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 PPP2R1A

Basic gene info.	Gene symbol	PPP2R1A
	Gene name	protein phosphatase 2, regulatory subunit A, alpha
	Synonyms	PP2A-Aalpha\|PP2AAALPHA\|PR65A
	Cytomap	UCSC genome browser: 19q13.41
	Genomic location	chr19 :52693054-52729678
	Type of gene	protein-coding
	RefGenes	NM_014225.5, NR_033500.1,
	Ensembl id	ENSG00000105568
	Description	PP2A subunit A isoform PR65-alphaPP2A subunit A isoform R1-alphamedium tumor antigen-associated 61 KDA proteinprotein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoformserine/threonine protein phosphatase 2A, 65 kDa regulatory su
	Modification date	20141207
dbXrefs	MIM : 605983
	HGNC : HGNC
	HPRD : 16184
Protein	UniProt: P30153 go to UniProt's Cross Reference DB Table
Expression	CleanEX: HS_PPP2R1A
	BioGPS: 5518
	Gene Expression Atlas: ENSG00000105568
	The Human Protein Atlas: ENSG00000105568
Pathway	NCI Pathway Interaction Database: PPP2R1A
	KEGG: PPP2R1A
	REACTOME: PPP2R1A
	ConsensusPathDB
	Pathway Commons: PPP2R1A
Metabolism	MetaCyc: PPP2R1A
	HUMANCyc: PPP2R1A
Regulation	Ensembl's Regulation: ENSG00000105568
	miRBase: chr19 :52,693,054-52,729,678
	TargetScan: NM_014225
	cisRED: ENSG00000105568
Context	iHOP: PPP2R1A
	cancer metabolism search in PubMed: PPP2R1A
	UCL Cancer Institute: PPP2R1A
Assigned class in ccmGDB	A - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PPP2R1A in cancer cell metabolism	1. Morvan D, Steyaert JM, Schwartz L, Israel M, Demidem A (2012) Normal human melanocytes exposed to chronic insulin and glucose supplementation undergo oncogenic changes and methyl group metabolism cellular redistribution. American Journal of Physiology-Endocrinology and Metabolism 302: E1407-E1418. go to article

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Phenotypic Information for PPP2R1A(metabolism pathway, cancer, disease, phenome)

Cancer Description
Cancer	CGAP: PPP2R1A
	Familial Cancer Database: PPP2R1A

* 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 UCEC ⁶,	Therapeutic Vulnerabilities in Cancer⁷

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,
6 http://www.nature.com/nature/journal/v497/n7447/full/nature12113.html,
7Therapeutic 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	605983; gene.
Orphanet
Disease	KEGG Disease: PPP2R1A
	MedGen: PPP2R1A (Human Medical Genetics with Condition)
	ClinVar: PPP2R1A
Phenotype	MGI: PPP2R1A (International Mouse Phenotyping Consortium)
Phenotype	PhenomicDB: PPP2R1A

Mutations for PPP2R1A

* 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	PPP2R1A	chr19	52700117	52700137	PPP2R1A	chr19	52713471	52713491

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 PPP2R1A 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
AW473090	PPP2R1A	9	166	19	52716252	52719077	PPP2R1A	163	615	19	52719071	52723114
CN418097	PPP2R1A	10	89	19	52724244	52724323	PPP2R1A	86	610	19	52716038	52719916
AI419727	WNT5B	3	251	12	1756150	1756398	PPP2R1A	248	404	19	52719277	52719887
W48816	RPL32	1	98	3	12877548	12877645	PPP2R1A	94	407	19	52716331	52719874
AL709013	ADAM12	5	290	10	127829031	127829315	PPP2R1A	273	384	19	52729560	52729671

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=44

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Somatic Mutation Counts per Tissue in COSMIC data

Stat. for Non-Synonymous SNVs (# total SNVs=176)	Stat. for Synonymous SNVs (# total SNVs=23)

Stat. for Deletions (# total SNVs=3)	Stat. for Insertions (# total SNVs=1)

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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
chr19:52715982-52715982	p.R183W	31
chr19:52715971-52715971	p.P179R	31
chr19:52716323-52716323	p.S256Y	17
chr19:52715983-52715983	p.R183Q	13
chr19:52716329-52716329	p.R258H	9
chr19:52715979-52715979	p.R182W	8
chr19:52716327-52716327	p.W257C	6
chr19:52709237-52709237	p.E64G	3
chr19:52716325-52716325	p.W257G	3
chr19:52709238-52709238	p.E64D	3

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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=10

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	3	2	18			5			1		6	10	4			4	11	2	28
# mutation	3	3	2	13			5			1		6	10	4			5	12	2	20
nonsynonymous SNV	1	1	2	9			2			1		5	7	4			2	10	2	17
synonymous SNV	2	2		4			3					1	3				3	2		3

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
chr19:52715971	p.P179R	9
chr19:52715982	p.R183W	8
chr19:52716323	p.S256F	4
chr19:52716329	p.R258H	4
chr19:52716217	p.S120L	2
chr19:52714601	p.R183Q	2
chr19:52715979	p.R28C	2
chr19:52709237	p.R221W	2
chr19:52715983	p.E64G	2
chr19:52716328	p.R258C	2

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 PPP2R1A 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 PPP2R1A

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


AKT1S1,EMC10,EPN1,HSPBP1,LENG1,MED25,NAT14, NOSIP,NR1H2,PNKP,PPP2R1A,PRPF31,PTOV1,RUVBL2, SCAF1,TBC1D17,TFPT,UBE2M,VRK3,ZNF444,ZNF579	ARF5,CHMP6,DRG2,EEFSEC,HSPBP1,MCRS1,MRPL4, MRPS12,NOC4L,NSUN5,NUDT22,OTUB1,PPP1CA,PPP2R1A, PTOV1,RNF187,SGTA,SSSCA1,TBL3,TIMM17B,TMEM134

EMC10,CHMP2A,EPN1,FIZ1,HSPBP1,NAPA,PNKP, PPP2R1A,PRPF31,RPL18,RUVBL2,SAE1,SCAF1,TRIM28, UBE2M,ZBTB45,ZNF444,ZNF524,ZNF574,ZNF784,ZNF787	ALDOA,ATP5D,AP5S1,CHCHD10,FAM129B,CPTP,GTF3C5, HIGD2A,IDH3G,LGALS4,NDUFV1,PGLS,PGM1,PPDPF, PPP2R1A,RAB1B,RCE1,SDSL,THAP4,UQCRC1,ZDHHC12

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 PPP2R1A

Cross-referenced pharmacological DB IDs from Uniprot

DB Category	DB Name	DB's ID and Url link
Organism-specific databases	PharmGKB	PA33666; -.
Organism-specific databases	CTD	5518; -.

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 A, alpha	experimental	2,6,8-Trimethyl-3-Amino-9-Benzyl-9-Methoxynonanoic Acid
DB06905	protein phosphatase 2, regulatory subunit A, alpha	experimental	(2S,3S,4E,6E,8S,9S)-3-amino-9-methoxy-2,6,8-trimethyl-10-phenyldeca-4,6-dienoic acid

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Cross referenced IDs for PPP2R1A

* 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