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 PDHA1
Basic gene info.Gene symbolPDHA1
Gene namepyruvate dehydrogenase (lipoamide) alpha 1
SynonymsPDHA|PDHAD|PDHCE1A|PHE1A
CytomapUCSC genome browser: Xp22.1
Genomic locationchrX :19362010-19379825
Type of geneprotein-coding
RefGenesNM_000284.3,
NM_001173454.1,NM_001173455.1,NM_001173456.1,
Ensembl idENSG00000131828
DescriptionPDHE1-A type Ipyruvate dehydrogenase E1 component subunit alpha, somatic form, mitochondrialpyruvate dehydrogenase complex, E1-alpha polypeptide 1
Modification date20141207
dbXrefs MIM : 300502
HGNC : HGNC
Ensembl : ENSG00000131828
HPRD : 02420
Vega : OTTHUMG00000021224
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDHA1
BioGPS: 5160
Gene Expression Atlas: ENSG00000131828
The Human Protein Atlas: ENSG00000131828
PathwayNCI Pathway Interaction Database: PDHA1
KEGG: PDHA1
REACTOME: PDHA1
ConsensusPathDB
Pathway Commons: PDHA1
MetabolismMetaCyc: PDHA1
HUMANCyc: PDHA1
RegulationEnsembl's Regulation: ENSG00000131828
miRBase: chrX :19,362,010-19,379,825
TargetScan: NM_000284
cisRED: ENSG00000131828
ContextiHOP: PDHA1
cancer metabolism search in PubMed: PDHA1
UCL Cancer Institute: PDHA1
Assigned class in ccmGDBC

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Phenotypic Information for PDHA1(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDHA1
Familial Cancer Database: PDHA1
* 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
KEGG_GLYCOLYSIS_GLUCONEOGENESIS
KEGG_PYRUVATE_METABOLISM
KEGG_BUTANOATE_METABOLISM
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE
REACTOME_PYRUVATE_METABOLISM

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PDHA1
MedGen: PDHA1 (Human Medical Genetics with Condition)
ClinVar: PDHA1
PhenotypeMGI: PDHA1 (International Mouse Phenotyping Consortium)
PhenomicDB: PDHA1

Mutations for PDHA1
* 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 PDHA1 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AM746210TMEM2233248116255922562559470PDHA12451004X1937260719377866
BF694498BOLA2296163007606130078604PDHA193582X1937261219377135
CB113851SUB1124653258566332591771PDHA1231556X1937356619377626

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=5

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=43)
Stat. for Synonymous SNVs
(# total SNVs=17)
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
chr23:19377730-19377730p.R378C3
chr23:19368115-19368115p.D60Y3
chr23:19367444-19367444p.L24L3
chr23:19369427-19369427p.G107D2
chr23:19367443-19367443p.L24P2
chr23:19373600-19373600p.G246D2
chr23:19368163-19368163p.L76L2
chr23:19373834-19373834p.E264K1
chr23:19368172-19368172p.D79Y1
chr23:19369486-19369486p.R127W1

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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
# sample13 91 3 2  441  12 8
# mutation13 91 3 2  341  12 9
nonsynonymous SNV 2 61 3 2  33   11 7
synonymous SNV11 3        11   1 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
chrX:19367444p.G107D,PDHA13
chrX:19369427p.L24L,PDHA13
chrX:19373600p.G215D,PDHA12
chrX:19372640p.L24P,PDHA12
chrX:19367443p.C181F,PDHA12
chrX:19371229p.D187Y,PDHA11
chrX:19373497p.G61R,PDHA11
chrX:19368118p.L191L,PDHA11
chrX:19371264p.D79Y,PDHA11
chrX:19373555p.G195G,PDHA11

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 PDHA1 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 PDHA1

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

ATP5C1,AURKB,CMC2,CDC20,ECE2,KARS,KIF2C,
MAGOH,NDUFAF4,PDCD5,PDHA1,PDSS1,PRDX4,PSMB2,
PSMG1,PTTG1,SHFM1,TOMM5,TUBA1C,UQCRH,UQCRHL
ACAT1,ADHFE1,BCL2L13,CS,DLD,DLST,ETFDH,
GPI,GPT2,KIAA0408,NDUFV3,PDHA1,PDK2,GATB,
PFKFB1,PGM1,PHYH,PLIN5,RNF157,SLC2A4,SLC6A8

AIFM1,APOO,BRCC3,CASK,CCDC22,EBP,EMD,
HCCS,HDAC8,HSD17B10,LAS1L,NDUFB11,PDHA1,JADE3,
POLA1,RBBP7,SCML1,SMS,SUV39H1,TIMM8A,TSR2
AIFM1,CS,DARS2,DNAJC11,GJB2,GOT1,GSS,
HMGB3,IARS2,IMMT,MCCC2,MIPEP,NDUFA10,NDUFS2,
NDUFV1,PDHA1,PKP2,SLC35A4,STARD7,SUPV3L1,TUFM
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 PDHA1
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
DB00157pyruvate dehydrogenase (lipoamide) alpha 1approved; nutraceuticalNADH


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Cross referenced IDs for PDHA1
* 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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