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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 MT3
check button Gene summary
Basic gene informationGene symbolMT3
Gene namemetallothionein 3
SynonymsGIF|GIFB|GRIF|ZnMT3
CytomapUCSC genome browser: 16q13
Type of geneprotein-coding
RefGenesNM_005954.2,
DescriptionMT-3MT-IIIgrowth inhibitory factormetallothionein 3 (growth inhibitory factor (neurotrophic))metallothionein-3metallothionein-III
Modification date20141207
dbXrefs MIM : 139255
HGNC : HGNC
Ensembl : ENSG00000087250
HPRD : 00752
Vega : OTTHUMG00000133282
ProteinUniProt:
go to UniProt's Cross Reference DB Table
ExpressionCleanEX: HS_MT3
BioGPS: 4504
PathwayNCI Pathway Interaction Database: MT3
KEGG: MT3
REACTOME: MT3
Pathway Commons: MT3
ContextiHOP: MT3
ligand binding site mutation search in PubMed: MT3
UCL Cancer Institute: MT3
Assigned class in TissGDB*C
Included tissue-specific gene expression resourcesHPA,TiGER
Specific-tissues in normal samples (assigned by TissGDB using HPA, TiGER, and GTEx)Brain
Cancer types related to the specific-tissues in cancer samples (assigned by TissGDB using TCGA)GBM,LGG
Reference showing the relevant tissue of MT3
Description by TissGene annotationsCancer gene
* 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:0000060protein import into nucleus, translocation18554677
GO:0001666response to hypoxia12763630
GO:0001934positive regulation of protein phosphorylation18295594
GO:0010628positive regulation of gene expression18295594
GO:0010940positive regulation of necrotic cell death15129022
GO:0010942positive regulation of cell death16387743
GO:0019430removal of superoxide radicals12383939
GO:0030308negative regulation of cell growth16601975
GO:0030517negative regulation of axon extension16601975
GO:0030949positive regulation of vascular endothelial growth factor receptor signaling pathway18295594
GO:0032148activation of protein kinase B activity18295594
GO:0035690cellular response to drug19536566
GO:0036091positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress18554677
GO:0043066negative regulation of apoptotic process15129022
GO:0043154negative regulation of cysteine-type endopeptidase activity involved in apoptotic process16387743
GO:0043491protein kinase B signaling18554677
GO:0045893positive regulation of transcription, DNA-templated18295594
GO:0050821protein stabilization18295594
GO:0051354negative regulation of oxidoreductase activity21320589
GO:0055069zinc ion homeostasis18157556
GO:0055073cadmium ion homeostasis18157556
GO:0060547negative regulation of necrotic cell death18554677
GO:0070371ERK1 and ERK2 cascade18554677
GO:0070374positive regulation of ERK1 and ERK2 cascade18295594
GO:0071276cellular response to cadmium ion16387743
GO:0071732cellular response to nitric oxide18157556
GO:2000117negative regulation of cysteine-type endopeptidase activity18554677
GO:2000378negative regulation of reactive oxygen species metabolic process18554677
GO:0000060protein import into nucleus, translocation18554677
GO:0001666response to hypoxia12763630
GO:0001934positive regulation of protein phosphorylation18295594
GO:0010628positive regulation of gene expression18295594
GO:0010940positive regulation of necrotic cell death15129022
GO:0010942positive regulation of cell death16387743
GO:0019430removal of superoxide radicals12383939
GO:0030308negative regulation of cell growth16601975
GO:0030517negative regulation of axon extension16601975
GO:0030949positive regulation of vascular endothelial growth factor receptor signaling pathway18295594
GO:0032148activation of protein kinase B activity18295594
GO:0035690cellular response to drug19536566
GO:0036091positive regulation of transcription from RNA polymerase II promoter in response to oxidative stress18554677
GO:0043066negative regulation of apoptotic process15129022
GO:0043154negative regulation of cysteine-type endopeptidase activity involved in apoptotic process16387743
GO:0043491protein kinase B signaling18554677
GO:0045893positive regulation of transcription, DNA-templated18295594
GO:0050821protein stabilization18295594
GO:0051354negative regulation of oxidoreductase activity21320589
GO:0055069zinc ion homeostasis18157556
GO:0055073cadmium ion homeostasis18157556
GO:0060547negative regulation of necrotic cell death18554677
GO:0070371ERK1 and ERK2 cascade18554677
GO:0070374positive regulation of ERK1 and ERK2 cascade18295594
GO:0071276cellular response to cadmium ion16387743
GO:0071732cellular response to nitric oxide18157556
GO:2000117negative regulation of cysteine-type endopeptidase activity18554677
GO:2000378negative regulation of reactive oxygen species metabolic process18554677


