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 PPP2R5D
Basic gene info.Gene symbolPPP2R5D
Gene nameprotein phosphatase 2, regulatory subunit B', delta
SynonymsB56D
CytomapUCSC genome browser: 6p21.1
Genomic locationchr6 :42952329-42980080
Type of geneprotein-coding
RefGenesNM_001270476.1,
NM_006245.3,NM_180976.2,NM_180977.2,
Ensembl idENSG00000112640
DescriptionPP2A B subunit isoform B'-deltaPP2A B subunit isoform B56-deltaPP2A B subunit isoform PR61-deltaPP2A B subunit isoform R5-deltaPP2A, B subunit, B' delta isoformPP2A, B subunit, B56 delta isoformPP2A, B subunit, PR61 delta isoformPP2A, B subunit, R5
Modification date20141207
dbXrefs MIM : 601646
HGNC : HGNC
Ensembl : ENSG00000112640
HPRD : 09039
Vega : OTTHUMG00000014716
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PPP2R5D
BioGPS: 5528
Gene Expression Atlas: ENSG00000112640
The Human Protein Atlas: ENSG00000112640
PathwayNCI Pathway Interaction Database: PPP2R5D
KEGG: PPP2R5D
REACTOME: PPP2R5D
ConsensusPathDB
Pathway Commons: PPP2R5D
MetabolismMetaCyc: PPP2R5D
HUMANCyc: PPP2R5D
RegulationEnsembl's Regulation: ENSG00000112640
miRBase: chr6 :42,952,329-42,980,080
TargetScan: NM_001270476
cisRED: ENSG00000112640
ContextiHOP: PPP2R5D
cancer metabolism search in PubMed: PPP2R5D
UCL Cancer Institute: PPP2R5D
Assigned class in ccmGDBC

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Phenotypic Information for PPP2R5D(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PPP2R5D
Familial Cancer Database: PPP2R5D
* 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_INTEGRATION_OF_ENERGY_METABOLISM
REACTOME_METABOLISM_OF_CARBOHYDRATES
REACTOME_GLUCOSE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PPP2R5D
MedGen: PPP2R5D (Human Medical Genetics with Condition)
ClinVar: PPP2R5D
PhenotypeMGI: PPP2R5D (International Mouse Phenotyping Consortium)
PhenomicDB: PPP2R5D

Mutations for PPP2R5D
* 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
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'.
SampleSymbol_aChr_aStart_aEnd_aSymbol_bChr_bStart_bEnd_b
pancreasPPP2R5Dchr64296875642968776chr64675796146757981
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 PPP2R5D related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a

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 # sample1                
GAIN (# sample)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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=35)
Stat. for Synonymous SNVs
(# total SNVs=15)
Stat. for Deletions
(# total SNVs=2)
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
chr6:42977143-42977143p.I445I2
chr6:42975942-42975942p.F287F2
chr6:42975737-42975737p.R264H2
chr6:42975745-42975745p.G267S2
chr6:42974938-42974938p.S176*2
chr6:42957352-42957352p.K13fs*942
chr6:42974675-42974675p.L117L2
chr6:42974972-42974972p.S187S1
chr6:42957397-42957397p.K26*1
chr6:42975938-42975938p.?1

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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=3

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample23161 3 1  5 1 116 11
# mutation23161 3 1  6 1 116 12
nonsynonymous SNV12 4  3    5 1  13 8
synonymous SNV11121   1  1   1 3 4
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
chr6:42975737p.R158H,PPP2R5D3
chr6:42974675p.L11L,PPP2R5D2
chr6:42975803p.R158C,PPP2R5D1
chr6:42974334p.G358R,PPP2R5D1
chr6:42977129p.F25F,PPP2R5D1
chr6:42974953p.E398Q,PPP2R5D1
chr6:42975942p.V26M,PPP2R5D1
chr6:42974371p.G161S,PPP2R5D1
chr6:42977150p.E404D,PPP2R5D1
chr6:42974956p.P29Q,PPP2R5D1

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 PPP2R5D 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 PPP2R5D

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

AARS2,ABCC10,RRP36,CDC5L,CUL7,GTPBP2,HSP90AB1,
KLHDC3,MEA1,MED20,MRPS10,MRPS18A,NFYA,POLH,
POLR1C,PPP2R5D,SLC29A1,SLC35B2,TJAP1,XPO5,ZNF318
AP2A1,ATG9A,APOPT1,NATD1,C21orf33,DLST,FZD9,
GPI,HADHA,HDLBP,PACS2,GATB,PPP2R5D,PRKACA,
PSMD2,SAMM50,SLC25A23,SLC6A8,ST3GAL3,VPS4A,WBSCR16

AARS2,BYSL,RRP36,ZC2HC1B,CCND3,CDCA3,CLDN25,
F11,KLHDC3,MAD2L1BP,MEA1,MED20,MRPL2,PPP2R5D,
RHAG,SRF,TAF8,TJAP1,TOMM6,XPO5,ZNF318
ABHD6,ANPEP,ADIRF,GBA3,GCNT4,GNB1,SLC52A1,
HEBP1,HOXC11,HOXC6,HOXC8,ING2,LOC148709,MARC2,
MSRA,PPP2R5D,PTGR1,SPAM1,SUSD2,AGMO,TTBK1
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 PPP2R5D
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
DB00675protein phosphatase 2, regulatory subunit B', deltaapprovedTamoxifen
DB01394protein phosphatase 2, regulatory subunit B', deltaapprovedColchicine
DB00864protein phosphatase 2, regulatory subunit B', deltaapproved; investigationalTacrolimus
DB00877protein phosphatase 2, regulatory subunit B', deltaapproved; investigationalSirolimus
DB00131protein phosphatase 2, regulatory subunit B', deltaapproved; nutraceuticalAdenosine monophosphate
DB00171protein phosphatase 2, regulatory subunit B', deltaapproved; nutraceuticalAdenosine triphosphate
DB00988protein phosphatase 2, regulatory subunit B', deltaapprovedDopamine


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Cross referenced IDs for PPP2R5D
* 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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