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Phenotypic Information (metabolism pathway, cancer, disease, phenome) | |
Gene-Gene Network Information: Co-Expression Network, Interacting Genes & KEGG | |
Gene Summary for GPX4 |
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Phenotypic Information for GPX4(metabolism pathway, cancer, disease, phenome) |
Cancer Description | |
Cancer | CGAP: GPX4 |
Familial Cancer Database: GPX4 |
* 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_GLUTATHIONE_METABOLISM KEGG_ARACHIDONIC_ACID_METABOLISM |
Others | |
OMIM | |
Orphanet | |
Disease | KEGG Disease: GPX4 |
MedGen: GPX4 (Human Medical Genetics with Condition) | |
ClinVar: GPX4 | |
Phenotype | MGI: GPX4 (International Mouse Phenotyping Consortium) |
PhenomicDB: GPX4 |
Mutations for GPX4 |
* 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 GPX4 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 |
BF111779 | TRA2B | 12 | 72 | 3 | 185635116 | 185635176 | GPX4 | 72 | 284 | 19 | 1105757 | 1106614 | |
BI055467 | TMEM8A | 1 | 213 | 16 | 421729 | 421940 | GPX4 | 203 | 279 | 19 | 1104846 | 1104923 |
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=7) | (# total SNVs=7) |
(# 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 |
chr19:1106407-1106407 | p.I170I | 2 |
chr19:1105195-1105195 | p.R32Q | 2 |
chr19:1105498-1105498 | p.F105L | 1 |
chr19:1105743-1105743 | p.G137G | 1 |
chr19:1105750-1105750 | p.A140T | 1 |
chr19:1105758-1105758 | p.P142P | 1 |
chr19:1106259-1106259 | p.F165F | 1 |
chr19:1106418-1106418 | p.G174A | 1 |
chr19:1105215-1105215 | p.R39C | 1 |
chr19:1106419-1106419 | p.G174G | 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 GPX4 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 GPX4 |
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 |
AES,ALKBH7,ATP5D,C19orf24,C19orf25,C19orf70,EDF1, FAM195A,GAMT,GPX4,MRPL53,MRPL54,NDUFS7,OAZ1, PHPT1,POLR2E,RPS15,STUB1,TIMM13,UQCR11,WDR18 | AGPAT2,AP1M1,ADIRF,CAMK1,CD81,GPX4,GYPC, INPP5K,LGALS1,PALM,PHLDA3,PLA2G16,PNPLA2,POLR2E, RRAS,ST6GALNAC6,TALDO1,TESK1,TST,VEGFB,VTI1B | ||||
C11orf31,C19orf25,C19orf53,WDR83OS,FAM89B,FAU,FDX1L, GADD45GIP1,GPX1,GPX4,LIN37,LSM7,NDUFA11,NDUFB7, NOSIP,NUBP2,PAFAH1B3,RNF181,RPS15,SNRPD2,TRMT112 | ACY1,HYKK,AIG1,APOM,BDH2,ADIRF,FUOM, TMEM256,CBR1,CYB5A,GATA5,GOLT1A,GPX4,HACL1, KRT14,LOC201651,MS4A15,PEBP1,PHEX,SAT2,TM4SF5 |
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 GPX4 |
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 4 | approved; nutraceutical | Glutathione |
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Cross referenced IDs for GPX4 |
* 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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