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TissGeneExp for MT3

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
STAD-3.765673256-1.783388881-1.9822843752.60E-075.79E-06
KIRP-2.9941326310.593326744-3.5874593751.20E-164.72E-15
COAD-1.636144411.033870975-2.6700153858.69E-064.06E-05
ESCA-3.591275529-1.281548256-2.3097272730.002390.025059155
KICH3.1529037440.4927037442.66020.000770.00169708
LIHC-2.125228256-3.6817682561.556540.0004290.00126872
HNSC-2.747766861-0.878469186-1.8692976742.03E-050.000107218


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TissGene-miRNA for MT3

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 MT3
TissGeneSNV for MT3

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.S10FHNSC1
p.C35FLUAD1
p.L44RSKCM1
p.D37NSKCM1
p.C66*UCEC1
p.C35*LUAD1
p.E58KSKCM1


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TissGeneCNV for MT3

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 MT3

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


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TissGeneNet for MT3

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)
BRCA (tumor)BRCA (normal)
MT3, TERF2IP, TTR (tumor)MT3, TERF2IP, TTR (normal)
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COAD (tumor)COAD (normal)
MT3, TERF2IP, TTR (tumor)MT3, TERF2IP, TTR (normal)
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HNSC (tumor)HNSC (normal)
MT3, TERF2IP, TTR (tumor)MT3, TERF2IP, TTR (normal)
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KICH (tumor)KICH (normal)
MT3, TERF2IP, TTR (tumor)MT3, TERF2IP, TTR (normal)
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KIRC (tumor)KIRC (normal)
MT3, TERF2IP, TTR (tumor)MT3, TERF2IP, TTR (normal)
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KIRP (tumor)KIRP (normal)
MT3, TERF2IP, TTR (tumor)MT3, TERF2IP, TTR (normal)
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LIHC (tumor)LIHC (normal)
MT3, TERF2IP, TTR (tumor)MT3, TERF2IP, TTR (normal)
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LUAD (tumor)LUAD (normal)
MT3, TERF2IP, TTR (tumor)MT3, TERF2IP, TTR (normal)
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LUSC (tumor)LUSC (normal)
MT3, TERF2IP, TTR (tumor)MT3, TERF2IP, TTR (normal)
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PRAD (tumor)PRAD (normal)
MT3, TERF2IP, TTR (tumor)MT3, TERF2IP, TTR (normal)
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STAD (tumor)STAD (normal)
MT3, TERF2IP, TTR (tumor)MT3, TERF2IP, TTR (normal)
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THCA (tumor)THCA (normal)
MT3, TERF2IP, TTR (tumor)MT3, TERF2IP, TTR (normal)
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TissGeneProg for MT3

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 MT3
TissGeneDrug for MT3

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


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TissGeneDisease for MT3

check button Disease information associated with TissGene
(DisGeNet, 2016-06-01)
Disease IDDisease name# pubmedsSource
umls:C0036572Seizures3BeFree,CTD_human,RGD
umls:C0001430Adenoma2BeFree
umls:C0007131Non-Small Cell Lung Carcinoma2BeFree,CTD_human
umls:C0085084Motor Neuron Disease2BeFree,RGD
umls:C1458155Mammary Neoplasms2BeFree,CTD_human
umls:C0000832Abruptio Placentae1LHGDN
umls:C0001418Adenocarcinoma1BeFree
umls:C0003469Anxiety Disorders1BeFree
umls:C0005695Bladder Neoplasm1CTD_human
umls:C0006023Borna Disease1RGD
umls:C0007137Squamous cell carcinoma1BeFree,LHGDN
umls:C0007787Transient Ischemic Attack1RGD
umls:C0011570Mental Depression1BeFree
umls:C0011581Depressive disorder1BeFree
umls:C0020676Hypothyroidism1RGD
umls:C0022336Creutzfeldt-Jakob disease1BeFree
umls:C0023418leukemia1BeFree
umls:C0023467Leukemia, Myelocytic, Acute1BeFree
umls:C0027626Neoplasm Invasiveness1CTD_human
umls:C0027627Neoplasm Metastasis1BeFree
umls:C0033578Prostatic Neoplasms1LHGDN
umls:C0153381Malignant neoplasm of mouth1BeFree
umls:C0206686Adrenocortical carcinoma1BeFree
umls:C0220621pediatric acute myeloblastic leukemia1BeFree
umls:C0220641Lip and Oral Cavity Carcinoma1BeFree
umls:C0242706Hyperoxia1RGD
umls:C0333463Senile Plaques1BeFree
umls:C0376618Endotoxemia1RGD
umls:C0699791Stomach Carcinoma1BeFree
umls:C0740392Infarction, Middle Cerebral Artery1RGD
umls:C0751922Median Neuropathy1RGD
umls:C1306856Megaloblastic anemia due to inborn errors of metabolism1BeFree
umls:C1394891Intrinsic Factor Deficiency1BeFree
umls:C1519670Tumor Angiogenesis1BeFree
umls:C2936349Plaque, Amyloid1BeFree
umls:C2937421Prostatic Hyperplasia1LHGDN