SETX [The Human Chemical-Genetic Interaction Map Project]

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======= SETX =======


== Gene Information ==
  * **<color #00a2e8>Official Symbol</color>**: SETX
  * **<color #00a2e8>Official Name</color>**: senataxin
  * **<color #00a2e8>Aliases and Previous Symbols</color>**: N/A
  * **<color #00a2e8>Entrez ID</color>**: [[https://www.ncbi.nlm.nih.gov/gene/?term=23064|23064]]
  * **<color #00a2e8>UniProt</color>**: [[https://www.uniprot.org/uniprot/Q7Z333|Q7Z333]]
  * **<color #00a2e8>Interactions</color>**: [[https://thebiogrid.org/search.php?search=SETX&organism=9606|BioGRID]]
  * **<color #00a2e8>PubMed articles</color>**: [[https://www.ncbi.nlm.nih.gov/pubmed/?term=gene%20SETX|Open PubMed]]
  * **<color #00a2e8>OMIM</color>**: [[https://omim.org/entry/608465|Open OMIM]]

== Function Summary ==
  * **<color #00a2e8>Entrez Summary</color>**:  This gene encodes a protein named for its homology to the Sen1p protein of fungi which has RNA helicase activity encoded by a domain at the C-terminal end of the protein. The protein encoded by this gene contains a DNA/RNA helicase domain at its C-terminal end which suggests that it may be involved in both DNA and RNA processing. Mutations in this gene have been associated with ataxia-ocular apraxia-2 (AOA2) and an autosomal dominant form of juvenile amyotrophic lateral sclerosis (ALS4). [provided by RefSeq, Jul 2008]. 
  * **<color #00a2e8>UniProt Summary</color>**:  Probable RNA/DNA helicase involved in diverse aspects of RNA metabolism and genomic integrity. Plays a role in transcription regulation by its ability to modulate RNA Polymerase II (Pol II) binding to chromatin and through its interaction with proteins involved in transcription (PubMed:19515850, PubMed:21700224). Contributes to the mRNA splicing efficiency and splice site selection (PubMed:19515850). Required for the resolution of R-loop RNA-DNA hybrid formation at G-rich pause sites located downstream of the poly(A) site, allowing XRN2 recruitment and XRN2-mediated degradation of the downstream cleaved RNA and hence efficient RNA polymerase II (RNAp II) transcription termination (PubMed:19515850, PubMed:21700224, PubMed:26700805). Required for the 3' transcriptional termination of PER1 and CRY2, thus playing an important role in the circadian rhythm regulation (By similarity). Involved in DNA double-strand breaks damage response generated by oxidative stress (PubMed:17562789). In association with RRP45, targets the RNA exosome complex to sites of transcription-induced DNA damage (PubMed:24105744). Plays a role in the development and maturation of germ cells: essential for male meiosis, acting at the interface of transcription and meiotic recombination, and in the process of gene silencing during meiotic sex chromosome inactivation (MSCI) (By similarity). May be involved in telomeric stability through the regulation of telomere repeat-containing RNA (TERRA) transcription (PubMed:21112256). Plays a role in neurite outgrowth in hippocampal cells through FGF8-activated signaling pathways. Inhibits retinoic acid-induced apoptosis (PubMed:21576111). {ECO:0000250|UniProtKB:A2AKX3, ECO:0000269|PubMed:17562789, ECO:0000269|PubMed:19515850, ECO:0000269|PubMed:21112256, ECO:0000269|PubMed:21576111, ECO:0000269|PubMed:21700224, ECO:0000269|PubMed:24105744, ECO:0000269|PubMed:26700805}.

<button type='default' 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'>
No Pfam Domain information is available for this gene.
</modal>

