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 PDP2
Basic gene info.Gene symbolPDP2
Gene namepyruvate dehyrogenase phosphatase catalytic subunit 2
SynonymsPPM2C2
CytomapUCSC genome browser: 16q22.1
Genomic locationchr16 :66914382-66925002
Type of geneprotein-coding
RefGenesNM_020786.2,
Ensembl idENSG00000172840
DescriptionPDPC 2[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 2, mitochondrialprotein phosphatase 2C, magnesium-dependent, catalytic subunit 2pyruvate dehydrogenase phosphatase catalytic subunit 2pyruvate dehydrogenase phosphatase isoenzyme 2pyruv
Modification date20141207
dbXrefs MIM : 615499
HGNC : HGNC
Ensembl : ENSG00000172840
HPRD : 15112
Vega : OTTHUMG00000137512
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDP2
BioGPS: 57546
Gene Expression Atlas: ENSG00000172840
The Human Protein Atlas: ENSG00000172840
PathwayNCI Pathway Interaction Database: PDP2
KEGG: PDP2
REACTOME: PDP2
ConsensusPathDB
Pathway Commons: PDP2
MetabolismMetaCyc: PDP2
HUMANCyc: PDP2
RegulationEnsembl's Regulation: ENSG00000172840
miRBase: chr16 :66,914,382-66,925,002
TargetScan: NM_020786
cisRED: ENSG00000172840
ContextiHOP: PDP2
cancer metabolism search in PubMed: PDP2
UCL Cancer Institute: PDP2
Assigned class in ccmGDBC

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Phenotypic Information for PDP2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDP2
Familial Cancer Database: PDP2
* 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: PDP2
MedGen: PDP2 (Human Medical Genetics with Condition)
ClinVar: PDP2
PhenotypeMGI: PDP2 (International Mouse Phenotyping Consortium)
PhenomicDB: PDP2

Mutations for PDP2
* 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 PDP2 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
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=3

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=30)
Stat. for Synonymous SNVs
(# total SNVs=12)
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
chr16:66918510-66918510p.R108Q2
chr16:66919604-66919604p.R473W2
chr16:66919297-66919297p.T370T2
chr16:66918530-66918530p.A115T2
chr16:66919155-66919155p.E323G2
chr16:66919560-66919560p.R458K2
chr16:66918646-66918646p.S153S1
chr16:66919576-66919576p.L463L1
chr16:66919107-66919107p.R307H1
chr16:66919259-66919259p.E358*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
# sample11161   1  441 196 5
# mutation11151   1  441 197 6
nonsynonymous SNV 1131   1  24  145 4
synonymous SNV1  2       2 1  52 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
chr16:66918510p.T370T2
chr16:66919297p.R108Q2
chr16:66919155p.E323G2
chr16:66918814p.S12F1
chr16:66919167p.P182L1
chr16:66918454p.W39L1
chr16:66919617p.L209L1
chr16:66918897p.A372S1
chr16:66919186p.S43S1
chr16:66919695p.R237I1

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 PDP2 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 PDP2

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

ADAT1,AP1G1,APOOL,ASXL2,ATXN1L,CCNT1,CHD9,
CNOT1,CTCF,DYNC1LI2,EXOC6B,CMTR2,GTF2A1,LMTK2,
NFATC3,PDP2,PHLPP2,REST,RSPRY1,SLC38A7,ZFP90
ABCD2,ACSS3,ACVR1C,ADIPOQ,ADRBK2,ALDH6A1,ANO6,
AQPEP,GPATCH11,EHHADH,EIF4EBP2,FAM13A,GABRE,GHR,
KCNIP2,OXCT1,PDE3B,PDP2,PEX19,SIK2,SLC16A7

ADAT1,ANAPC1,ARFGEF2,ASXL2,ATXN1L,C9orf129,CCNT1,
CNOT1,DDI2,MON1B,NEU3,NUP153,PDP2,PRKAR2A,
PTPLB,RAPGEF6,SERINC5,SHPRH,STRN,TGFBRAP1,UHMK1
ACVR1B,ADAM10,APAF1,ARFGEF1,ARFGEF2,ARHGAP32,ATP11B,
ATP6V1A,BROX,PRR14L,CTNND1,FHDC1,FNIP2,LGR4,
MARVELD2,MCTP2,NAPEPLD,NUMB,PDP2,PLD1,UTP14C
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 PDP2


There's no related Drug.
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Cross referenced IDs for PDP2
* 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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