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 PDP1
Basic gene info.Gene symbolPDP1
Gene namepyruvate dehyrogenase phosphatase catalytic subunit 1
SynonymsPDH|PDP|PDPC|PPM2C
CytomapUCSC genome browser: 8q22.1
Genomic locationchr8 :94929991-94938296
Type of geneprotein-coding
RefGenesNM_001161779.1,
NM_001161780.1,NM_001161781.1,NM_018444.3,NM_001161778.1,
Ensembl idENSG00000164951
DescriptionPDP 1PDPC 1[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrialprotein phosphatase 2C, magnesium-dependent, catalytic subunitpyruvate dehydrogenase (Lipoamide) phosphatase-phosphatasepyruvate dehydrogenase phosphatase catalytic
Modification date20141222
dbXrefs MIM : 605993
HGNC : HGNC
Ensembl : ENSG00000164951
HPRD : 16185
Vega : OTTHUMG00000164356
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDP1
BioGPS: 54704
Gene Expression Atlas: ENSG00000164951
The Human Protein Atlas: ENSG00000164951
PathwayNCI Pathway Interaction Database: PDP1
KEGG: PDP1
REACTOME: PDP1
ConsensusPathDB
Pathway Commons: PDP1
MetabolismMetaCyc: PDP1
HUMANCyc: PDP1
RegulationEnsembl's Regulation: ENSG00000164951
miRBase: chr8 :94,929,991-94,938,296
TargetScan: NM_001161779
cisRED: ENSG00000164951
ContextiHOP: PDP1
cancer metabolism search in PubMed: PDP1
UCL Cancer Institute: PDP1
Assigned class in ccmGDBC

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Phenotypic Information for PDP1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDP1
Familial Cancer Database: PDP1
* 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_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE
REACTOME_PYRUVATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PDP1
MedGen: PDP1 (Human Medical Genetics with Condition)
ClinVar: PDP1
PhenotypeMGI: PDP1 (International Mouse Phenotyping Consortium)
PhenomicDB: PDP1

Mutations for PDP1
* 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 PDP1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
DB075386PDP1148689492917594934596ZNRD1-AS1486558613093591309431
BG776390PDP119789493043294930528APPL19368135730689357307480

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=50)
Stat. for Synonymous SNVs
(# total SNVs=11)
Stat. for Deletions
(# total SNVs=1)
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
chr8:94934315-94934315p.P10S3
chr8:94934356-94934356p.T23T2
chr8:94935030-94935030p.S248F2
chr8:94934897-94934897p.A204S1
chr8:94935503-94935503p.L406I1
chr8:94934294-94934294p.A3S1
chr8:94934449-94934450p.T54_F55insT1
chr8:94935099-94935099p.G271V1
chr8:94935783-94935783p.R499H1
chr8:94934764-94934764p.L159L1

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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
# sample2  13  11 1 343 15318
# mutation2  12  11 1 343 153110
nonsynonymous SNV2  8  11 1 143 13  7
synonymous SNV   4       2    2313
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
chr8:94934356p.T23T,PDP12
chr8:94935250p.L159L,PDP11
chr8:94934247p.E321E,PDP11
chr8:94934619p.I12T,PDP11
chr8:94935737p.A179T,PDP11
chr8:94934860p.R367T,PDP11
chr8:94935387p.P20S,PDP11
chr8:94934270p.A3S,PDP11
chr8:94934630p.R184W,PDP11
chr8:94935750p.N377H,PDP11

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 PDP1 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 PDP1

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

ASAP1,AZIN1,CPNE3,ESRP1,INTS8,KIAA1429,MTDH,
MTFR1,NBN,NIPAL2,OSGIN2,PDP1,RBM12B,RNF19A,
STK3,TMEM65,TMEM67,TRAM1,VCPIP1,YTHDF3,ZBTB21
C18orf25,C5orf22,CUL3,G3BP2,HSF2,MARCH7,MIOS,
MLF1,MOB4,MOSPD1,MTM1,NEDD1,NPHP1,PDP1,
PGM2L1,PPP1CB,PPP1R2,PTP4A1,RRP15,SLMAP,VEZF1

ARFGEF1,ATP6V1C1,CPNE3,DERL1,FAM91A1,INTS8,KIAA0196,
KIAA1429,OSGIN2,OXR1,PDP1,PLEKHF2,PTK2,SLC25A32,
SP6,STK3,TAF2,EMC2,VCPIP1,YTHDF3,YWHAZ
ARSJ,B3GNT7,PRAC2,FAM71D,FOXA2,GLDN,HOXB13,
KAZ,KCTD12,KIF13A,NOV,PDP1,PROS1,PTAR1,
RARRES2,RBM24,RTN4R,SFTPA2,SPINK5,SPON1,ST6GALNAC6
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 PDP1
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
DB02494pyruvate dehyrogenase phosphatase catalytic subunit 1experimentalAlpha-Hydroxy-Beta-Phenyl-Propionic Acid
DB03884pyruvate dehyrogenase phosphatase catalytic subunit 1experimental3-Phenylpyruvic Acid


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Cross referenced IDs for PDP1
* 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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