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 PDK3
Basic gene info.Gene symbolPDK3
Gene namepyruvate dehydrogenase kinase, isozyme 3
SynonymsCMTX6|GS1-358P8.4
CytomapUCSC genome browser: Xp22.11
Genomic locationchrX :24483343-24552542
Type of geneprotein-coding
RefGenesNM_001142386.2,
NM_005391.4,
Ensembl idENSG00000067992
Description[Pyruvate dehydrogenase (acetyl-transferring)] kinase isozyme 3, mitochondrialpyruvate dehydrogenase kinase, isoenzyme 3pyruvate dehydrogenase, lipoamide, kinase isozyme 3, mitochondrial
Modification date20141207
dbXrefs MIM : 300906
HGNC : HGNC
Ensembl : ENSG00000067992
HPRD : 03956
Vega : OTTHUMG00000021269
ProteinUniProt: Q15120
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDK3
BioGPS: 5165
Gene Expression Atlas: ENSG00000067992
The Human Protein Atlas: ENSG00000067992
PathwayNCI Pathway Interaction Database: PDK3
KEGG: PDK3
REACTOME: PDK3
ConsensusPathDB
Pathway Commons: PDK3
MetabolismMetaCyc: PDK3
HUMANCyc: PDK3
RegulationEnsembl's Regulation: ENSG00000067992
miRBase: chrX :24,483,343-24,552,542
TargetScan: NM_001142386
cisRED: ENSG00000067992
ContextiHOP: PDK3
cancer metabolism search in PubMed: PDK3
UCL Cancer Institute: PDK3
Assigned class in ccmGDBA - This gene has a literature evidence and it belongs to cancer gene.
References showing role of PDK3 in cancer cell metabolism1. Kluza J, Corazao-Rozas P, Touil Y, Jendoubi M, Maire C, et al. (2012) Inactivation of the HIF-1α/PDK3 signaling axis drives melanoma toward mitochondrial oxidative metabolism and potentiates the therapeutic activity of pro-oxidants. Cancer research 72: 5035-5047. go to article
2. Prigione A, Rohwer N, Hoffmann S, Mlody B, Drews K, et al. (2014) HIF1α modulates cell fate reprogramming through early glycolytic shift and upregulation of PDK1–3 and PKM2. Stem Cells 32: 364-376. go to article

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Phenotypic Information for PDK3(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDK3
Familial Cancer Database: PDK3
* 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 300905; phenotype.
300906; gene.
Orphanet 352675; X-linked Charcot-Marie-Tooth disease type 6.
DiseaseKEGG Disease: PDK3
MedGen: PDK3 (Human Medical Genetics with Condition)
ClinVar: PDK3
PhenotypeMGI: PDK3 (International Mouse Phenotyping Consortium)
PhenomicDB: PDK3

Mutations for PDK3
* 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 PDK3 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AV755280PDK372149X2451854524518622PDK3150505X2451751824517868
BU674003PDK318220X2456838124568583PDK3219341X2456815724568279

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=7

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=42)
Stat. for Synonymous SNVs
(# total SNVs=14)
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
chr23:24537111-24537111p.E219E4
chr23:24546235-24546235p.R299C2
chr23:24544369-24544369p.H243R2
chr23:24552052-24552052p.S362T2
chr23:24521580-24521580p.R153W2
chr23:24521596-24521596p.R158H2
chr23:24521458-24521458p.L112Q1
chr23:24523382-24523382p.D188H1
chr23:24552116-24552116p.T383M1
chr23:24483633-24483633p.R21C1

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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=4

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample 1 11    1  432 153110
# mutation 1 6    1  432 153111
nonsynonymous SNV   5    1  332  4218
synonymous SNV 1 2       1   111 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
chrX:24537111p.E219E,PDK35
chrX:24546235p.R299C,PDK33
chrX:24552052p.S362T,PDK32
chrX:24521592p.P24P,PDK31
chrX:24545705p.T383M,PDK31
chrX:24483644p.D38Y,PDK31
chrX:24552116p.E222D,PDK31
chrX:24523330p.T383T,PDK31
chrX:24545733p.S87I,PDK31
chrX:24512864p.V234L,PDK31

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 PDK3 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 PDK3

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

BCAR4,ABRACL,FAM171A1,FOXC1,HORMAD1,ID4,LMAN1L,
NUDT3,OGFRL1,OR5AU1,PDK3,PIR,PRM1,PRM2,
PTCHD1,RIPK2,RNASE13,SLC26A7,STATH,TNP2,TPPP2
ABI2,B3GALNT1,CXADR,DSC2,EXPH5,ITGA2,KLHL42,
LRRC8D,MTMR1,OAT,PDK3,PRKCI,RBBP4,PTBP3,
SLC11A2,SLC9A7,SRPK1,SUDS3,TRIM59,ZNF286A,ZNF93

AIFM1,APEX2,APOO,DKC1,ELK1,FANCB,FTSJ1,
HCCS,HPRT1,NDUFB11,NKAP,NSDHL,PDK3,JADE3,
PRPS1,PRPS2,SMS,SUV39H1,TIMM8A,TMLHE,VBP1
CALM1,CDS2,EFR3A,EXOC6B,FREM1,HOXC10,HOXC4,
IRS4,KCTD4,MEGF9,MYLK3,NR1D1,NRBP1,OR51E1,
PDK3,PSG5,RARB,RPS6KA5,SEC23A,TAC3,ZACN
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 PDK3
check002.gifCross-referenced pharmacological DB IDs from Uniprot
DB CategoryDB NameDB's ID and Url link
ChemistryChEMBL CHEMBL2096665; -.
Organism-specific databasesPharmGKB PA33156; -.
Organism-specific databasesCTD 5165; -.

check002.gifDrug-Gene Interaction Network
* Gene Centered Interaction Network.
* Drug Centered Interaction Network.
DrugBank IDTarget NameDrug GroupsGeneric NameDrug Centered NetworkDrug Structure
DB03758pyruvate dehydrogenase kinase, isozyme 3experimentalRadicicol
DB03760pyruvate dehydrogenase kinase, isozyme 3experimentalDihydrolipoic Acid


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Cross referenced IDs for PDK3
* 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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