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Browse TDG

Summary
SymbolTDG
Namethymine DNA glycosylase
Aliases G/T mismatch-specific thymine DNA glycosylase; hTDG; thymine-DNA glycosylase
Chromosomal Location12q24.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Basic function annotation.
> Subcellular Location, Domain and Function
> Gene Ontology
> KEGG and Reactome Pathway
> Subcellular Location, Domain and Function
 
Subcellular Location Nucleus
Domain PF03167 Uracil DNA glycosylase superfamily
Function

DNA glycosylase that plays a key role in active DNA demethylation: specifically recognizes and binds 5-formylcytosine (5fC) and 5-carboxylcytosine (5caC) in the context of CpG sites and mediates their excision through base-excision repair (BER) to install an unmethylated cytosine. Cannot remove 5-hydroxymethylcytosine (5hmC). According to an alternative model, involved in DNA demethylation by mediating DNA glycolase activity toward 5-hydroxymethyluracil (5hmU) produced by deamination of 5hmC. Also involved in DNA repair by acting as a thymine-DNA glycosylase that mediates correction of G/T mispairs to G/C pairs: in the DNA of higher eukaryotes, hydrolytic deamination of 5-methylcytosine to thymine leads to the formation of G/T mismatches. Its role in the repair of canonical base damage is however minor compared to its role in DNA demethylation. It is capable of hydrolyzing the carbon-nitrogen bond between the sugar-phosphate backbone of the DNA and a mispaired thymine. In addition to the G/T, it can remove thymine also from C/T and T/T mispairs in the order G/T >> C/T > T/T. It has no detectable activity on apyrimidinic sites and does not catalyze the removal of thymine from A/T pairs or from single-stranded DNA. It can also remove uracil and 5-bromouracil from mispairs with guanine.

> Gene Ontology
 
Biological Process GO:0006220 pyrimidine nucleotide metabolic process
GO:0006244 pyrimidine nucleotide catabolic process
GO:0006284 base-excision repair
GO:0006285 base-excision repair, AP site formation
GO:0006298 mismatch repair
GO:0006304 DNA modification
GO:0009166 nucleotide catabolic process
GO:0009219 pyrimidine deoxyribonucleotide metabolic process
GO:0009223 pyrimidine deoxyribonucleotide catabolic process
GO:0009262 deoxyribonucleotide metabolic process
GO:0009264 deoxyribonucleotide catabolic process
GO:0009394 2'-deoxyribonucleotide metabolic process
GO:0016925 protein sumoylation
GO:0018205 peptidyl-lysine modification
GO:0019439 aromatic compound catabolic process
GO:0019692 deoxyribose phosphate metabolic process
GO:0032091 negative regulation of protein binding
GO:0034655 nucleobase-containing compound catabolic process
GO:0035510 DNA dealkylation
GO:0035511 oxidative DNA demethylation
GO:0035561 regulation of chromatin binding
GO:0035562 negative regulation of chromatin binding
GO:0040029 regulation of gene expression, epigenetic
GO:0043393 regulation of protein binding
GO:0044270 cellular nitrogen compound catabolic process
GO:0044728 DNA methylation or demethylation
GO:0045008 depyrimidination
GO:0046386 deoxyribose phosphate catabolic process
GO:0046434 organophosphate catabolic process
GO:0046700 heterocycle catabolic process
GO:0051098 regulation of binding
GO:0051100 negative regulation of binding
GO:0070988 demethylation
GO:0070989 oxidative demethylation
GO:0072527 pyrimidine-containing compound metabolic process
GO:0072529 pyrimidine-containing compound catabolic process
GO:0080111 DNA demethylation
GO:1901136 carbohydrate derivative catabolic process
GO:1901292 nucleoside phosphate catabolic process
GO:1901361 organic cyclic compound catabolic process
GO:1901565 organonitrogen compound catabolic process
Molecular Function GO:0000700 mismatch base pair DNA N-glycosylase activity
GO:0001076 transcription factor activity, RNA polymerase II transcription factor binding
GO:0001104 RNA polymerase II transcription cofactor activity
GO:0003684 damaged DNA binding
GO:0004844 uracil DNA N-glycosylase activity
GO:0005080 protein kinase C binding
GO:0008134 transcription factor binding
GO:0008263 pyrimidine-specific mismatch base pair DNA N-glycosylase activity
GO:0016798 hydrolase activity, acting on glycosyl bonds
GO:0016799 hydrolase activity, hydrolyzing N-glycosyl compounds
GO:0019104 DNA N-glycosylase activity
GO:0030983 mismatched DNA binding
GO:0032182 ubiquitin-like protein binding
GO:0032183 SUMO binding
GO:0043566 structure-specific DNA binding
GO:0097506 deaminated base DNA N-glycosylase activity
Cellular Component GO:0016604 nuclear body
GO:0016605 PML body
> KEGG and Reactome Pathway
 
