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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for PGP |
Basic gene info. | Gene symbol | PGP |
Gene name | phosphoglycolate phosphatase | |
Synonyms | PGPase | |
Cytomap | UCSC genome browser: 16p13.3 | |
Genomic location | chr16 :2261602-2264822 | |
Type of gene | protein-coding | |
RefGenes | NM_001042371.2, | |
Ensembl id | ENSG00000184207 | |
Description | - | |
Modification date | 20141207 | |
dbXrefs | MIM : 172280 | |
HGNC : HGNC | ||
Ensembl : ENSG00000184207 | ||
Vega : OTTHUMG00000177047 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_PGP | |
BioGPS: 283871 | ||
Gene Expression Atlas: ENSG00000184207 | ||
The Human Protein Atlas: ENSG00000184207 | ||
Pathway | NCI Pathway Interaction Database: PGP | |
KEGG: PGP | ||
REACTOME: PGP | ||
ConsensusPathDB | ||
Pathway Commons: PGP | ||
Metabolism | MetaCyc: PGP | |
HUMANCyc: PGP | ||
Regulation | Ensembl's Regulation: ENSG00000184207 | |
miRBase: chr16 :2,261,602-2,264,822 | ||
TargetScan: NM_001042371 | ||
cisRED: ENSG00000184207 | ||
Context | iHOP: PGP | |
cancer metabolism search in PubMed: PGP | ||
UCL Cancer Institute: PGP | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for PGP(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: PGP |
Familial Cancer Database: PGP |
* This gene is included in those cancer gene databases. |
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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_GLYOXYLATE_AND_DICARBOXYLATE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: PGP |
MedGen: PGP (Human Medical Genetics with Condition) | |
ClinVar: PGP | |
Phenotype | MGI: PGP (International Mouse Phenotyping Consortium) |
PhenomicDB: PGP |
Mutations for PGP |
* 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 PGP 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 |
AA653505 | PGP | 2 | 73 | 16 | 2263682 | 2263753 | AUTS2 | 58 | 369 | 7 | 69645460 | 69645771 | |
BC080619 | PGP | 18 | 1079 | 16 | 2263693 | 2264838 | CSNK1D | 1077 | 2843 | 17 | 80202238 | 80231293 |
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=4) | (# total SNVs=6) |
(# 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 |
chr16:2263765-2263765 | p.D310D | 2 |
chr16:2264226-2264226 | p.L185L | 2 |
chr16:2263949-2263949 | p.G249D | 2 |
chr16:2263992-2263992 | p.K235* | 1 |
chr16:2264017-2264017 | p.A226A | 1 |
chr16:2264032-2264032 | p.A221A | 1 |
chr16:2264143-2264143 | p.I212I | 1 |
chr16:2264199-2264199 | p.L194M | 1 |
chr16:2263803-2263803 | p.V298M | 1 |
chr16:2264506-2264506 | p.G91G | 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 |   |   |   |   | 1 |   | 1 |   |   |   |   | 1 |   |   |   |   | 2 | 1 |   |   |
# mutation |   |   |   |   | 1 |   | 1 |   |   |   |   | 1 |   |   |   |   | 2 | 1 |   |   |
nonsynonymous SNV |   |   |   |   | 1 |   | 1 |   |   |   |   | 1 |   |   |   |   | 1 | 1 |   |   |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   | 1 |   |   |   |
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 |
chr16:2263803 | p.V298M | 1 |
chr16:2263819 | p.N292K | 1 |
chr16:2263929 | p.V256F | 1 |
chr16:2264143 | p.I212I | 1 |
chr16:2264177 | p.D201G | 1 |
chr16:2264251 | p.F176L | 1 |
Other DBs for Point Mutations |
Copy Number for PGP 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 PGP |
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 |
TSR3,C16orf91,ECI1,FAM173A,FAM195A,FLYWCH2,GFER, MLST8,MPG,MRPL28,MRPS34,NARFL,NDUFB10,NME3, NUBP2,PGP,RPUSD1,STUB1,TBL3,TCEB2,PAM16 | AIMP2,COX17,COX8A,ENDOG,FAM195A,FASTK,LSM10, LINC00116,NDUFB10,NDUFB2,NDUFS7,NDUFS8,PGP,PHPT1, SLC25A11,STK25,EMC6,TWF2,UBAC1,UQCR11,UQCRC1 |
BRMS1,UQCC3,C16orf13,TSR3,C16orf59,EMC8,FAM195A, EEF2KMT,HMOX2,MRPS34,NDUFB10,NUBP2,PGP,PKMYT1, POLR3K,PPP4C,RPUSD1,SAC3D1,SNRNP25,STUB1,TUFM | ADRM1,ARPC5L,ASL,ATP5G1,BRMS1,TMEM234,C9orf142, DDX39A,IDH3A,MPV17L2,NDUFS6,NOL12,PDF,PGP, PMM2,PSMC4,PTGES2,PUSL1,TBC1D7,TUBA1C,YIF1B |
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 PGP |
There's no related Drug. |
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Cross referenced IDs for PGP |
* 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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