VPS39 [The Human Chemical-Genetic Interaction Map Project]

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======= VPS39 =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: VPS39
  * **<color #00a2e8>Official Name</color>**: VPS39 subunit of HOPS complex
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=23339|23339]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/Q96JC1|Q96JC1]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=VPS39&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20VPS39|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/612188|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**: N/A
  * **<color #00a2e8>UniProt Summary</color>**:  Regulator of TGF-beta/activin signaling, inhibiting SMAD3- and activating SMAD2-dependent transcription. Acts by interfering with SMAD3/SMAD4 complex formation, this would lead to inhibition of SMAD3-dependent transcription and relieve SMAD3 inhibition of SMAD2-dependent promoters, thus increasing SMAD2- dependent transcription. Does not affect TGF-beta-induced SMAD2 or SMAD3 phosphorylation, nor SMAD2/SMAD4 complex formation. {ECO:0000269|PubMed:12941698}.

<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'>
|Vps39 1|
|Vps39 2|
|Clathrin|
|CNH|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|late endosome to lysosome transport|
|endosomal vesicle fusion|
|AP-3 adaptor complex|
|HOPS complex|
|retrograde transport, endosome to plasma membrane|
|endosome to lysosome transport|
|vesicle fusion|
|organelle membrane fusion|
|vesicle-mediated transport to the plasma membrane|
|organelle fusion|
|lysosomal transport|
|late endosome membrane|
|membrane fusion|
|vacuolar transport|
|endosomal transport|
|autophagy|
|process utilizing autophagic mechanism|
|vesicle organization|
|lysosomal membrane|
|membrane organization|
|intracellular protein transport|
|protein transport|
|intracellular transport|
|peptide transport|
|amide transport|
|cellular protein localization|
|cellular macromolecule localization|
|establishment of protein localization|
|cellular catabolic process|
|establishment of localization in cell|
|nitrogen compound transport|
|vesicle-mediated transport|
</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:exp246|UM0011500 10μM R05 exp246]]|-2.44|
|[[:results:exp241|QNZ 0.01μM R05 exp241]]|-2.06|
|[[:results:exp175|3-Bromopyruvate 7μM R04 exp175]]|1.86|
</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: 3/739
^Tissue^Fraction Of Cell Lines Where Essential^
|1290807.0|0/1|
|909776.0|0/1|
|bile duct|0/28|
|blood|0/28|
|bone|0/26|
|breast|0/33|
|central nervous system|0/56|
|cervix|0/4|
|colorectal|0/17|
|esophagus|0/13|
|fibroblast|0/1|
|gastric|0/16|
|kidney|0/21|
|liver|0/20|
|lung|0/75|
|lymphocyte|0/16|
|ovary|0/26|
|pancreas|0/24|
|peripheral nervous system|0/16|
|plasma cell|0/15|
|prostate|0/1|
|skin|0/24|
|soft tissue|1/9|
|thyroid|0/2|
|upper aerodigestive|0/22|
|urinary tract|0/29|
|uterus|0/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 2267
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 6.57 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='VPS39 Expression in NALM6 Cells: 6.57'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>