KEGG hsa03410 Base excision repair
Reactome R-HSA-73884: Base Excision Repair
R-HSA-73929: Base-Excision Repair, AP Site Formation
R-HSA-110329: Cleavage of the damaged pyrimidine
R-HSA-73894: DNA Repair
R-HSA-73928: Depyrimidination
R-HSA-110357: Displacement of DNA glycosylase by APEX1
R-HSA-212165: Epigenetic regulation of gene expression
R-HSA-74160: Gene Expression
R-HSA-392499: Metabolism of proteins
R-HSA-597592: Post-translational protein modification
R-HSA-110328: Recognition and association of DNA glycosylase with site containing an affected pyrimidine
R-HSA-73933: Resolution of Abasic Sites (AP sites)
R-HSA-3108232: SUMO E3 ligases SUMOylate target proteins
R-HSA-2990846: SUMOylation
R-HSA-3108214: SUMOylation of DNA damage response and repair proteins
R-HSA-5221030: TET1,2,3 and TDG demethylate DNA
Summary
SymbolTDG
Namethymine DNA glycosylase
Aliases G/T mismatch-specific thymine DNA glycosylase; hTDG; thymine-DNA glycosylase
Chromosomal Location12q24.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between TDG and anti-tumor immunity. The specific mechanism were also collected if the literature reports that a gene specifically promotes or inhibits the infiltration or function of T/NK cells.
> Text Mining
 

There is no record.
Summary
SymbolTDG
Namethymine DNA glycosylase
Aliases G/T mismatch-specific thymine DNA glycosylase; hTDG; thymine-DNA glycosylase
Chromosomal Location12q24.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content High-throughput screening data (e.g. CRISPR-Cas9, shRNA and RNAi) for T cell-mediated killing. Genetic screen techniques can identify mechanisms of tumor cell resistance (e.g., PTPN2) and sensitivity (e.g., APLNR) to killing by cytotoxic T cells, the central effectors of anti-tumor immunity. After comprehensively searching, eight groups of screening data sets were collected in the current database. In this tab, users can check whether their selected genes cause resistance or increase sensitivity to T cell-mediated killing in various data sets.
> High-throughput Screening
  Statistical results of TDG in screening data sets for detecting immune reponses.
PMID Screening System Cancer Type Cell Line Data Set Statistical Results Relation to immunity
29301958CRISPR-Cas9 melanomaB16F10Pmel-1 T cell NA/NSNA/NS
29301958CRISPR-Cas9 melanomaB16F10OT-1 T cell NA/NSNA/NS
28783722CRISPR-Cas9 melanomaMel6242CT-CRISPR NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX+Anti-PD1 NA/NSNA/NS
28723893CRISPR-Cas9 melanomaB16GVAX NA/NSNA/NS
25691366RNAiBreast cancerMCF7Luc-CTL assay NA/NSNA/NS
24476824shRNAmelanomaB16Primary screen NA/NSNA/NS
24476824shRNAmelanomaB16Secondary screen NA/NSNA/NS
Summary
SymbolTDG
Namethymine DNA glycosylase
Aliases G/T mismatch-specific thymine DNA glycosylase; hTDG; thymine-DNA glycosylase
Chromosomal Location12q24.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Transcriptomic and genomic profiling of pre-treated tumor biopsies from responders and non-responders to immunotherapy. These data were used to identify signatures and mechanisms of response to checkpoint blockade (e.g., anti-PDL1 and anti-PD1). One example is that mutations in the gene PBRM1 benefit clinical survival of patients with clear cell renal cell carcinoma. After comprehensively searching, we collected 5 and 6 of transcriptomic and genomic data sets, respectively. In this tab, users can check whether their selected genes have significant difference of expression or mutation between responders and non-responders in various data sets.
> Expression difference between responders and non-responders
> Mutation difference between responders and non-responders
> Expression difference between responders and non-responders
 
