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Bioinformatics and Systems Medicine Laboratory Bioinformatics and Systems Medicine Laboratory

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TissGeneSummary

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TissGeneExp

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TissGene-miRNA

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TissGeneMut: TissGeneSNV, TissGeneCNV, and TissGeneFusions

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TissGeneNet

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TissGeneProg

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TissGeneClin: TissGeneDrug and TissGeneDisease

TissGeneSummary for GPX3
check button Gene summary
Basic gene informationGene symbolGPX3
Gene nameglutathione peroxidase 3 (plasma)
SynonymsGPx-P|GSHPx-3|GSHPx-P
CytomapUCSC genome browser: 5q23
Type of geneprotein-coding
RefGenesNM_002084.3,
DescriptionGPx-3extracellular glutathione peroxidaseglutathione peroxidase 3plasma glutathione peroxidase
Modification date20141222
dbXrefs MIM : 138321
HGNC : HGNC
Ensembl : ENSG00000211445
HPRD : 11750
Vega : OTTHUMG00000163693
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_GPX3
BioGPS: 2878
PathwayNCI Pathway Interaction Database: GPX3
KEGG: GPX3
REACTOME: GPX3
Pathway Commons: GPX3
ContextiHOP: GPX3
ligand binding site mutation search in PubMed: GPX3
UCL Cancer Institute: GPX3
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesTiGER,GTEx
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)KidneyEye
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)KIRC,KIRP,KICHUVM
Reference showing the relevant tissue of GPX3
Description by TissGene annotationsProtective TissGene in OS
Cancer gene
Fused withTSGene
* Class A consists of genes with literature evidence and is part of the cTissGenes. Class B consists of only cTissGenes without additional evidence. The remaining genes belong to Class C.

check button Gene ontology having evidence of Inferred from Direct Assay (IDA) from Entrez
GO IDGO termPubMed ID
GO:0051289protein homotetramerization3693360
GO:0051289protein homotetramerization3693360


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TissGeneExp for GPX3

check button Gene expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
gene exp


check button Gene isoform expressions across 28 cancer types (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA pan-cancer tcga_rsem_isoform_tpm, version 2016-09-01)
gene isoform exp


check button Gene expressions across normal tissues of GTEx data
(GTEx GTEx_Analysis_v6_RNA-seq_RNA-SeQCv1.1.8_gene_rpkm.gct)
- Here, we shows the matched tissue types only among our 28 cancer types.
normal gene exp


check button Different expressions across 14 cancer types with more than 10 samples between matched tumors and normals (X-axis: cancer type and Y-axis: log2(norm_counts+1))
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
DEG exp

- Significantly differentially expressed cancer types and information. (|Fold change|>1 and FDR<0.05)
Cancer typeMean(exp) in tumorMean(exp) in matched normalLog2FCP-val.FDR
HNSC-1.1371175881.636184738-2.7733023261.32E-136.19E-12
COAD-2.025662310.38748769-2.413155.63E-095.43E-08
KIRP3.2617497095.646868459-2.385118751.33E-055.40E-05
BRCA-1.282006982.10779302-3.38982.33E-375.20E-36
PRAD-0.8141815410.489808843-1.3039903851.60E-114.91E-10
STAD-0.8710627911.553940334-2.4250031253.29E-114.62E-09
LUSC-0.4901335023.28087238-3.7710058824.10E-312.15E-29
LUAD0.658206393.071890873-2.4136844836.26E-231.90E-21
BLCA-1.6820104891.022957933-2.7049684212.33E-081.84E-06
KICH2.5453444594.286460459-1.7411160.0006740.001500501
ESCA-2.0757769961.12447755-3.2002545457.81E-060.000913862


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TissGene-miRNA for GPX3

check button Significantly anti-correlated miRNAs of TissGene across 28 cancer types
(Gene-miRNA relations from TargetScanHuman Relsease 7.1, Conserved_Site_Context_Scores.txt.zip, 06.01.2016)
(TCGA IlluminaHiSeq_miRNASeq, log2(RPM+1) data, version 2016-11-21)
(TCGA IlluminaHiSeq_RNASeqV2, log2(normalized_count+1) data, version 2016-08-16)
(Spearman’s Rank Correlation (p-value<0.05 and coefficient<-0.25))
Cancer typemiRNA idmiRNA accessionP-val.Coeff.# samples


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TissGeneMut for GPX3
TissGeneSNV for GPX3

check button nsSNV counts per each loci.
Different colors of circles represent different cancer types. Circle size denotes number of samples.
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
* Click on the image to enlarge it in a new window.
SNV lollipop
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check button Somatic nucleotide variants of TissGene across 28 cancer types
(X-axis: cancer type and Y-axis: % of mutated samples)
The numbers in parentheses are numbers of samples with mutation (nsSNVs).
(TCGA somatic mutation (SNPs and small INDELs) data, version 2016-04-25)
SNV distribution

