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 PDHA2
Basic gene info.Gene symbolPDHA2
Gene namepyruvate dehydrogenase (lipoamide) alpha 2
SynonymsPDHAL
CytomapUCSC genome browser: 4q22-q23
Genomic locationchr4 :96761238-96762625
Type of geneprotein-coding
RefGenesNM_005390.4,
Ensembl idENSG00000163114
DescriptionPDHE1-A type IIpyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrialpyruvate dehydrogenase, E1-alpha polypeptide, testis specific
Modification date20141207
dbXrefs MIM : 179061
HGNC : HGNC
Ensembl : ENSG00000163114
HPRD : 01531
Vega : OTTHUMG00000130990
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_PDHA2
BioGPS: 5161
Gene Expression Atlas: ENSG00000163114
The Human Protein Atlas: ENSG00000163114
PathwayNCI Pathway Interaction Database: PDHA2
KEGG: PDHA2
REACTOME: PDHA2
ConsensusPathDB
Pathway Commons: PDHA2
MetabolismMetaCyc: PDHA2
HUMANCyc: PDHA2
RegulationEnsembl's Regulation: ENSG00000163114
miRBase: chr4 :96,761,238-96,762,625
TargetScan: NM_005390
cisRED: ENSG00000163114
ContextiHOP: PDHA2
cancer metabolism search in PubMed: PDHA2
UCL Cancer Institute: PDHA2
Assigned class in ccmGDBC

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Phenotypic Information for PDHA2(metabolism pathway, cancer, disease, phenome)
check002.gifCancer Description
Cancer CGAP: PDHA2
Familial Cancer Database: PDHA2
* 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

check002.gifOthers
OMIM
Orphanet
DiseaseKEGG Disease: PDHA2
MedGen: PDHA2 (Human Medical Genetics with Condition)
ClinVar: PDHA2
PhenotypeMGI: PDHA2 (International Mouse Phenotyping Consortium)
PhenomicDB: PDHA2

Mutations for PDHA2
* 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 PDHA2 related fusion information.
IDHead GeneTail Gene
AccessionGene_aqStart_aqEnd_aChromosome_atStart_atEnd_aGene_aqStart_aqEnd_aChromosome_atStart_atEnd_a
AI393336CIAPIN115136165746247457462595PDHA213334949676161796761833

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=6

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check002.gifSomatic Mutation Counts per Tissue in COSMIC data
Stat. for Non-Synonymous SNVs
(# total SNVs=111)
Stat. for Synonymous SNVs
(# total SNVs=32)
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
chr4:96761854-96761854p.D185N5
chr4:96761557-96761557p.R86C4
chr4:96762199-96762199p.R300S4
chr4:96762427-96762427p.R376C3
chr4:96761326-96761326p.V9M3
chr4:96761853-96761853p.N184N3
chr4:96762205-96762205p.R302*3
chr4:96761627-96761627p.S109L3
chr4:96761738-96761738p.G146E3
chr4:96761886-96761886p.G195G3

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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=5

Point Mutation/ Tissue ID1234567891011121314151617181920
# sample221214 9 1  2210   21839
# mutation221214 9 1  2310   188312
nonsynonymous SNV121152 4    178   153210
synonymous SNV1  62 5 1  62   3512
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
chr4:96761557p.R86C5
chr4:96761854p.D185N4
chr4:96762427p.R300C3
chr4:96762199p.R376C3
chr4:96761377p.R26S3
chr4:96761394p.D31D3
chr4:96761853p.G195G2
chr4:96761711p.R70S2
chr4:96761738p.T137M2
chr4:96762054p.R71H2

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 PDHA2 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 PDHA2

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

CALB1,CCL24,CDA,COL7A1,CSF2,DCBLD2,DEFB103B,
IFNK,IL1A,KRT14,KRT6A,KRTAP11-1,LAMC2,NEU2,
PDHA2,SPINK7,TMPRSS11D,TRIML2,UCN2,WNT7A,ZBED2
ADAMTS20,C10orf120,PTCHD4,CCL1,CRYGC,EFNA2,EGR4,
EPHA8,IGFBP1,IGSF1,KRTAP9-2,LCE1D,OR2V2,PDHA2,
PRSS21,PRSS41,RBMXL3,SLC30A8,SNORA80E,SNORA58,SST

ATP8B3,MROH9,C1QL2,CCL21,CGB5,CLEC4M,CSMD3,
CXorf51A,FAM25A,FMR1NB,GML,HBD,KPRP,KRT34,
LOC100216001,MUC15,MYL2,OR9G9,PDHA2,SUN3,VCX
CPXCR1,CTRB2,DEFB119,DEFB125,ENDOG,FAM173A,HIST1H4B,
KRTAP10-1,KRTAP10-5,LGALS9C,LOC284379,LOC390858,OR52L1,PDHA2,
PHGR1,RBPJL,SCAND1,SCGB1D1,SNORA14A,SNORA77,SPINK8
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 PDHA2
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 2approved; nutraceuticalNADH


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Cross referenced IDs for PDHA2
* 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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