Points in the above scatter plot represent the expression difference of TDG in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)1412-0.2790.245
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)65-0.1020.95
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)87-0.4120.739
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 916-0.5830.0495
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59-0.4990.771
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 47-0.690.746
729033130MelanomaallAnti-PD-1 (nivolumab) 26230.0060.987
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 15110.0050.997
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 11120.0820.958
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 480.1170.9
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 280.4940.734
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 682300.1190.415
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of TDG in various data sets.
No PMID Cancer type Group Drug # Res # NRes % Mut/Res % Mut/NRes % Diff (R vs NR) Pval Anno
125765070Non-small cell lung cancer (NSCLC)allAnti-PD-1 (pembrolizumab) 14170001
225765070Non-small cell lung cancer (NSCLC)smokingAnti-PD-1 (pembrolizumab) 1030001
325765070Non-small cell lung cancer (NSCLC)non-smokingAnti-PD-1 (pembrolizumab) 4140001
426359337MelanomaallAnti-CTLA-4 (ipilimumab) 277302.7-2.71
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 275903.4-3.41
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21179.509.50.492
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)8612.5012.51
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13117.707.71
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160001
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 590001
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 38275.33.71.61
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22139.109.10.519
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 161407.1-7.10.467
1629301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 11130001
1729301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 610001
1829301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 5120001
Summary
SymbolTDG
Namethymine DNA glycosylase
Aliases G/T mismatch-specific thymine DNA glycosylase; hTDG; thymine-DNA glycosylase
Chromosomal Location12q24.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of TDG. The immune-related signatures of 28 TIL types from Charoentong's study, which can be viewed in the download page. For each cancer type, the relative abundance of TILs were inferred by using gene set variation analysis (GSVA) based on gene expression profile. In this tab, users can examine which kinds of TILs might be regulated by the current gene.
> Lymphocyte
 
Summary
SymbolTDG
Namethymine DNA glycosylase
Aliases G/T mismatch-specific thymine DNA glycosylase; hTDG; thymine-DNA glycosylase
Chromosomal Location12q24.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of TDG. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by TDG.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolTDG
Namethymine DNA glycosylase
Aliases G/T mismatch-specific thymine DNA glycosylase; hTDG; thymine-DNA glycosylase
Chromosomal Location12q24.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of TDG. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolTDG
Namethymine DNA glycosylase
Aliases G/T mismatch-specific thymine DNA glycosylase; hTDG; thymine-DNA glycosylase
Chromosomal Location12q24.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of TDG expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolTDG
Namethymine DNA glycosylase
Aliases G/T mismatch-specific thymine DNA glycosylase; hTDG; thymine-DNA glycosylase
Chromosomal Location12q24.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between TDG and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolTDG
Namethymine DNA glycosylase
Aliases G/T mismatch-specific thymine DNA glycosylase; hTDG; thymine-DNA glycosylase
Chromosomal Location12q24.1
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting TDG collected from DrugBank database.
> Drugs from DrugBank database
 

There is no record.