VIMP [The Human Chemical-Genetic Interaction Map Project]

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======= VIMP =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: SELENOS
  * **<color #00a2e8>Official Name</color>**: selenoprotein S
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=55829|55829]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/Q9BQE4|Q9BQE4]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=VIMP&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20VIMP|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/607918|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**:  This gene encodes a transmembrane protein that is localized in the endoplasmic reticulum (ER). It is involved in the degradation process of misfolded proteins in the ER, and may also have a role in inflammation control. This protein is a selenoprotein, containing the rare amino acid selenocysteine (Sec). Sec is encoded by the UGA codon, which normally signals translation termination. The 3' UTRs of selenoprotein mRNAs contain a conserved stem-loop structure, designated the Sec insertion sequence (SECIS) element, that is necessary for the recognition of UGA as a Sec codon, rather than as a stop signal. Two additional phylogenetically conserved stem-loop structures (Stem-loop 1 and Stem-loop 2) in the 3' UTR of this mRNA have been shown to function as modulators of Sec insertion. An alternatively spliced transcript variant, lacking the SECIS element and encoding a non-Sec containing shorter isoform, has been described for this gene (PMID:23614019). [provided by RefSeq, Jul 2017]. 
  * **<color #00a2e8>UniProt Summary</color>**:  Involved in the degradation process of misfolded endoplasmic reticulum (ER) luminal proteins. Participates in the transfer of misfolded proteins from the ER to the cytosol, where they are destroyed by the proteasome in a ubiquitin-dependent manner. Probably acts by serving as a linker between DERL1, which mediates the retrotranslocation of misfolded proteins into the cytosol, and the ATPase complex VCP, which mediates the translocation and ubiquitination. {ECO:0000269|PubMed:15215856}.

