Cancer Cell Metabolism Gene Database

  Cancer Cell Metabolism Gene DB

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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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 symbolPPP2R2A
Gene nameprotein phosphatase 2, regulatory subunit B, alpha
SynonymsB55A|B55ALPHA|PR52A|PR55A
CytomapUCSC genome browser: 8p21.2
Genomic locationchr8 :26150731-26230195
Type of geneprotein-coding
RefGenesNM_001177591.1,
NM_002717.3,
Ensembl idENSG00000221914
Descriptionprotein 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 date20141207
dbXrefs MIM : 604941
HGNC : HGNC
Ensembl : ENSG00000221914
HPRD : 09223
Vega : OTTHUMG00000163850
ProteinUniProt: P63151
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PPP2R2A
BioGPS: 5520
Gene Expression Atlas: ENSG00000221914
The Human Protein Atlas: ENSG00000221914
PathwayNCI Pathway Interaction Database: PPP2R2A
KEGG: PPP2R2A
REACTOME: PPP2R2A
ConsensusPathDB
Pathway Commons: PPP2R2A
MetabolismMetaCyc: PPP2R2A
HUMANCyc: PPP2R2A
RegulationEnsembl's Regulation: ENSG00000221914
miRBase: chr8 :26,150,731-26,230,195
TargetScan: NM_001177591
cisRED: ENSG00000221914
ContextiHOP: PPP2R2A
cancer metabolism search in PubMed: PPP2R2A
UCL Cancer Institute: PPP2R2A
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PPP2R2A in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA

check002.gifOthers
OMIM 604941; gene.
Orphanet
DiseaseKEGG Disease: PPP2R2A
MedGen: PPP2R2A (Human Medical Genetics with Condition)
ClinVar: PPP2R2A
PhenotypeMGI: PPP2R2A (International Mouse Phenotyping Consortium)
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.

check002.gifStructural Variants in COSMIC: go to COSMIC mutation histogram

- Statistics for Tissue and Mutation typeTop
- 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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
ovaryPPP2R2Achr82615769326157713PPP2R2Achr82621709126217111
ovaryPPP2R2Achr82615848926158509PPP2R2Achr82616174026161760
ovaryPPP2R2Achr82615971726159737PPP2R2Achr82616169026161710
ovaryPPP2R2Achr82616670826166728PPP2R2Achr82618525326185273
ovaryPPP2R2Achr82617001126170031PPP2R2Achr82617342626173446
ovaryPPP2R2Achr82617524026175260chr123408623534086255
prostatePPP2R2Achr82619103926193039chr204662522246627222
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)

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PPP2R2A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a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check002.gifOther DBs for Structural Variants
Structural Variants in Ensembl: go to Ensembl Structural variation
Structural Variants in dbVar: go to dbVar

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check002.gifCopy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr
 
Mutation type/ Tissue IDbrcacnscervendomehaematopokidnLintestliverlungnsovarypancreprostskinstomathyrourina
Total # sample2     1   4 1    
GAIN (# sample)1                
LOSS (# sample)1     1   4 1    
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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check002.gifSNV 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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check002.gifSomatic 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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check002.gifTop 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 positionMutation(aa)Unique sampleID count
chr8:26220313-26220313p.I251V1
chr8:26227731-26227731p.S382S1
chr8:26227751-26227751p.R389H1
chr8:26227853-26227853p.A423V1

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check002.gifSNV 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 ID1234567891011121314151617181920
# sample12 5    1  412  25 9
# mutation12 9    1  412  26 11
nonsynonymous SNV 1 4    1  412  14 9
synonymous SNV11 5            12 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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check002.gifTop 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 PositionMutation(aa)Unique sampleID count
chr8:26227731p.S392S,PPP2R2A2
chr8:26217719p.R154I,PPP2R2A1
chr8:26227853p.I295I,PPP2R2A1
chr8:26220315p.V456M,PPP2R2A1
chr8:26223851p.P165S,PPP2R2A1
chr8:26217736p.R308Q,PPP2R2A1
chr8:26227900p.V166V,PPP2R2A1
chr8:26220316p.M310T,PPP2R2A1
chr8:26223870p.P169P,PPP2R2A1
chr8:26217769p.M310I,PPP2R2A1

check002.gifOther 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

check002.gifCopy 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

check002.gifGene 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.

check002.gifDifferential 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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check002.gifCNV 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
check002.gifCo-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
check002.gifCo-Expressed gene's Protein-protein interaction 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

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check002.gifInteracting 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
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryBindingDB P63151; -.
ChemistryChEMBL CHEMBL4284; -.
Organism-specific databasesPharmGKB PA33668; -.
Organism-specific databasesCTD 5520; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02506protein phosphatase 2, regulatory subunit B, alphaexperimental2,6,8-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



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