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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PGD |
Basic gene info. | Gene symbol | PGD |
Gene name | phosphogluconate dehydrogenase | |
Synonyms | 6PGD | |
Cytomap | UCSC genome browser: 1p36.22 | |
Genomic location | chr1 :10459084-10480201 | |
Type of gene | protein-coding | |
RefGenes | NM_002631.2, | |
Ensembl id | ENSG00000142657 | |
Description | 6-phosphogluconate dehydrogenase, decarboxylating | |
Modification date | 20141207 | |
dbXrefs | MIM : 172200 | |
HGNC : HGNC | ||
Ensembl : ENSG00000142657 | ||
HPRD : 01391 | ||
Vega : OTTHUMG00000001905 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PGD | |
BioGPS: 5226 | ||
Gene Expression Atlas: ENSG00000142657 | ||
The Human Protein Atlas: ENSG00000142657 | ||
Pathway | NCI Pathway Interaction Database: PGD | |
KEGG: PGD | ||
REACTOME: PGD | ||
ConsensusPathDB | ||
Pathway Commons: PGD | ||
Metabolism | MetaCyc: PGD | |
HUMANCyc: PGD | ||
Regulation | Ensembl's Regulation: ENSG00000142657 | |
miRBase: chr1 :10,459,084-10,480,201 | ||
TargetScan: NM_002631 | ||
cisRED: ENSG00000142657 | ||
Context | iHOP: PGD | |
cancer metabolism search in PubMed: PGD | ||
UCL Cancer Institute: PGD | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PGD(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PGD |
Familial Cancer Database: PGD |
* 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_GLUTATHIONE_METABOLISM REACTOME_METABOLISM_OF_CARBOHYDRATES |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PGD |
MedGen: PGD (Human Medical Genetics with Condition) | |
ClinVar: PGD | |
Phenotype | MGI: PGD (International Mouse Phenotyping Consortium) |
PhenomicDB: PGD |
Mutations for PGD |
* 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 PGD 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 |
CV813939 | PGD | 1 | 76 | 1 | 10464228 | 10464303 | ZNF335 | 73 | 525 | 20 | 44581025 | 44582531 | |
DA454694 | PGD | 1 | 340 | 1 | 10459126 | 10463154 | ESRP1 | 335 | 563 | 8 | 95683825 | 95690584 | |
BF032755 | PGD | 1 | 248 | 1 | 10464287 | 10471601 | C11orf24 | 248 | 668 | 11 | 68029511 | 68029941 | |
AA654860 | PGD | 8 | 241 | 1 | 10479911 | 10480144 | PGD | 238 | 462 | 1 | 10479702 | 10479926 |
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=31) | (# total SNVs=11) |
(# total SNVs=0) | (# total SNVs=0) |
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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 |
chr1:10473196-10473196 | p.D244D | 4 |
chr1:10460485-10460485 | p.D40D | 4 |
chr1:10479678-10479678 | p.? | 2 |
chr1:10477169-10477169 | p.R324W | 2 |
chr1:10477453-10477453 | p.I332I | 2 |
chr1:10477466-10477466 | p.Q337K | 2 |
chr1:10477468-10477468 | p.Q337Q | 2 |
chr1:10473290-10473290 | p.V276I | 2 |
chr1:10479557-10479557 | p.D431E | 2 |
chr1:10460491-10460491 | p.F42L | 2 |
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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 | 2 | 2 | 7 |   |   | 1 |   | 1 |   |   | 4 | 2 | 1 |   |   | 12 | 5 |   | 4 |
# mutation | 2 | 2 | 2 | 7 |   |   | 1 |   | 1 |   |   | 4 | 2 | 1 |   |   | 13 | 6 |   | 5 |
nonsynonymous SNV | 1 | 2 | 2 | 6 |   |   | 1 |   |   |   |   | 3 | 1 | 1 |   |   | 7 | 6 |   | 3 |
synonymous SNV | 1 |   |   | 1 |   |   |   |   | 1 |   |   | 1 | 1 |   |   |   | 6 |   |   | 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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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 |
chr1:10477466 | p.V276I | 2 |
chr1:10473290 | p.I332I | 2 |
chr1:10477468 | p.Q337K | 2 |
chr1:10477453 | p.Q337Q | 2 |
chr1:10477456 | p.S405F | 1 |
chr1:10460560 | p.F42L | 1 |
chr1:10479551 | p.R288W | 1 |
chr1:10473253 | p.A416T | 1 |
chr1:10460573 | p.S57S | 1 |
chr1:10479585 | p.R288Q | 1 |
Other DBs for Point Mutations |
Copy Number for PGD 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 PGD |
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 |
AKR1A1,SZRD1,CTNNBIP1,DDOST,DNAJC11,ENO1,G6PD, GALE,ICMT,KIAA2013,LYPLA2,LYPLA2P1,NOC2L,PGD, PRDX1,PSMB2,PSMD14,RCC2,SDHB,SLC25A33,TUBA1C | ACO1,AIFM2,ALDH2,CALB2,COL4A1,EPHX1,ESYT1, FAH,GDPD5,GPD1,ITPK1,LIPE,MYO1C,PGD, PJA1,SURF4,TFE3,TKT,TUSC5,TYRO3,VTI1B | ||||
ACOT7,AKR7A2,APITD1,PITHD1,AUNIP,SZRD1,MINOS1, DDOST,DNAJC11,DNAJC16,ENO1,EXOSC10,ICMT,LZIC, MFN2,MRTO4,PARK7,PGD,SDHB,TMEM201,USP48 | ASF1B,ATAD2,BRIP1,C16orf59,CHAF1B,CHEK1,DTL, E2F1,E2F7,EXO1,GGCT,GMDS,HELLS,NEK6, ORC1,PAQR4,PGD,PKMYT1,RAD54L,SLC5A6,ZNF367 |
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 PGD |
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 |
DB00789 | phosphogluconate dehydrogenase | approved | Gadopentetate dimeglumine | ||
DB00851 | phosphogluconate dehydrogenase | approved | Dacarbazine | ||
DB00920 | phosphogluconate dehydrogenase | approved | Ketotifen | ||
DB02076 | phosphogluconate dehydrogenase | experimental | 6-Phosphogluconic Acid | ||
DB02212 | phosphogluconate dehydrogenase | experimental | Pyrophosphate 2- | ||
DB03962 | phosphogluconate dehydrogenase | experimental | Nicotinamide 8-Bromo-Adenine Dinucleotide Phosphate |
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Cross referenced IDs for PGD |
* 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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