|
Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PDHA2 |
Basic gene info. | Gene symbol | PDHA2 |
Gene name | pyruvate dehydrogenase (lipoamide) alpha 2 | |
Synonyms | PDHAL | |
Cytomap | UCSC genome browser: 4q22-q23 | |
Genomic location | chr4 :96761238-96762625 | |
Type of gene | protein-coding | |
RefGenes | NM_005390.4, | |
Ensembl id | ENSG00000163114 | |
Description | PDHE1-A type IIpyruvate dehydrogenase E1 component subunit alpha, testis-specific form, mitochondrialpyruvate dehydrogenase, E1-alpha polypeptide, testis specific | |
Modification date | 20141207 | |
dbXrefs | MIM : 179061 | |
HGNC : HGNC | ||
Ensembl : ENSG00000163114 | ||
HPRD : 01531 | ||
Vega : OTTHUMG00000130990 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PDHA2 | |
BioGPS: 5161 | ||
Gene Expression Atlas: ENSG00000163114 | ||
The Human Protein Atlas: ENSG00000163114 | ||
Pathway | NCI Pathway Interaction Database: PDHA2 | |
KEGG: PDHA2 | ||
REACTOME: PDHA2 | ||
ConsensusPathDB | ||
Pathway Commons: PDHA2 | ||
Metabolism | MetaCyc: PDHA2 | |
HUMANCyc: PDHA2 | ||
Regulation | Ensembl's Regulation: ENSG00000163114 | |
miRBase: chr4 :96,761,238-96,762,625 | ||
TargetScan: NM_005390 | ||
cisRED: ENSG00000163114 | ||
Context | iHOP: PDHA2 | |
cancer metabolism search in PubMed: PDHA2 | ||
UCL Cancer Institute: PDHA2 | ||
Assigned class in ccmGDB | C |
Top |
Phenotypic Information for PDHA2(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PDHA2 |
Familial Cancer Database: PDHA2 |
* This gene is included in those cancer gene databases. |
Oncogene 1 | Significant driver gene in |
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/ |
Metabolic Pathway Description | |
KEGG_GLYCOLYSIS_GLUCONEOGENESIS KEGG_PYRUVATE_METABOLISM KEGG_BUTANOATE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PDHA2 |
MedGen: PDHA2 (Human Medical Genetics with Condition) | |
ClinVar: PDHA2 | |
Phenotype | MGI: 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. |
Structural Variants in COSMIC: go to COSMIC mutation histogram |
There's no structural variation information in COSMIC data for this gene. |
Related fusion transcripts : go to Chitars2.0 |
* From mRNA Sanger sequences, Chitars2.0 arranged chimeric transcripts. This table shows PDHA2 related fusion information. |
ID | Head Gene | Tail Gene | Accession | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a | Gene_a | qStart_a | qEnd_a | Chromosome_a | tStart_a | tEnd_a |
AI393336 | CIAPIN1 | 15 | 136 | 16 | 57462474 | 57462595 | PDHA2 | 133 | 349 | 4 | 96761617 | 96761833 |
Other DBs for Structural Variants |
Top |
Copy Number Variations in COSMIC: go to COSMIC mutation CNV/Expr |
There's no copy number variation information in COSMIC data for this gene. |
Top |
SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
|
Top |
Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=111) | (# total SNVs=32) |
(# total SNVs=0) | (# total SNVs=0) |
Top |
Top 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 position | Mutation(aa) | Unique sampleID count |
chr4:96761854-96761854 | p.D185N | 5 |
chr4:96761557-96761557 | p.R86C | 4 |
chr4:96762199-96762199 | p.R300S | 4 |
chr4:96761738-96761738 | p.G146E | 3 |
chr4:96761886-96761886 | p.G195G | 3 |
chr4:96762427-96762427 | p.R376C | 3 |
chr4:96761853-96761853 | p.N184N | 3 |
chr4:96761326-96761326 | p.V9M | 3 |
chr4:96762205-96762205 | p.R302* | 3 |
chr4:96761627-96761627 | p.S109L | 3 |
Top |
SNV Counts per Each Loci in TCGA data |
|
Point Mutation/ Tissue ID | 1 | 2 | 3 | 4 | 5 | 6 | 7 | 8 | 9 | 10 | 11 | 12 | 13 | 14 | 15 | 16 | 17 | 18 | 19 | 20 |
# sample | 2 | 2 | 1 | 21 | 4 |   | 9 |   | 1 |   |   | 22 | 10 |   |   |   | 21 | 8 | 3 | 9 |
# mutation | 2 | 2 | 1 | 21 | 4 |   | 9 |   | 1 |   |   | 23 | 10 |   |   |   | 18 | 8 | 3 | 12 |
nonsynonymous SNV | 1 | 2 | 1 | 15 | 2 |   | 4 |   |   |   |   | 17 | 8 |   |   |   | 15 | 3 | 2 | 10 |
synonymous SNV | 1 |   |   | 6 | 2 |   | 5 |   | 1 |   |   | 6 | 2 |   |   |   | 3 | 5 | 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]) |
Top |
Top 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 Position | Mutation(aa) | Unique sampleID count |
chr4:96761557 | p.R86C | 5 |
chr4:96761854 | p.D185N | 4 |
chr4:96761394 | p.R300C | 3 |
chr4:96762427 | p.R376C | 3 |
chr4:96762199 | p.R26S | 3 |
chr4:96761377 | p.D31D | 3 |
chr4:96761853 | p.G195G | 2 |
chr4:96761711 | p.R70S | 2 |
chr4:96761738 | p.T137M | 2 |
chr4:96762054 | p.R71H | 2 |
Other DBs for Point Mutations |
Copy 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] |
Top |
Gene Expression for PDHA2 |
Gene 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. |
Differential 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)) |
Top |
CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
Top |
Gene-Gene Network Information |
Co-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 |
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 |
Co-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 |
Top |
Interacting Genes (from Pathway Commons) |
Top |
Pharmacological Information for PDHA2 |
Cross-referenced pharmacological DB IDs from Uniprot |
DB Category | DB Name | DB's ID and Url link |
Drug-Gene Interaction Network |
* Gene Centered Interaction Network. |
* Drug Centered Interaction Network. |
DrugBank ID | Target Name | Drug Groups | Generic Name | Drug Centered Network | Drug Structure |
DB00157 | pyruvate dehydrogenase (lipoamide) alpha 2 | approved; nutraceutical | NADH |
Top |
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 |
Copyright © 2016-Present - The Univsersity of Texas Health Science Center at Houston @ |