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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PDP1 |
Basic gene info. | Gene symbol | PDP1 |
Gene name | pyruvate dehyrogenase phosphatase catalytic subunit 1 | |
Synonyms | PDH|PDP|PDPC|PPM2C | |
Cytomap | UCSC genome browser: 8q22.1 | |
Genomic location | chr8 :94929991-94938296 | |
Type of gene | protein-coding | |
RefGenes | NM_001161779.1, NM_001161780.1,NM_001161781.1,NM_018444.3,NM_001161778.1, | |
Ensembl id | ENSG00000164951 | |
Description | PDP 1PDPC 1[Pyruvate dehydrogenase [acetyl-transferring]]-phosphatase 1, mitochondrialprotein phosphatase 2C, magnesium-dependent, catalytic subunitpyruvate dehydrogenase (Lipoamide) phosphatase-phosphatasepyruvate dehydrogenase phosphatase catalytic | |
Modification date | 20141222 | |
dbXrefs | MIM : 605993 | |
HGNC : HGNC | ||
Ensembl : ENSG00000164951 | ||
HPRD : 16185 | ||
Vega : OTTHUMG00000164356 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PDP1 | |
BioGPS: 54704 | ||
Gene Expression Atlas: ENSG00000164951 | ||
The Human Protein Atlas: ENSG00000164951 | ||
Pathway | NCI Pathway Interaction Database: PDP1 | |
KEGG: PDP1 | ||
REACTOME: PDP1 | ||
ConsensusPathDB | ||
Pathway Commons: PDP1 | ||
Metabolism | MetaCyc: PDP1 | |
HUMANCyc: PDP1 | ||
Regulation | Ensembl's Regulation: ENSG00000164951 | |
miRBase: chr8 :94,929,991-94,938,296 | ||
TargetScan: NM_001161779 | ||
cisRED: ENSG00000164951 | ||
Context | iHOP: PDP1 | |
cancer metabolism search in PubMed: PDP1 | ||
UCL Cancer Institute: PDP1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PDP1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PDP1 |
Familial Cancer Database: PDP1 |
* 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 | |
REACTOME_PYRUVATE_METABOLISM_AND_CITRIC_ACID_TCA_CYCLE REACTOME_PYRUVATE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PDP1 |
MedGen: PDP1 (Human Medical Genetics with Condition) | |
ClinVar: PDP1 | |
Phenotype | MGI: PDP1 (International Mouse Phenotyping Consortium) |
PhenomicDB: PDP1 |
Mutations for PDP1 |
* 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 PDP1 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 |
DB075386 | PDP1 | 1 | 486 | 8 | 94929175 | 94934596 | ZNRD1-AS1 | 486 | 558 | 6 | 1309359 | 1309431 | |
BG776390 | PDP1 | 1 | 97 | 8 | 94930432 | 94930528 | APPL1 | 93 | 681 | 3 | 57306893 | 57307480 |
Other DBs for Structural Variants |
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Copy 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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SNV Counts per Each Loci in COSMIC data: go to COSMIC point mutation |
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Somatic Mutation Counts per Tissue in COSMIC data |
Stat. for Non-Synonymous SNVs (# total SNVs=50) | (# total SNVs=11) |
(# total SNVs=1) | (# total SNVs=1) |
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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 |
chr8:94934315-94934315 | p.P10S | 3 |
chr8:94934356-94934356 | p.T23T | 2 |
chr8:94935030-94935030 | p.S248F | 2 |
chr8:94935011-94935011 | p.R242G | 1 |
chr8:94935614-94935616 | p.Q444delQ | 1 |
chr8:94934355-94934355 | p.T23I | 1 |
chr8:94935128-94935128 | p.G281S | 1 |
chr8:94935867-94935867 | p.S527Y | 1 |
chr8:94934604-94934604 | p.V106G | 1 |
chr8:94934831-94934831 | p.S182G | 1 |
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SNV Counts per Each Loci in TCGA data |
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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 |   |   | 13 |   |   | 1 | 1 |   | 1 |   | 3 | 4 | 3 |   | 1 | 5 | 3 | 1 | 8 |
# mutation | 2 |   |   | 12 |   |   | 1 | 1 |   | 1 |   | 3 | 4 | 3 |   | 1 | 5 | 3 | 1 | 10 |
nonsynonymous SNV | 2 |   |   | 8 |   |   | 1 | 1 |   | 1 |   | 1 | 4 | 3 |   | 1 | 3 |   |   | 7 |
synonymous SNV |   |   |   | 4 |   |   |   |   |   |   |   | 2 |   |   |   |   | 2 | 3 | 1 | 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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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 |
chr8:94934356 | p.T23T,PDP1 | 2 |
chr8:94935499 | p.L190L,PDP1 | 1 |
chr8:94935840 | p.L406I,PDP1 | 1 |
chr8:94934717 | p.Y26H,PDP1 | 1 |
chr8:94935031 | p.Q191Q,PDP1 | 1 |
chr8:94935503 | p.H425Y,PDP1 | 1 |
chr8:94934363 | p.H31Y,PDP1 | 1 |
chr8:94934764 | p.A204S,PDP1 | 1 |
chr8:94935067 | p.V430F,PDP1 | 1 |
chr8:94935560 | p.S37S,PDP1 | 1 |
Other DBs for Point Mutations |
Copy Number for PDP1 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 PDP1 |
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)) |
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CNV vs Gene Expression Plot |
* This plots show the correlation between CNV and gene expression. |
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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 |
ASAP1,AZIN1,CPNE3,ESRP1,INTS8,KIAA1429,MTDH, MTFR1,NBN,NIPAL2,OSGIN2,PDP1,RBM12B,RNF19A, STK3,TMEM65,TMEM67,TRAM1,VCPIP1,YTHDF3,ZBTB21 | C18orf25,C5orf22,CUL3,G3BP2,HSF2,MARCH7,MIOS, MLF1,MOB4,MOSPD1,MTM1,NEDD1,NPHP1,PDP1, PGM2L1,PPP1CB,PPP1R2,PTP4A1,RRP15,SLMAP,VEZF1 | ||||
ARFGEF1,ATP6V1C1,CPNE3,DERL1,FAM91A1,INTS8,KIAA0196, KIAA1429,OSGIN2,OXR1,PDP1,PLEKHF2,PTK2,SLC25A32, SP6,STK3,TAF2,EMC2,VCPIP1,YTHDF3,YWHAZ | ARSJ,B3GNT7,PRAC2,FAM71D,FOXA2,GLDN,HOXB13, KAZ,KCTD12,KIF13A,NOV,PDP1,PROS1,PTAR1, RARRES2,RBM24,RTN4R,SFTPA2,SPINK5,SPON1,ST6GALNAC6 |
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 |
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Interacting Genes (from Pathway Commons) |
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Pharmacological Information for PDP1 |
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 |
DB02494 | pyruvate dehyrogenase phosphatase catalytic subunit 1 | experimental | Alpha-Hydroxy-Beta-Phenyl-Propionic Acid | ||
DB03884 | pyruvate dehyrogenase phosphatase catalytic subunit 1 | experimental | 3-Phenylpyruvic Acid |
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Cross referenced IDs for PDP1 |
* We obtained these cross-references from Uniprot database. It covers 150 different DBs, 18 categories. http://www.uniprot.org/help/cross_references_section |
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