<modal id='GO_terms' size='lg' title='GO Terms'>
|positive regulation of termination of RNA polymerase II transcription, poly(A)-coupled|
|positive regulation of DNA-templated transcription, termination|
|positive regulation of termination of RNA polymerase II transcription|
|transcription termination site sequence-specific DNA binding|
|regulation of termination of RNA polymerase II transcription|
|regulation of termination of RNA polymerase II transcription, poly(A)-coupled|
|regulation of DNA-templated transcription, termination|
|positive regulation of DNA-templated transcription, initiation|
|nuclear chromosome|
|mRNA splice site selection|
|positive regulation of RNA splicing|
|termination of RNA polymerase II transcription|
|regulation of DNA-templated transcription, initiation|
|positive regulation of protein complex disassembly|
|protein kinase B signaling|
|chromosome, telomeric region|
|spliceosomal complex assembly|
|intercellular bridge|
|DNA helicase activity|
|cellular response to retinoic acid|
|cellular response to hydrogen peroxide|
|DNA-templated transcription, termination|
|fibroblast growth factor receptor signaling pathway|
|cellular response to fibroblast growth factor stimulus|
|response to retinoic acid|
|DNA duplex unwinding|
|regulation of protein complex disassembly|
|response to fibroblast growth factor|
|cellular response to antibiotic|
|response to hydrogen peroxide|
|DNA geometric change|
|growth cone|
|cellular response to reactive oxygen species|
|regulation of RNA splicing|
|circadian rhythm|
|double-strand break repair|
|response to reactive oxygen species|
|cellular response to acid chemical|
|cellular response to toxic substance|
|DNA recombination|
|ribonucleoprotein complex assembly|
|cellular response to oxidative stress|
|ribonucleoprotein complex subunit organization|
|rhythmic process|
|positive regulation of neuron projection development|
|nuclear body|
|axon|
|DNA conformation change|
|mRNA splicing, via spliceosome|
|RNA splicing, via transesterification reactions with bulged adenosine as nucleophile|
|RNA splicing, via transesterification reactions|
|response to antibiotic|
|response to acid chemical|
|positive regulation of neuron differentiation|
|MAPK cascade|
|positive regulation of cell projection organization|
|response to oxidative stress|
|signal transduction by protein phosphorylation|
|RNA splicing|
|cellular response to drug|
|ribonucleoprotein complex biogenesis|
|positive regulation of neurogenesis|
|mRNA processing|
|transcription by RNA polymerase II|
|regulation of neuron projection development|
|cellular response to growth factor stimulus|
|response to toxic substance|
|DNA repair|
|transmembrane receptor protein tyrosine kinase signaling pathway|
|cellular response to lipid|
|response to growth factor|
|response to inorganic substance|
|positive regulation of nervous system development|
|positive regulation of cell development|
|spermatogenesis|
|male gamete generation|
|transcription, DNA-templated|
|nucleic acid-templated transcription|
|RNA biosynthetic process|
|regulation of neuron differentiation|
|gamete generation|
|regulation of plasma membrane bounded cell projection organization|
|mRNA metabolic process|
|regulation of cell projection organization|
|enzyme linked receptor protein signaling pathway|
|DNA metabolic process|
|cellular response to DNA damage stimulus|
|regulation of neurogenesis|
|multicellular organismal reproductive process|
|sexual reproduction|
|cellular protein-containing complex assembly|
|multicellular organism reproduction|
|response to lipid|
|nucleolus|
|RNA processing|
|negative regulation of apoptotic process|
|negative regulation of programmed cell death|
|regulation of nervous system development|
|regulation of cell development|
|positive regulation of cell differentiation|
|protein phosphorylation|
|multi-organism reproductive process|
|negative regulation of cell death|
|response to drug|
|cellular response to oxygen-containing compound|
|chromosome organization|
|identical protein binding|
|nucleobase-containing compound biosynthetic process|
|heterocycle biosynthetic process|
|aromatic compound biosynthetic process|
|positive regulation of cellular component organization|
|positive regulation of transcription by RNA polymerase II|
|cellular response to endogenous stimulus|
|phosphorylation|
|organic cyclic compound biosynthetic process|
|positive regulation of developmental process|
|RNA binding|
|reproductive process|
|reproduction|
|DNA binding|
|response to endogenous stimulus|
|ATP binding|
|generation of neurons|
|positive regulation of transcription, DNA-templated|
|regulation of apoptotic process|
|response to oxygen-containing compound|
|protein-containing complex assembly|
|regulation of programmed cell death|
|neurogenesis|
|cellular nitrogen compound biosynthetic process|
|positive regulation of nucleic acid-templated transcription|
|positive regulation of RNA biosynthetic process|
|RNA metabolic process|
|regulation of cell death|
|intracellular signal transduction|
|cellular response to stress|
|cellular macromolecule biosynthetic process|
|positive regulation of RNA metabolic process|
|positive regulation of multicellular organismal process|
|macromolecule biosynthetic process|
|regulation of cell differentiation|
|protein-containing complex subunit organization|
|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|
|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:exp139|Nicotinamide Riboside 100μM R03 exp139]]|-2.17|
|[[:results:exp422|Wiskostatin 3μM R07 exp422]]|-2.17|
|[[:results:exp466|Cannabidiol 20μM R08 exp466]]|-1.97|
|[[:results:exp426|FBS-Wisent 0.1 R07 exp426]]|-1.95|
|[[:results:exp38|Wortmannin 5μM R00 exp38]]|-1.95|
|[[:results:exp321|ABT-702 5μM plus Deferoxamine 11μM R07 exp321]]|-1.92|
|[[:results:exp75|MK-1775 0.32μM R02 exp75]]|-1.77|
|[[:results:exp216|Erlotinib 10μM R05 exp216]]|-1.75|
|[[:results:exp72|LB-100 4.1μM R02 exp72]]|-1.75|
|[[:results:exp14|Cycloheximide 0.02μM R00 exp14]]|1.73|
|[[:results:exp506|Momordin-Ic 10μM R08 exp506]]|1.74|
</modal>

<modal id='Most_Correlated_Genes' size='lg' title='Most Correlated Genes in Chemogenomics'>
^Gene^Correlation^
|[[:human genes:r:rrm1|RRM1]]|0.443|
</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>**: 3842
    * **<color #00a2e8>Expression level (log2 read counts)</color>**: 7.98 
<button type='primary' size='small' modal='Dist_expr'>Expression Distribution</button>
<modal id='Dist_expr' size='lg' title='SETX Expression in NALM6 Cells: 7.98'>
{{:chemogenomics:nalm6 dist.png?nolink |}}
</modal>