- nsSNVs sorted by frequency.
AAchangeCancer type# samples
p.R123GLUAD1
p.G44ESKCM1
p.R180SKIRC1
p.G93SBLCA1
p.M174ISKCM1
p.F151VUCEC1
p.S28LSTAD1
p.R123*BLCA1
p.G110ESKCM1
p.K147IKIRC1
p.D139NSKCM1
p.E136QBLCA1
p.S20LLUAD1
p.V69MLUAD1
p.V223ISKCM1
p.I193MSTAD1
p.E42KSKCM1
p.A220VUCEC1
p.L162FBLCA1


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TissGeneCNV for GPX3

check button Copy number variations of TissGene across 28 cancer types (X-axis: cancer type and Y-axis: % of CNV samples)
(TCGA Gistic2_CopyNumber_Gistic2_all_data_by_genes, Gistic2 copy number data, version 2016-08-16)
CNV


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TissGeneFusions for GPX3

check button Fusion genes including TissGene
(ChimerDB 3.0, 2016-12-01 and TCGA fusion Portal 2015-12-01)
DatabaseSrcCancer typeSampleFusion geneORF5'-gene BP3'-gene BP
Chimerdb3.0ChiTaRsNACV421185GPX3-NSMCE1chr5:150408290chr16:27238452
Chimerdb3.0ChiTaRsNAAA740310GPX3-RPN2chr5:150408522chr20:35812585
Chimerdb3.0ChiTaRsNABG430541GPX3-GPX3chr5:150407832chr5:150406467
Chimerdb3.0ChiTaRsNABG896291GPX3-GPX3chr5:150408090chr5:150408072
Chimerdb3.0ChiTaRsNABG927502GPX3-GPX3chr5:150407992chr5:150407030
Chimerdb3.0ChiTaRsNABF878552GPX3-GPX3chr5:150407052chr5:150404898
Chimerdb3.0ChiTaRsNAAW794509GPX3-S100A8chr5:150407982chr1:153362669
Chimerdb3.0ChiTaRsNACB044109INPP4B-GPX3chr4:142963356chr5:150406475
Chimerdb3.0ChiTaRsNABG990596AFAP1L2-GPX3chr10:116057013chr5:150406494
Chimerdb3.0ChiTaRsNAW25873GPX3-GPX3chr5:150407578chr5:150407726
Chimerdb3.0ChiTaRsNABF848871AARS-GPX3chr16:70287931chr5:150407985
TCGAfusionPortalPRADATHCATCGA-BJ-A2N8-01AGPX3-SEC63NAChr5:150408548Chr6:108214782
TCGAfusionPortalPRADATHCATCGA-DJ-A4UR-01AGPX3-SQSTM13UTR-CDSChr5:150408548Chr5:179250858
TCGAfusionPortalPRADATHCATCGA-DJ-A4V2-01AGPX3-CHD4NAChr5:150408515Chr12:6710696
TCGAfusionPortalPRADATHCATCGA-EM-A22L-01AGPX3-SEC63NAChr5:150408548Chr6:108214782
TCGAfusionPortalPRADATHCATCGA-FY-A3W9-01AGPX3-CHD4NAChr5:150408515Chr12:6710696


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TissGeneNet for GPX3

check button Co-expressed gene networks based on protein-protein interaction data (CePIN)
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(PINA2 ppi data)


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TissGeneProg for GPX3

check button Kaplan-Meier plots with logrank tests of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image to enlarge it in a new window.
survival 1

check button Kaplan-Meier plots with logrank test of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.
survival 2

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of overall survival (OS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.
survival 3

check button Forest plot of Cox proportional hazard ratio (HR) and 95% CI of relapse free survival (RFS) using 28 cancer types
(TCGA IlluminaHiSeq_RNASeqV2, pan-cancer normalized log2(norm_counts+1) data, version 2016-08-16)
(TCGA clinicalMatrix, phenotype data, version 2016-04-27)
* Click on the image enlarge it in a new window.
survival 4

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TissGeneClin for GPX3
TissGeneDrug for GPX3

check button Drug information targeting TissGene
(DrugBank Version 5.0.6, 2017-04-01)
DrugBank IDDrug nameDrug activityDrug typeDrug status
DB00143GlutathioneCofactorSmall moleculeApproved|Nutraceutical


