5	133598689	133598689

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 PPP2CA 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
AA598481	PPP2CA	1	57	5	133532933	133532989	PPP2CA	56	506	5	133532869	133533318
CD722562	PPP2CA	23	280	5	133532781	133533038	PPP2CA	277	519	5	133533382	133534865
DB352016	PPP2CA	1	224	5	133532782	133533005	SAMD12	218	538	8	119271563	119271883
AK124366	SAMD12	1	2387	8	119271563	119274046	PPP2CA	2381	2604	5	133532782	133533005
BI870214	PPP2CA	108	328	5	133532781	133533001	PIK3CA	319	341	3	178893499	178893521
T39914	PPP2CA	24	77	5	133532954	133533007	PPP2CA	73	271	5	133532791	133532989

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=25)	Stat. for Synonymous SNVs (# total SNVs=9)

Stat. for Deletions (# total SNVs=2)	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
chr5:133537696-133537696	p.R110H	2
chr5:133536100-133536100	p.Q222E	2
chr5:133536147-133536147	p.R206H	2
chr5:133537662-133537662	p.R121R	2
chr5:133541780-133541780	p.R49*	2
chr5:133536739-133536739	p.S171S	2
chr5:133536760-133536760	p.F164L	1
chr5:133537694-133537694	p.I111F	1
chr5:133536091-133536091	p.S225P	1
chr5:133536763-133536763	p.I163I	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=3

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		6					1			2	1	1			2	4		6
# mutation	2	1		5					1			2	1	1			2	5		6
nonsynonymous SNV	1	1		2					1			1		1			1	4		5
synonymous SNV	1			3								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
chr5:133537696	p.R121R	2
chr5:133536739	p.R110H	2
chr5:133536147	p.R206H	2
chr5:133537662	p.S171S	2
chr5:133537663	p.F164L	1
chr5:133536726	p.I163I	1
chr5:133537691	p.P154S	1
chr5:133536734	p.D131D	1
chr5:133541666	p.V126A	1
chr5:133534831	p.R268H	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 PPP2CA 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 PPP2CA

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


C5orf15,SMIM15,COMMD10,CSNK1A1,DCTN4,GIN1,H2AFY, HSPA4,MED7,MRPS36,NDFIP1,PGGT1B,PPP2CA,RIOK2, RNF14,SAR1B,SKP1,TAF9,TMED7,UBE2B,ZCCHC10	BCAS2,GSKIP,SPTSSA,CHMP1B,CSNK1A1,DPM1,EEF1E1, HAT1,MAPK1IP1L,MED31,MOB4,MOSPD1,MRPL42,PNO1, PPP2CA,TRMT10C,TMEM9B,TPRKB,UBE2N,VAPA,VTA1

CCNB1,CDC42SE2,COX7C,HINT1,MRPL22,MRPS36,NDUFA2, NUDCD2,PFDN1,PPP2CA,SAR1B,SREK1IP1,SKP1,SRA1, TAF9,TBCA,TTC1,UBE2B,UBE2D2,UQCRQ,ZCCHC10	AMD1,BZW1,SLIRP,EMC7,C20orf24,RRP36,CCNH, CHUK,EMC8,GTF2A2,MRPL20,MRPL47,POMP,PPP2CA, PSMC6,PSMD13,RAB1A,TAF13,TIMM17A,UBE2N,UCHL3

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 PPP2CA

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Chemistry	BindingDB	P67775; -.
Chemistry	ChEMBL	CHEMBL4703; -.
Organism-specific databases	PharmGKB	PA33663; -.
Organism-specific databases	CTD	5515; -.

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, alpha isozyme	approved; nutraceutical	Vitamin E
DB02506	protein phosphatase 2, catalytic subunit, alpha isozyme	experimental	2,6,8-Trimethyl-3-Amino-9-Benzyl-9-Methoxynonanoic Acid
DB06905	protein phosphatase 2, catalytic subunit, alpha isozyme	experimental	(2S,3S,4E,6E,8S,9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid
DB00877	protein phosphatase 2, catalytic subunit, alpha isozyme	approved; investigational	Sirolimus

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Cross referenced IDs for PPP2CA

* 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