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 PPP1CA
Basic gene info.Gene symbolPPP1CA
Gene nameprotein phosphatase 1, catalytic subunit, alpha isozyme
SynonymsPP-1A|PP1A|PP1alpha|PPP1A
CytomapUCSC genome browser: 11q13
Genomic locationchr11 :67165651-67169376
Type of geneprotein-coding
RefGenesNM_001008709.1,
NM_002708.3,NM_206873.1,
Ensembl idENSG00000172531
Descriptionprotein phosphatase 1, catalytic subunit, alpha isoformserine/threonine protein phosphatase PP1-alpha 1 catalytic subunitserine/threonine-protein phosphatase PP1-alpha catalytic subunit
Modification date20141222
dbXrefs MIM : 176875
HGNC : HGNC
Ensembl : ENSG00000172531
HPRD : 15942
Vega : OTTHUMG00000167671
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PPP1CA
BioGPS: 5499
Gene Expression Atlas: ENSG00000172531
The Human Protein Atlas: ENSG00000172531
PathwayNCI Pathway Interaction Database: PPP1CA
KEGG: PPP1CA
REACTOME: PPP1CA
ConsensusPathDB
Pathway Commons: PPP1CA
MetabolismMetaCyc: PPP1CA
HUMANCyc: PPP1CA
RegulationEnsembl's Regulation: ENSG00000172531
miRBase: chr11 :67,165,651-67,169,376
TargetScan: NM_001008709
cisRED: ENSG00000172531
ContextiHOP: PPP1CA
cancer metabolism search in PubMed: PPP1CA
UCL Cancer Institute: PPP1CA
Assigned class in ccmGDBC

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Phenotypic Information for PPP1CA(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PPP1CA
Familial Cancer Database: PPP1CA
* 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_LIPIDS_AND_LIPOPROTEINS

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PPP1CA
MedGen: PPP1CA (Human Medical Genetics with Condition)
ClinVar: PPP1CA
PhenotypeMGI: PPP1CA (International Mouse Phenotyping Consortium)
PhenomicDB: PPP1CA

Mutations for PPP1CA
* 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
There's no structural variation information in COSMIC data for this gene.

check002.gifRelated fusion transcripts : go to Chitars2.0
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PPP1CA related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
BI029138RAD9A31246116716576867165982PPP1CA245357116716835567168615

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
There's no copy number variation information in COSMIC data for this gene.

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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=4

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=15)
Stat. for Synonymous SNVs
(# total SNVs=8)
Stat. for Deletions
(# total SNVs=1)
Stat. for Insertions
(# total SNVs=0)
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
chr11:67168653-67168653p.G25C4
chr11:67167127-67167127p.R143H2
chr11:67166051-67166051p.G316G2
chr11:67168290-67168290p.R96S2
chr11:67166321-67166321p.E252K1
chr11:67167109-67167110p.W149fs*51
chr11:67168367-67168367p.D71H1
chr11:67166500-67166500p.D220N1
chr11:67167114-67167114p.K147N1
chr11:67168577-67168577p.P50H1

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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=1

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample21 4    1  21   32 2
# mutation41 4    1  21   32 2
nonsynonymous SNV4  2    1  21   22 2
synonymous SNV 1 2            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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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
chr11:67166500p.D150N,PPP1CA1
chr11:67168665p.T149T,PPP1CA1
chr11:67166506p.R147W,PPP1CA1
chr11:67168700p.R99H,PPP1CA1
chr11:67166578p.Y93C,PPP1CA1
chr11:67166579p.E82D,PPP1CA1
chr11:67166015p.E72D,PPP1CA1
chr11:67166587p.A284A,PPP1CA1
chr11:67166084p.P61H,PPP1CA1
chr11:67167127p.K261K,PPP1CA1

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 PPP1CA 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 PPP1CA

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

ADRBK1,AIP,ANKRD13D,BRMS1,C11orf24,CDK2AP2,CHKA,
CORO1B,LOC645332,MRPL21,NDUFS8,NDUFV1,POLD4,PPP1CA,
RAD9A,RBM4,RHOD,RPS6KB2,SSH3,TMEM134,UNC93B1
ARF5,ATP6V0B,COPE,FIBP,HSPBP1,LSM4,LSM7,
LYPLA2,MRPL52,MRPS12,OTUB1,POP7,PPP1CA,PPP1R14B,
PPP2R1A,PPP4C,PSMG3,RALY,TBCB,TMEM134,TSPAN17

BANF1,TMEM258,LAMTOR1,UQCC3,CFL1,COA4,COPE,
COX8A,FAU,MRPL11,NUBP2,POLR2G,PPP1CA,PPP4C,
RPS6KB2,SDHAF2,PAM16,TIMM8B,TMEM179B,TMEM223,YIF1A
BLOC1S1,CIB1,COX6A1,COX8A,HN1,MAD2L1BP,NOSIP,
NT5C,NUDT22,OTUB1,PLEKHJ1,POLD4,PPP1CA,PPP4C,
PRSS3,RAB4B,RER1,TAF10,TMSB4XP8,TSG101,WIBG
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 PPP1CA
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB02506protein phosphatase 1, catalytic subunit, alpha isozymeexperimental2,6,8-Trimethyl-3-Amino-9-Benzyl-9-Methoxynonanoic Acid
DB00171protein phosphatase 1, catalytic subunit, alpha isozymeapproved; nutraceuticalAdenosine triphosphate
DB00988protein phosphatase 1, catalytic subunit, alpha isozymeapprovedDopamine


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Cross referenced IDs for PPP1CA
* 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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