Browse KDM1B

Summary
SymbolKDM1B
Namelysine (K)-specific demethylase 1B
Aliases FLJ34109; FLJ33898; dJ298J15.2; bA204B7.3; FLJ43328; LSD2; C6orf193; AOF1; amine oxidase, flavin containing ......
Chromosomal Location6p22.3
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 PF01593 Flavin containing amine oxidoreductase
PF04433 SWIRM domain
PF07496 CW-type Zinc Finger
Function

Histone demethylase that demethylates 'Lys-4' of histone H3, a specific tag for epigenetic transcriptional activation, thereby acting as a corepressor. Required for de novo DNA methylation of a subset of imprinted genes during oogenesis. Acts by oxidizing the substrate by FAD to generate the corresponding imine that is subsequently hydrolyzed. Demethylates both mono- and di-methylated 'Lys-4' of histone H3. Has no effect on tri-methylated 'Lys-4', mono-, di- or tri-methylated 'Lys-9', mono-, di- or tri-methylated 'Lys-27', mono-, di- or tri-methylated 'Lys-36' of histone H3, or on mono-, di- or tri-methylated 'Lys-20' of histone H4.

> Gene Ontology
 
Biological Process GO:0006304 DNA modification
GO:0006305 DNA alkylation
GO:0006306 DNA methylation
GO:0006349 regulation of gene expression by genetic imprinting
GO:0006482 protein demethylation
GO:0008214 protein dealkylation
GO:0016570 histone modification
GO:0016577 histone demethylation
GO:0032259 methylation
GO:0034720 histone H3-K4 demethylation
GO:0040029 regulation of gene expression, epigenetic
GO:0043046 DNA methylation involved in gamete generation
GO:0043414 macromolecule methylation
GO:0044030 regulation of DNA methylation
GO:0044728 DNA methylation or demethylation
GO:0051052 regulation of DNA metabolic process
GO:0070076 histone lysine demethylation
GO:0070988 demethylation
GO:0071514 genetic imprinting
Molecular Function GO:0016705 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen
GO:0032451 demethylase activity
GO:0032452 histone demethylase activity
GO:0032453 histone demethylase activity (H3-K4 specific)
GO:0034648 histone demethylase activity (H3-dimethyl-K4 specific)
GO:0034649 histone demethylase activity (H3-monomethyl-K4 specific)
GO:0048037 cofactor binding
GO:0050660 flavin adenine dinucleotide binding
GO:0050662 coenzyme binding
Cellular Component -
> KEGG and Reactome Pathway
 
KEGG -
Reactome R-HSA-3247509: Chromatin modifying enzymes
R-HSA-4839726: Chromatin organization
R-HSA-5688426: Deubiquitination
R-HSA-3214842: HDMs demethylate histones
R-HSA-392499: Metabolism of proteins
R-HSA-597592: Post-translational protein modification
R-HSA-5689603: UCH proteinases
Summary
SymbolKDM1B
Namelysine (K)-specific demethylase 1B
Aliases FLJ34109; FLJ33898; dJ298J15.2; bA204B7.3; FLJ43328; LSD2; C6orf193; AOF1; amine oxidase, flavin containing ......
Chromosomal Location6p22.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Literatures that report relations between KDM1B 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
SymbolKDM1B
Namelysine (K)-specific demethylase 1B
Aliases FLJ34109; FLJ33898; dJ298J15.2; bA204B7.3; FLJ43328; LSD2; C6orf193; AOF1; amine oxidase, flavin containing ......
Chromosomal Location6p22.3
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 KDM1B 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
SymbolKDM1B
Namelysine (K)-specific demethylase 1B
Aliases FLJ34109; FLJ33898; dJ298J15.2; bA204B7.3; FLJ43328; LSD2; C6orf193; AOF1; amine oxidase, flavin containing ......
Chromosomal Location6p22.3
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 KDM1B in various data sets.
No PMID Cancer type Group Drug # Res # NRes Log2 (Fold Change) P value Anno
126997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)14120.6780.0147
226997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)650.8580.532
326997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)870.5430.615
428552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 9160.2230.534
528552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59-0.0950.952
628552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470.6320.773
729033130MelanomaallAnti-PD-1 (nivolumab) 26230.0120.974
829033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 15110.0840.959
929033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 1112-0.0360.984
1029301960Clear cell renal cell carcinoma (ccRCC)allAnti-PD-1 (nivolumab) 480.0890.929
1129301960Clear cell renal cell carcinoma (ccRCC)VEGFRiAnti-PD-1 (nivolumab) 2001
1229301960Clear cell renal cell carcinoma (ccRCC)non-VEGFRiAnti-PD-1 (nivolumab) 280.4880.729
1329443960Urothelial cancerallAnti-PD-L1 (atezolizumab) 682300.1370.118
> Mutation difference between responders and non-responders
 
