KDM6B [The Human Chemical-Genetic Interaction Map Project]

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======= KDM6B =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: KDM6B
  * **<color #00a2e8>Official Name</color>**: lysine demethylase 6B
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=23135|23135]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/O15054|O15054]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=KDM6B&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20KDM6B|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/611577|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**:  The protein encoded by this gene is a lysine-specific demethylase that specifically demethylates di- or tri-methylated lysine 27 of histone H3 (H3K27me2 or H3K27me3). H3K27 trimethylation is a repressive epigenetic mark controlling chromatin organization and gene silencing. This protein can also demethylate non-histone proteins such as retinoblastoma protein. Through its demethylation actvity this gene influences cellular differentiation and development, tumorigenesis, inflammatory diseases, and neurodegenerative diseases. This protein has two classical nuclear localization signals at its N-terminus. Alternative splicing results in multiple transcript variants encoding distinct isoforms. [provided by RefSeq, Feb 2017]. 
  * **<color #00a2e8>UniProt Summary</color>**:  Histone demethylase that specifically demethylates 'Lys- 27' of histone H3, thereby playing a central role in histone code (PubMed:17825402, PubMed:17851529, PubMed:17713478, PubMed:18003914). Demethylates trimethylated and dimethylated H3 'Lys-27' (PubMed:17825402, PubMed:17851529, PubMed:17713478, PubMed:18003914). Plays a central role in regulation of posterior development, by regulating HOX gene expression (PubMed:17851529). Involved in inflammatory response by participating in macrophage differentiation in case of inflammation by regulating gene expression and macrophage differentiation (PubMed:17825402). Plays a demethylase-independent role in chromatin remodeling to regulate T-box family member-dependent gene expression by acting as a link between T-box factors and the SMARCA4-containing SWI/SNF remodeling complex (By similarity). {ECO:0000250|UniProtKB:Q5NCY0, ECO:0000269|PubMed:17713478, ECO:0000269|PubMed:17825402, ECO:0000269|PubMed:17851529, ECO:0000269|PubMed:18003914, ECO:0000269|PubMed:28262558}.

<button type='primary' size='sm' modal='Pfam_Domains'>Pfam Domains</button>
<button type='primary' size='sm' modal='GO_terms'>GO Terms</button>


<modal id='Pfam_Domains' size='lg' title='Pfam Domains'>
|JmjC|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|histone demethylase activity (H3-K27 specific)|
|histone H3-K27 demethylation|
|response to fungicide|
|MLL3/4 complex|
|dioxygenase activity|
|inflammatory response to antigenic stimulus|
|mesodermal cell differentiation|
|histone lysine demethylation|
|histone demethylation|
|protein demethylation|
|protein dealkylation|
|demethylation|
|response to activity|
|mesoderm formation|
|mesoderm morphogenesis|
|cellular response to hydrogen peroxide|
|chromatin DNA binding|
|hippocampus development|
|endothelial cell differentiation|
|beta-catenin binding|
|cardiac muscle cell differentiation|
|endothelium development|
|positive regulation of cold-induced thermogenesis|
|limbic system development|
|formation of primary germ layer|
|cardiocyte differentiation|
|cellular response to antibiotic|
|response to hydrogen peroxide|
|mesoderm development|
|cellular response to reactive oxygen species|
|regulation of cold-induced thermogenesis|
|gastrulation|
|chromatin remodeling|
|cardiac muscle tissue development|
|pallium development|
|response to reactive oxygen species|
|striated muscle cell differentiation|
|cellular response to toxic substance|
|cellular response to oxidative stress|
|muscle cell differentiation|
|cell fate commitment|
|telencephalon development|
|striated muscle tissue development|
|muscle tissue development|
|response to antibiotic|
|histone modification|
|covalent chromatin modification|
|response to oxidative stress|
|forebrain development|
|chromatin binding|
|cellular response to drug|
|sequence-specific DNA binding|
|muscle structure development|
|inflammatory response|
|RNA polymerase II proximal promoter sequence-specific DNA binding|
|response to toxic substance|
|heart development|
|response to inorganic substance|
|tissue morphogenesis|
|embryonic morphogenesis|
|epithelial cell differentiation|
|chromatin organization|
|brain development|
|head development|
|circulatory system development|
|anatomical structure formation involved in morphogenesis|
|oxidation-reduction process|
|embryo development|
|central nervous system development|
|response to drug|
|cellular response to oxygen-containing compound|
|chromosome organization|
|epithelium development|
|positive regulation of transcription by RNA polymerase II|
|defense response|
|positive regulation of transcription, DNA-templated|
|response to oxygen-containing compound|
|positive regulation of nucleic acid-templated transcription|
|positive regulation of RNA biosynthetic process|
|cellular response to stress|
|positive regulation of RNA metabolic process|
|positive regulation of multicellular organismal process|
|tissue development|
|immune response|
|positive regulation of nucleobase-containing compound metabolic process|
|positive regulation of macromolecule biosynthetic process|
|positive regulation of cellular biosynthetic process|
|positive regulation of gene expression|
|positive regulation of biosynthetic process|
</modal>
\\

 === CRISPR Data ===
<button type='primary' size='small' modal='Compound_Hit'>Compound Hit</button>
<button type='primary' size='small' modal='Most_Correlated_Genes'>Most Correlated Genes in Chemogenomics</button>
<button type='primary' size='small' modal='Essential_Avana'>Tissues where Essential in the Avana Dataset (DepMap 20Q1)</button>

<modal id='Compound_Hit' size='lg' title='Compound Hit'>
^Screen^Score^
|[[:results:exp389|PF-06409577 20μM R07 exp389]]|-2.13|
|[[:results:exp165|RO-3306 3 to 4μM on day4 R04 exp165]]|-1.98|
|[[:results:exp50|Nicotinamide 2000μM R01 exp50]]|-1.89|
|[[:results:exp210|LB-100 2μM R05 exp210]]|-1.77|
|[[:results:exp52|Ribavirin 10μM R01 exp52]]|-1.76|
|[[:results:exp489|Hippuristanol 0.12μM R08 exp489 no dilution day6]]|-1.75|
|[[:results:exp451|Atovaquone 15μM R08 exp451]]|1.73|
|[[:results:exp264|Arsenate 40μM R06 exp264]]|1.78|
|[[:results:exp282|Fluvastatin 2.2μM R06 exp282]]|1.83|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
^Gene^Correlation^
|[[:human genes:h:hars|HARS]]|0.496|
|[[:human genes:i:id3|ID3]]|0.406|
</modal>

<modal id='Essential_Avana' size='lg' title='Tissues where Essential in the Avana Dataset (DepMap 20Q1)'>
Global Fraction of Cell Lines Where Essential: 0/726
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|0/1|
|bile duct|0/28|
|blood|0/28|
|bone|0/25|
|breast|0/33|
|central nervous system|0/56|
|cervix|0/4|
|colorectal|0/17|
|esophagus|0/13|
|fibroblast|0/1|
|gastric|0/15|
|kidney|0/21|
|liver|0/20|
|lung|0/75|
|lymphocyte|0/14|
|ovary|0/26|
|pancreas|0/24|
|peripheral nervous system|0/16|
|plasma cell|0/15|
|prostate|0/1|
|skin|0/24|
|soft tissue|0/7|
|thyroid|0/2|
|upper aerodigestive|0/22|
|urinary tract|0/29|
|uterus|0/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 11523
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 5.06 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='KDM6B Expression in NALM6 Cells: 5.06'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>