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TissGeneDisease for GPX3

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0027627Neoplasm Metastasis6BeFree
umls:C0596263Carcinogenesis6BeFree
umls:C0006142Malignant neoplasm of breast5BeFree
umls:C0376358Malignant neoplasm of prostate5BeFree
umls:C0600139Prostate carcinoma5BeFree
umls:C0678222Breast Carcinoma5BeFree
umls:C0686619Secondary malignant neoplasm of lymph node5BeFree
umls:C0001418Adenocarcinoma4BeFree,CTD_human,LHGDN
umls:C0024623Malignant neoplasm of stomach4BeFree
umls:C0028754Obesity4BeFree,CTD_human,RGD
umls:C0038454Cerebrovascular accident4BeFree
umls:C0699791Stomach Carcinoma4BeFree
umls:C0948008Ischemic stroke3BeFree,GAD
umls:C2239176Liver carcinoma3BeFree
umls:C3272363Ischemic Cerebrovascular Accident3BeFree
umls:C0001430Adenoma2BeFree,GAD
umls:C0014175Endometriosis2CTD_human
umls:C0023903Liver neoplasms2BeFree,CTD_human
umls:C0024115Lung diseases2BeFree,RGD
umls:C0024121Lung Neoplasms2CTD_human
umls:C0040136Thyroid Neoplasm2GAD,LHGDN
umls:C0085580Essential Hypertension2BeFree
umls:C0242379Malignant neoplasm of lung2GAD
umls:C0002736Amyotrophic Lateral Sclerosis1BeFree
umls:C0004096Asthma1BeFree
umls:C0004153Atherosclerosis1GAD
umls:C0004763Barrett Esophagus1LHGDN
umls:C0005586Bipolar Disorder1BeFree
umls:C0005684Malignant neoplasm of urinary bladder1GAD
umls:C0007102Malignant tumor of colon1BeFree
umls:C0007113Rectal Carcinoma1BeFree
umls:C0007115Malignant neoplasm of thyroid1BeFree
umls:C0007134Renal Cell Carcinoma1BeFree
umls:C0007222Cardiovascular Diseases1LHGDN
umls:C0007787Transient Ischemic Attack1BeFree
umls:C0008497Choriocarcinoma1BeFree
umls:C0009404Colorectal Neoplasms1GAD
umls:C0011849Diabetes Mellitus1LHGDN
umls:C0011853Diabetes Mellitus, Experimental1RGD
umls:C0011860Diabetes Mellitus, Non-Insulin-Dependent1GAD
umls:C0013080Down Syndrome1BeFree
umls:C0013264Muscular Dystrophy, Duchenne1BeFree
umls:C0014170Endometrial Neoplasms1RGD
umls:C0015230Exanthema1BeFree
umls:C0015624Fanconi Syndrome1CTD_human
umls:C0017636Glioblastoma1BeFree
umls:C0019693HIV Infections1LHGDN
umls:C0021655Insulin Resistance1CTD_human
umls:C0023418leukemia1BeFree
umls:C0023895Liver diseases1GAD
umls:C0024117Chronic Obstructive Airway Disease1GAD
umls:C0024305Lymphoma, Non-Hodgkin1GAD
umls:C0025202melanoma1BeFree
umls:C0029925Ovarian Carcinoma1BeFree
umls:C0033578Prostatic Neoplasms1CTD_human
umls:C0038356Stomach Neoplasms1GAD
umls:C0042487Venous Thrombosis1LHGDN
umls:C0085110Severe Combined Immunodeficiency1BeFree
umls:C0151942Arterial thrombosis1BeFree
umls:C0151945Thrombosis of cerebral veins1BeFree
umls:C0178874Tumor Progression1BeFree
umls:C0206681Adenocarcinoma, Clear Cell1LHGDN
umls:C0206701Cystadenocarcinoma, Serous1BeFree
umls:C0238463Papillary thyroid carcinoma1BeFree
umls:C0278601Inflammatory Breast Carcinoma1BeFree
umls:C0278996Cancer of Head and Neck1BeFree
umls:C0279626Squamous cell carcinoma of esophagus1BeFree
umls:C0279702Conventional (Clear Cell) Renal Cell Carcinoma1BeFree
umls:C0374997Helicobacter pylori (H. pylori) infection in conditions classified elsewhere and of unspecified site1BeFree
umls:C0524851Neurodegenerative Disorders1CTD_human
umls:C0549473Thyroid carcinoma1BeFree
umls:C0677886Epithelial ovarian cancer1BeFree
umls:C0699790Colon Carcinoma1BeFree
umls:C0848332Spots on skin1BeFree
umls:C1134719Invasive Ductal Breast Carcinoma1BeFree
umls:C1335177Ovarian Serous Adenocarcinoma1BeFree
umls:C1337013Differentiated Thyroid Gland Carcinoma1BeFree
umls:C1378703Renal carcinoma1BeFree
umls:C1449563Cardiomyopathy, Familial Idiopathic1BeFree