Points in the above scatter plot represent the mutation difference of KDM1B 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) 27733.71.42.30.469
526359337MelanomaBRAFiAnti-CTLA-4 (ipilimumab) 0140001
626359337Melanomanon-BRAFiAnti-CTLA-4 (ipilimumab) 27593.71.720.532
726997480MelanomaallAnti-PD-1 (pembrolizumab and nivolumab)21170001
826997480MelanomaMAPKiAnti-PD-1 (pembrolizumab and nivolumab)860001
926997480Melanomanon-MAPKiAnti-PD-1 (pembrolizumab and nivolumab)13110001
1028552987Urothelial cancerallAnti-PD-L1 (atezolizumab) 91606.2-6.21
1128552987Urothelial cancersmokingAnti-PD-L1 (atezolizumab) 59011.1-11.11
1228552987Urothelial cancernon-smokingAnti-PD-L1 (atezolizumab) 470001
1329033130MelanomaallAnti-PD-1 (nivolumab) 38270001
1429033130MelanomaNIV3-PROGAnti-PD-1 (nivolumab) 22130001
1529033130MelanomaNIV3-NAIVEAnti-PD-1 (nivolumab) 16140001
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
SymbolKDM1B
Namelysine (K)-specific demethylase 1B
Aliases FLJ34109; FLJ33898; dJ298J15.2; bA204B7.3; FLJ43328; LSD2; C6orf193; AOF1; amine oxidase, flavin containing ......
Chromosomal Location6p22.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between abundance of tumor-infiltrating lymphocytes (TILs) and expression, copy number, methylation, or mutation of KDM1B. 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
SymbolKDM1B
Namelysine (K)-specific demethylase 1B
Aliases FLJ34109; FLJ33898; dJ298J15.2; bA204B7.3; FLJ43328; LSD2; C6orf193; AOF1; amine oxidase, flavin containing ......
Chromosomal Location6p22.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between three kinds of immunomodulators and expression, copy number, methylation, or mutation of KDM1B. These immunomo-dulators were collected from Charoentong's study. In this tab, users can examine which immunomodulators might be regulated by KDM1B.
> Immunoinhibitor
> Immunostimulator
> MHC molecule
> Immunoinhibitor
 
> Immunostimulator
 
> MHC molecule
 
Summary
SymbolKDM1B
Namelysine (K)-specific demethylase 1B
Aliases FLJ34109; FLJ33898; dJ298J15.2; bA204B7.3; FLJ43328; LSD2; C6orf193; AOF1; amine oxidase, flavin containing ......
Chromosomal Location6p22.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Relations between chemokines (or receptors) and expression, copy number, methylation, or mutation of KDM1B. In this tab, users can examine which chemokines (or receptors) might be regulated by the current gene.
> Chemokine
> Receptor
> Chemokine
 
> Receptor
 
Summary
SymbolKDM1B
Namelysine (K)-specific demethylase 1B
Aliases FLJ34109; FLJ33898; dJ298J15.2; bA204B7.3; FLJ43328; LSD2; C6orf193; AOF1; amine oxidase, flavin containing ......
Chromosomal Location6p22.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Distribution of KDM1B expression across immune and molecular subtypes.
> Immune subtype
> Molecular subtype
> Immune subtype
 
> Molecular subtype
 
Summary
SymbolKDM1B
Namelysine (K)-specific demethylase 1B
Aliases FLJ34109; FLJ33898; dJ298J15.2; bA204B7.3; FLJ43328; LSD2; C6orf193; AOF1; amine oxidase, flavin containing ......
Chromosomal Location6p22.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Associations between KDM1B and clinical features.
> Overall survival analysis
> Cancer stage
> Tumor grade
> Overall survival
 
> Stage
 
> Grade
 
Summary
SymbolKDM1B
Namelysine (K)-specific demethylase 1B
Aliases FLJ34109; FLJ33898; dJ298J15.2; bA204B7.3; FLJ43328; LSD2; C6orf193; AOF1; amine oxidase, flavin containing ......
Chromosomal Location6p22.3
External Links HGNC, NCBI, Ensembl, Uniprot, GeneCards
Content Drugs targeting KDM1B collected from DrugBank database.
> Drugs from DrugBank database
 

There is no record.