Cancer Cell Metabolism Gene Database

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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 symbolPPP2R1A
Gene nameprotein phosphatase 2, regulatory subunit A, alpha
SynonymsPP2A-Aalpha|PP2AAALPHA|PR65A
CytomapUCSC genome browser: 19q13.41
Genomic locationchr19 :52693054-52729678
Type of geneprotein-coding
RefGenesNM_014225.5,
NR_033500.1,
Ensembl idENSG00000105568
DescriptionPP2A 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 date20141207
dbXrefs MIM : 605983
HGNC : HGNC
HPRD : 16184
ProteinUniProt: P30153
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PPP2R1A
BioGPS: 5518
Gene Expression Atlas: ENSG00000105568
The Human Protein Atlas: ENSG00000105568
PathwayNCI Pathway Interaction Database: PPP2R1A
KEGG: PPP2R1A
REACTOME: PPP2R1A
ConsensusPathDB
Pathway Commons: PPP2R1A
MetabolismMetaCyc: PPP2R1A
HUMANCyc: PPP2R1A
RegulationEnsembl's Regulation: ENSG00000105568
miRBase: chr19 :52,693,054-52,729,678
TargetScan: NM_014225
cisRED: ENSG00000105568
ContextiHOP: PPP2R1A
cancer metabolism search in PubMed: PPP2R1A
UCL Cancer Institute: PPP2R1A
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PPP2R1A in cancer cell metabolism1. 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)
check002.gifCancer 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/

check002.gifMetabolic Pathway Description
REACTOME_INTEGRATION_OF_ENERGY_METABOLISM
REACTOME_METABOLISM_OF_MRNA
REACTOME_METABOLISM_OF_RNA
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM 605983; gene.
Orphanet
DiseaseKEGG Disease: PPP2R1A
MedGen: PPP2R1A (Human Medical Genetics with Condition)
ClinVar: PPP2R1A
PhenotypeMGI: PPP2R1A (International Mouse Phenotyping Consortium)
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.

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
ovaryPPP2R1Achr195270011752700137PPP2R1Achr195271347152713491
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 PPP2R1A related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AW473090PPP2R1A9166195271625252719077PPP2R1A163615195271907152723114
CN418097PPP2R1A1089195272424452724323PPP2R1A86610195271603852719916
AI419727WNT5B32511217561501756398PPP2R1A248404195271927752719887
W48816RPL3219831287754812877645PPP2R1A94407195271633152719874
AL709013ADAM12529010127829031127829315PPP2R1A273384195272956052729671

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 # sample   1    1 1      
GAIN (# sample)   1    1 1      
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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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=44

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check002.gifSomatic 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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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
chr19:52715971-52715971p.P179R31
chr19:52715982-52715982p.R183W31
chr19:52716323-52716323p.S256Y17
chr19:52715983-52715983p.R183Q13
chr19:52716329-52716329p.R258H9
chr19:52715979-52715979p.R182W8
chr19:52716327-52716327p.W257C6
chr19:52709237-52709237p.E64G3
chr19:52716325-52716325p.W257G3
chr19:52709238-52709238p.E64D3

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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=10

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample33218  5  1 6104  411228
# mutation33213  5  1 6104  512220
nonsynonymous SNV1129  2  1 574  210217
synonymous SNV22 4  3    13   32 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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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
chr19:52715971p.P179R9
chr19:52715982p.R183W8
chr19:52716323p.S256F4
chr19:52716329p.R258H4
chr19:52715979p.R28C2
chr19:52709237p.R221W2
chr19:52715983p.E64G2
chr19:52716328p.R258C2
chr19:52705200p.R182W2
chr19:52716217p.S120L2

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 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

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

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
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 PPP2R1A
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
Organism-specific databasesPharmGKB PA33666; -.
Organism-specific databasesCTD 5518; -.

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 A, alphaexperimental2,6,8-Trimethyl-3-Amino-9-Benzyl-9-Methoxynonanoic Acid
DB06905protein phosphatase 2, regulatory subunit A, alphaexperimental(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



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