<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'>
|Selenoprotein S|
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|regulation of nitric oxide metabolic process|
|Derlin-1-VIMP complex|
|negative regulation of nitric-oxide synthase biosynthetic process|
|negative regulation of acute inflammatory response to antigenic stimulus|
|negative regulation of glycogen biosynthetic process|
|negative regulation of macrophage apoptotic process|
|negative regulation of glycogen metabolic process|
|Derlin-1 retrotranslocation complex|
|regulation of macrophage apoptotic process|
|negative regulation of glucose import|
|ER overload response|
|negative regulation of inflammatory response to antigenic stimulus|
|negative regulation of acute inflammatory response|
|regulation of acute inflammatory response to antigenic stimulus|
|response to redox state|
|low-density lipoprotein particle|
|negative regulation of myeloid cell apoptotic process|
|ubiquitin-specific protease binding|
|negative regulation of glucose transmembrane transport|
|endoplasmic reticulum to cytosol transport|
|retrograde protein transport, ER to cytosol|
|antioxidant activity|
|regulation of nitric-oxide synthase biosynthetic process|
|negative regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway|
|very-low-density lipoprotein particle|
|regulation of inflammatory response to antigenic stimulus|
|protein exit from endoplasmic reticulum|
|regulation of glucan biosynthetic process|
|regulation of myeloid cell apoptotic process|
|regulation of glycogen biosynthetic process|
|regulation of endoplasmic reticulum stress-induced intrinsic apoptotic signaling pathway|
|regulation of glycogen metabolic process|
|ER-nucleus signaling pathway|
|regulation of polysaccharide biosynthetic process|
|negative regulation of cellular carbohydrate metabolic process|
|regulation of polysaccharide metabolic process|
|negative regulation of interleukin-6 production|
|regulation of acute inflammatory response|
|negative regulation of response to endoplasmic reticulum stress|
|regulation of gluconeogenesis|
|negative regulation of leukocyte apoptotic process|
|negative regulation of carbohydrate metabolic process|
|cytoplasmic microtubule|
|regulation of glucose import|
|negative regulation of tumor necrosis factor production|
|negative regulation of tumor necrosis factor superfamily cytokine production|
|ubiquitin-dependent ERAD pathway|
|regulation of glucose transmembrane transport|
|cell redox homeostasis|
|ATPase binding|
|regulation of leukocyte apoptotic process|
|regulation of response to endoplasmic reticulum stress|
|ERAD pathway|
|cellular oxidant detoxification|
|regulation of carbohydrate biosynthetic process|
|negative regulation of intrinsic apoptotic signaling pathway|
|cellular detoxification|
|endoplasmic reticulum unfolded protein response|
|integral component of endoplasmic reticulum membrane|
|regulation of glucose metabolic process|
|negative regulation of transmembrane transport|
|cellular response to unfolded protein|
|detoxification|
|negative regulation of inflammatory response|
|response to glucose|
|regulation of cellular carbohydrate metabolic process|
|regulation of interleukin-6 production|
|response to hexose|
|regulation of tumor necrosis factor production|
|response to monosaccharide|
|negative regulation of immune response|
|cellular response to topologically incorrect protein|
|regulation of tumor necrosis factor superfamily cytokine production|
|regulation of generation of precursor metabolites and energy|
|regulation of intrinsic apoptotic signaling pathway|
|response to unfolded protein|
|cellular response to insulin stimulus|
|response to carbohydrate|
|regulation of reactive oxygen species metabolic process|
|cellular response to lipopolysaccharide|
|response to topologically incorrect protein|
|cellular response to molecule of bacterial origin|
|signaling receptor activity|
|regulation of carbohydrate metabolic process|
|negative regulation of defense response|
|cellular response to toxic substance|
|cellular response to biotic stimulus|
|negative regulation of apoptotic signaling pathway|
|response to insulin|
|cellular response to oxidative stress|
|response to endoplasmic reticulum stress|
|cellular response to peptide hormone stimulus|
|negative regulation of cytokine production|
|response to lipopolysaccharide|
|proteasome-mediated ubiquitin-dependent protein catabolic process|
|response to molecule of bacterial origin|
|cellular response to peptide|
|regulation of inflammatory response|
|enzyme binding|
|proteasomal protein catabolic process|
|regulation of neurotransmitter levels|
|negative regulation of response to external stimulus|
|response to oxidative stress|
|response to peptide hormone|
|regulation of apoptotic signaling pathway|
|regulation of small molecule metabolic process|
|negative regulation of immune system process|
|response to peptide|
|negative regulation of transport|
|negative regulation of intracellular signal transduction|
|response to toxic substance|
|cellular response to lipid|
|ubiquitin-dependent protein catabolic process|
|modification-dependent protein catabolic process|
|modification-dependent macromolecule catabolic process|
|regulation of transmembrane transport|
|proteolysis involved in cellular protein catabolic process|
|cellular response to organonitrogen compound|
|cellular response to hormone stimulus|
|cellular protein catabolic process|
|cellular response to nitrogen compound|
|protein catabolic process|
|protein ubiquitination|
|response to bacterium|
|regulation of cytokine production|
|regulation of cellular response to stress|
|regulation of defense response|
|protein modification by small protein conjugation|
|response to lipid|
|negative regulation of apoptotic process|
|cellular homeostasis|
|negative regulation of programmed cell death|
|cellular macromolecule catabolic process|
|response to hormone|
|endoplasmic reticulum membrane|
|protein modification by small protein conjugation or removal|
|negative regulation of cell death|
|intracellular protein transport|
|response to organonitrogen compound|
|endoplasmic reticulum|
|macromolecule catabolic process|
|cellular response to oxygen-containing compound|
|organonitrogen compound catabolic process|
|response to nitrogen compound|
|regulation of response to external stimulus|
|regulation of immune response|
|negative regulation of multicellular organismal process|
|cellular response to endogenous stimulus|
|negative regulation of signal transduction|
|proteolysis|
|response to other organism|
|response to external biotic stimulus|
|response to biotic stimulus|
|negative regulation of cell communication|
|negative regulation of signaling|
|negative regulation of cellular macromolecule biosynthetic process|
|negative regulation of macromolecule biosynthetic process|
|response to endogenous stimulus|
|regulation of response to stress|
|protein transport|
|negative regulation of cellular biosynthetic process|
|intracellular transport|
|peptide transport|
|regulation of apoptotic process|
|negative regulation of biosynthetic process|
|response to oxygen-containing compound|
|regulation of programmed cell death|
|amide transport|
|cellular protein localization|
|cellular macromolecule localization|
|establishment of protein localization|
|negative regulation of response to stimulus|
|homeostatic process|
|regulation of immune system process|
|regulation of cell death|
|cellular response to stress|
|organic substance catabolic process|
|cellular catabolic process|
|regulation of intracellular signal transduction|
|establishment of localization in cell|
|nitrogen compound transport|
|regulation of 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:exp10|CCCP 0.1μM R00 exp10]]|1.87|
</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: 0/739
^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|0/9|
|thyroid|0/2|
|upper aerodigestive|0/22|
|urinary tract|0/29|
|uterus|0/5|
</modal>

== Essentiality in NALM6  ==
    * **<color #00a2e8>Essentiality Rank</color>**: 5010
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 5.03 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='VIMP Expression in NALM6 Cells: 5.03'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>