KDM5C [The Human Chemical-Genetic Interaction Map Project]

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======= KDM5C =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: KDM5C
  * **<color #00a2e8>Official Name</color>**: lysine demethylase 5C
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=8242|8242]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/P41229|P41229]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=KDM5C&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20KDM5C|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/314690|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**:  This gene is a member of the SMCY homolog family and encodes a protein with one ARID domain, one JmjC domain, one JmjN domain and two PHD-type zinc fingers. The DNA-binding motifs suggest this protein is involved in the regulation of transcription and chromatin remodeling. Mutations in this gene have been associated with X-linked cognitive disability. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]. 
  * **<color #00a2e8>UniProt Summary</color>**:  Histone demethylase that specifically demethylates 'Lys- 4' of histone H3, thereby playing a central role in histone code (PubMed:28262558). Does not demethylate histone H3 'Lys-9', H3 'Lys-27', H3 'Lys-36', H3 'Lys-79' or H4 'Lys-20'. Demethylates trimethylated and dimethylated but not monomethylated H3 'Lys-4'. Participates in transcriptional repression of neuronal genes by recruiting histone deacetylases and REST at neuron-restrictive silencer elements. Represses the CLOCK-ARNTL/BMAL1 heterodimer- mediated transcriptional activation of the core clock component PER2 (By similarity). {ECO:0000250|UniProtKB:P41230, ECO:0000269|PubMed:17320160, ECO:0000269|PubMed:17320161, ECO:0000269|PubMed:17468742, ECO:0000269|PubMed:26645689, 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'>
|JmjN|
|ARID|
|JmjC|
|zf-C5HC2|
|PHD|
|PLU-1|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|histone demethylase activity (H3-trimethyl-K4 specific)|
|histone H3-K4 demethylation, trimethyl-H3-K4-specific|
|histone demethylase activity (H3-K4 specific)|
|histone H3-K4 demethylation|
|histone demethylase activity|
|dioxygenase activity|
|histone lysine demethylation|
|histone demethylation|
|protein demethylation|
|protein dealkylation|
|histone methyltransferase complex|
|demethylation|
|chromatin remodeling|
|rhythmic process|
|histone modification|
|covalent chromatin modification|
|chromatin organization|
|zinc ion binding|
|oxidation-reduction process|
|chromosome organization|
|negative regulation of transcription, DNA-templated|
|negative regulation of nucleic acid-templated transcription|
|negative regulation of RNA biosynthetic process|
|negative regulation of RNA metabolic process|
|negative regulation of cellular macromolecule biosynthetic process|
|negative regulation of nucleobase-containing compound metabolic process|
|DNA binding|
|negative regulation of macromolecule biosynthetic process|
|negative regulation of cellular biosynthetic process|
|negative regulation of biosynthetic process|
|DNA-binding transcription factor activity, RNA polymerase II-specific|
|negative regulation of gene expression|
</modal>
\\

 === CRISPR Data ===
<button type='primary' size='small' modal='Compound_Hit'>Compound Hit</button>
<button type='default' 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:exp330|5-Azacytidine 2μM R07 exp330]]|1.7|
|[[:results:exp67|BVD-523 15μM R02 exp67]]|1.74|
|[[:results:exp526|Sulforaphane 9μM R08 exp526 no dilution day6]]|1.88|
|[[:results:exp162|BI-D1870 2μM R04 exp162]]|1.94|
|[[:results:exp106|UM131593 0.2μM R03 exp106]]|1.98|
|[[:results:exp274|Citral 50μM R06 exp274]]|2.03|
|[[:results:exp228|Demecolcine 0.03μM R05 exp228]]|2.51|
|[[:results:exp514|Phorbol-12-myristate-13-acetate 0.57μM R08 exp514]]|2.73|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
No correlation found to any other genes in chemogenomics.
</modal>

<modal id='Essential_Avana' size='lg' title='Tissues where Essential in the Avana Dataset (DepMap 20Q1)'>
Global Fraction of Cell Lines Where Essential: 2/683
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|0/1|
|bile duct|0/28|
|blood|0/26|
|bone|0/25|
|breast|0/30|
|central nervous system|0/49|
|cervix|0/4|
|colorectal|0/17|
|esophagus|0/11|
|fibroblast|0/1|
|gastric|0/14|
|kidney|0/18|
|liver|0/19|
|lung|1/72|
|lymphocyte|0/14|
|ovary|0/25|
|pancreas|0/22|
|peripheral nervous system|0/15|
|plasma cell|1/12|
|prostate|0/1|
|skin|0/20|
|soft tissue|0/7|
|thyroid|0/2|
|upper aerodigestive|0/22|
|urinary tract|0/28|
|uterus|0/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 1572
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 7.15 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='KDM5C Expression in NALM6 Cells: 7.15'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>