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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GPX1 |
Basic gene info. | Gene symbol | GPX1 |
Gene name | glutathione peroxidase 1 | |
Synonyms | GPXD|GSHPX1 | |
Cytomap | UCSC genome browser: 3p21.3 | |
Genomic location | chr3 :49394608-49395791 | |
Type of gene | protein-coding | |
RefGenes | NM_000581.2, NM_201397.1, | |
Ensembl id | ENSG00000233276 | |
Description | GPx-1GSHPx-1cellular glutathione peroxidase | |
Modification date | 20141222 | |
dbXrefs | MIM : 138320 | |
HGNC : HGNC | ||
Ensembl : ENSG00000233276 | ||
HPRD : 11749 | ||
Vega : OTTHUMG00000156837 | ||
Protein | UniProt: go to UniProt's Cross Reference DB Table | |
Expression | CleanEX: HS_GPX1 | |
BioGPS: 2876 | ||
Gene Expression Atlas: ENSG00000233276 | ||
The Human Protein Atlas: ENSG00000233276 | ||
Pathway | NCI Pathway Interaction Database: GPX1 | |
KEGG: GPX1 | ||
REACTOME: GPX1 | ||
ConsensusPathDB | ||
Pathway Commons: GPX1 | ||
Metabolism | MetaCyc: GPX1 | |
HUMANCyc: GPX1 | ||
Regulation | Ensembl's Regulation: ENSG00000233276 | |
miRBase: chr3 :49,394,608-49,395,791 | ||
TargetScan: NM_000581 | ||
cisRED: ENSG00000233276 | ||
Context | iHOP: GPX1 | |
cancer metabolism search in PubMed: GPX1 | ||
UCL Cancer Institute: GPX1 | ||
Assigned class in ccmGDB | C |
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Phenotypic Information for GPX1(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GPX1 |
Familial Cancer Database: GPX1 |
* 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 KEGG_ARACHIDONIC_ACID_METABOLISM REACTOME_METABOLISM_OF_NUCLEOTIDES REACTOME_PURINE_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GPX1 |
MedGen: GPX1 (Human Medical Genetics with Condition) | |
ClinVar: GPX1 | |
Phenotype | MGI: GPX1 (International Mouse Phenotyping Consortium) |
PhenomicDB: GPX1 |
Mutations for GPX1 |
* 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 GPX1 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 |
BP429026 | GPX1 | 7 | 292 | 3 | 49394925 | 49395489 | RPL3 | 291 | 388 | 22 | 39709703 | 39710177 | |
AA995621 | GPX1 | 16 | 159 | 3 | 49394609 | 49394752 | SLC35B3 | 150 | 315 | 6 | 8435434 | 8435599 |
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=15) | (# total SNVs=2) |
(# 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 |
chr3:49395482-49395482 | p.P77R | 11 |
chr3:49395688-49395688 | p.A8A | 1 |
chr3:49395053-49395053 | p.A127V | 1 |
chr3:49395694-49395694 | p.L6L | 1 |
chr3:49395068-49395069 | p.A122fs*44 | 1 |
chr3:49395695-49395695 | p.L6R | 1 |
chr3:49395097-49395097 | p.F112L | 1 |
chr3:49394857-49394857 | p.I192I | 1 |
chr3:49395100-49395100 | p.L111L | 1 |
chr3:49394909-49394909 | p.P175L | 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 |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
# mutation |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
nonsynonymous SNV |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
synonymous SNV |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |   |
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 |
Other DBs for Point Mutations |
Copy Number for GPX1 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 GPX1 |
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 |
APOE,ARL6IP4,AURKAIP1,BCL7C,C19orf24,C19orf60,C1orf86, LAMTOR4,C9orf16,CCDC12,CCM2,GPX1,NDUFA11,NDUFS7, OAZ1,INAFM1,RPS19BP1,THAP3,TWF2,UQCR11,ZNHIT1 | ANXA11,ARL2,CCDC107,CCM2,CD151,CD63,CD81, GPX1,GPX4,ITFG3,LGALS1,LRP3,MYL6,NAGLU, NME4,NUCB1,POLR2L,PRR5,RNPEPL1,SNX17,UROD | ||||
ASNA1,C11orf31,ELP6,FAU,GADD45GIP1,GEMIN7,GPX1, GSTO1,MED31,MRPL43,MRPL54,MYEOV2,NDUFA11,NDUFA13, NDUFA2,NDUFB7,PFDN5,RPSA,RPSAP58,TIMM8B,UQCR11 | ADSL,ANAPC11,ASNA1,C19orf53,ATRAID,GPX1,HAX1, HSCB,MRPL57,MRPL43,MRPL54,NDUFA11,NDUFA7,POP7, RPL27A,RPL35,RPS10,RPS14,SNRPD2,STOML2,ZNF511 |
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 GPX1 |
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 |
DB00143 | glutathione peroxidase 1 | approved; nutraceutical | Glutathione | ||
DB01694 | glutathione peroxidase 1 | experimental | D-tartaric acid | ||
DB01942 | glutathione peroxidase 1 | experimental | Formic Acid | ||
DB01975 | glutathione peroxidase 1 | experimental | AMPCPR | ||
DB02059 | glutathione peroxidase 1 | experimental | Adenosine-5-Diphosphoribose | ||
DB03148 | glutathione peroxidase 1 | experimental | Phosphomethylphosphonic Acid Adenosyl Ester | ||
DB01992 | glutathione peroxidase 1 | experimental | Coenzyme A | ||
DB03014 | glutathione peroxidase 1 | experimental | Heme | ||
DB03766 | glutathione peroxidase 1 | experimental | Propanoic Acid | ||
DB03247 | glutathione peroxidase 1 | experimental | Riboflavin Monophosphate | ||
DB03382 | glutathione peroxidase 1 | experimental | S-Oxy Cysteine | ||
DB03661 | glutathione peroxidase 1 | experimental | Cysteinesulfonic Acid | ||
DB04580 | glutathione peroxidase 1 | experimental | 1-Methyl-2-quinolone | ||
DB04605 | glutathione peroxidase 1 | experimental | 5-Aminoisoquinoline | ||
DB00515 | glutathione peroxidase 1 | approved | Cisplatin | ||
DB00171 | glutathione peroxidase 1 | approved; nutraceutical | Adenosine triphosphate | ||
DB01205 | glutathione peroxidase 1 | approved | Flumazenil | ||
DB00997 | glutathione peroxidase 1 | approved; investigational | Doxorubicin | ||
DB00783 | glutathione peroxidase 1 | approved; investigational | Estradiol | ||
DB00675 | glutathione peroxidase 1 | approved | Tamoxifen |
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Cross referenced IDs for GPX1 |
* 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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