KDM5A [The Human Chemical-Genetic Interaction Map Project]

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======= KDM5A =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: KDM5A
  * **<color #00a2e8>Official Name</color>**: lysine demethylase 5A
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=5927|5927]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/P29375|P29375]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=KDM5A&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20KDM5A|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/180202|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**:  This gene encodes a member of the Jumonji, AT-rich interactive domain 1 (JARID1) histone demethylase protein family. The encoded protein plays a role in gene regulation through the histone code by specifically demethylating lysine 4 of histone H3. The encoded protein interacts with many other proteins, including retinoblastoma protein, and is implicated in the transcriptional regulation of Hox genes and cytokines. This gene may play a role in tumor progression. [provided by RefSeq, Aug 2013]. 
  * **<color #00a2e8>UniProt Summary</color>**:  Histone demethylase that specifically demethylates 'Lys- 4' of histone H3, thereby playing a central role in histone code. 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'. Regulates specific gene transcription through DNA-binding on 5'-CCGCCC-3' motif (PubMed:18270511). May stimulate transcription mediated by nuclear receptors. Involved in transcriptional regulation of Hox proteins during cell differentiation (PubMed:19430464). May participate in transcriptional repression of cytokines such as CXCL12. Plays a role in the regulation of the circadian rhythm and in maintaining the normal periodicity of the circadian clock. In a histone demethylase-independent manner, acts as a coactivator of the CLOCK-ARNTL/BMAL1-mediated transcriptional activation of PER1/2 and other clock-controlled genes and increases histone acetylation at PER1/2 promoters by inhibiting the activity of HDAC1 (By similarity). Seems to act as a transcriptional corepressor for some genes such as MT1F and to favor the proliferation of cancer cells (PubMed:27427228). {ECO:0000250|UniProtKB:Q3UXZ9, ECO:0000269|PubMed:11358960, ECO:0000269|PubMed:15949438, ECO:0000269|PubMed:17320160, ECO:0000269|PubMed:17320161, ECO:0000269|PubMed:17320163, ECO:0000269|PubMed:18270511, ECO:0000269|PubMed:19430464, ECO:0000269|PubMed:27427228}.

<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|
|JmjC|
|zf-C5HC2|
|ARID|
|PLU-1|
|PHD|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|negative regulation of deacetylase activity|
|negative regulation of histone deacetylase activity|
|histone demethylase activity (H3-dimethyl-K4 specific)|
|histone H3-K4 demethylation, trimethyl-H3-K4-specific|
|histone demethylase activity (H3-trimethyl-K4 specific)|
|negative regulation of histone deacetylation|
|histone H3-K4 demethylation|
|regulation of histone deacetylase activity|
|regulation of deacetylase activity|
|histone demethylase activity (H3-K9 specific)|
|histone H3-K9 demethylation|
|histone demethylase activity|
|dioxygenase activity|
|histone lysine demethylation|
|regulation of histone deacetylation|
|histone demethylation|
|protein dealkylation|
|protein demethylation|
|negative regulation of histone modification|
|histone methyltransferase complex|
|regulation of protein deacetylation|
|protein-DNA complex|
|negative regulation of chromatin organization|
|methylated histone binding|
|circadian regulation of gene expression|
|demethylation|
|chromatin DNA binding|
|histone binding|
|male gonad development|
|negative regulation of chromosome organization|
|development of primary male sexual characteristics|
|circadian rhythm|
|regulation of histone modification|
|male sex differentiation|
|chromatin remodeling|
|regulation of chromatin organization|
|gonad development|
|development of primary sexual characteristics|
|transcription regulatory region DNA binding|
|sex differentiation|
|rhythmic process|
|transcription coactivator activity|
|regulation of chromosome organization|
|histone modification|
|negative regulation of organelle organization|
|covalent chromatin modification|
|reproductive structure development|
|regulation of DNA-binding transcription factor activity|
|reproductive system development|
|negative regulation of hydrolase activity|
|spermatogenesis|
|male gamete generation|
|negative regulation of protein modification process|
|developmental process involved in reproduction|
|DNA-binding transcription factor activity|
|gamete generation|
|chromatin organization|
|negative regulation of cellular component organization|
|negative regulation of catalytic activity|
|multicellular organismal reproductive process|
|sexual reproduction|
|zinc ion binding|
|multicellular organism reproduction|
|nucleolus|
|negative regulation of transcription by RNA polymerase II|
|oxidation-reduction process|
|multi-organism reproductive process|
|negative regulation of cellular protein metabolic process|
|chromosome organization|
|negative regulation of protein metabolic process|
|negative regulation of molecular function|
|negative regulation of transcription, DNA-templated|
|negative regulation of nucleic acid-templated transcription|
|negative regulation of RNA biosynthetic process|
|regulation of hydrolase activity|
|regulation of organelle organization|
|negative regulation of RNA metabolic process|
|negative regulation of cellular macromolecule biosynthetic process|
|reproductive process|
|reproduction|
|negative regulation of nucleobase-containing compound metabolic process|
|DNA binding|
|negative regulation of macromolecule biosynthetic process|
|negative regulation of cellular biosynthetic process|
|positive regulation of transcription, DNA-templated|
|negative regulation of biosynthetic process|
|DNA-binding transcription factor activity, RNA polymerase II-specific|
|positive regulation of nucleic acid-templated transcription|
|positive regulation of RNA biosynthetic process|
|negative regulation of gene expression|
|positive regulation of RNA metabolic process|
|regulation of protein modification process|
|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='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:exp351|Dexamethasone 0.006μM R07 exp351]]|-2.24|
|[[:results:exp480|ETC-159 50μM R08 exp480]]|-1.94|
|[[:results:exp19|Etoposide 1μM R00 exp19]]|-1.77|
|[[:results:exp233|EPZ-5676 30μM R05 exp233]]|-1.7|
</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: 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>**: 16282
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 7.32 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='KDM5A Expression in NALM6 Cells: 7.32'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>