http://narada.bio/assets/FAQ-c4522716.js

1import{y as h,r as p,f as a,o as e,c as n,b as t,g as m,w as o,F as b,k as g,A as u,s as v,p as y,a as f,_ as A}from"./index-70eb8fe8.js";const R=i=>(y("data-v-1349485a"),i=i(),f(),i),T={class:"faq-section"},D=R(()=>t("span",{class:"faq-title"},"FAQs for NaRaDa",-1)),C={class:"container"},P=v('<div class="header-bar" data-v-1349485a><span class="header-text" data-v-1349485a>1. How to contact us?</span></div><div class="content" data-v-1349485a> If you have any questions or need further information, please send an email to &#39;narada_bio [at] 163.com&#39; </div><div class="header-bar" data-v-1349485a><span class="header-text" data-v-1349485a>2. Which TREs will be shown when using “search TREs by Gene”?</span></div><div class="content" data-v-1349485a> The TREs exhibited in this function are determined by the distance between target genes and TREs. Automatically, the distance is set to 10 kb. Users can easily change the distance setting (&lt; 1,000 kb) on the result page according to their requirements.</div><div class="header-bar" data-v-1349485a><span class="header-text" data-v-1349485a>3. What is the definition of TSS region and gene body region?</span></div><div class="content" data-v-1349485a> The TSS region is defined as [-30 bp, to +300 bp] around the TSS. The gene body is defined as the region beginning from +301 bp to the transcription end site (TES). For genes &lt; 500 bp, the gene body is defined as the whole gene without any truncation. </div><div class="header-bar" data-v-1349485a><span class="header-text" data-v-1349485a>4. What is the definition of promoter in the Pol II pause/release analysis of “Comparison”?</span></div><div class="content" data-v-1349485a> In this section, we defined the TSS region described above as the promoter.</div><div class="header-bar" data-v-1349485a><span class="header-text" data-v-1349485a>5. How to define distal TREs?</span></div><div class="content" data-v-1349485a> We assume distal bidirectional transcripts are mainly from enhancer RNA transcription. To discriminate candidate enhancers from the pool of all TREs, we use bedtools (“intersect” function) to extract distal TREs from proximal TREs (500 bp regions flanking TSS of protein-coding transcripts)</div><div class="header-bar" data-v-1349485a><span class="header-text" data-v-1349485a>6. How to download?</span></div><div class="content" data-v-1349485a> All relevant information can be downloaded from the corresponding pages. Additionally, we provide a comprehensive download page where you can access quantitative data for all groups within any selected species. Moreover, overall TRE information is available for each species as well as for various tissues within them. </div><div class="header-bar" data-v-1349485a><span class="header-text" data-v-1349485a>7. What are the details of the treatment?</span></div>',13),S=["innerHTML"],w=h({__name:"FAQ",setup(i){const s=p({"1-NM-PP1":"CDK12 and CDK13 inhibitor.","1,6-HD (1,6-hexanediol)":"An aliphatic alcohol that disassembles phase-separated ribonucleoprotein (RNP) granules and membraneless structures by disrupting weak hydrophobic interactions.","2,5-HD (2,5-hexanediol)":"A similar aliphatic alcohol that has minimal impact on the phase behavior of disordered proteins.","2i":"Mitogen-activated protein kinase kinase (MEK) and glycogen synthase kinase 3 (GSK3) inhibitors: PD0325901 (PD) and CHIR99021 (CHIR).","3-MB-PP1":"Analog-sensitive (AS) kinase inhibitor for mcs6N84T-L87G (mcsas) and cdk9T120G  (cdk9as) , CDK8as but not for  lsk1F353G (lsk1 F353G).","5-aza-2'-deoxycytidine":"DNA methylation inhibitor.","5iLA/t2iGo":"hESCs cultured in primed or naïve (5iLA or t2iGo) medium.","A23187 (calcium ionophore)":"A highly selective calcium ionophore that increases intracellular Ca2+ levels by forming a stable complex with Ca2+ and passing through the cell membrane.","A-485":"CBP/p300 acetyltransferase inhibitors.","A771726 (teriflunomide)":"Active metabolite of leflunomide, inhibits DHODH, reducing pyrimidine levels.",ActinomycinD:"Transcription inhibitor.","actinomycin D (ActD)":"Inhibition of transcription by inserting DNA","Activin A":"Activates Activin/SMAD2,3 signaling pathway.","Afghan Desert Particulate Matter (APM)":"Can induce physiologic responses relevant to deployment-related lung diseases (DLD).","Akti-1/2":"Allosteric small molecule AKT inhibitor.",AID:"Auxin-inducible degron.","antiCD40/IL4":"Induces immunoglobulin (Ig) heavy chain class switch recombination (CSR) to Sγ1 and 

1Sε.","ASO (antisense oligonucleotide)":"Selective inhibition of the translation of disease-associated genes is achieved via Ribonuclease H (RNase H)-mediated cleavage or steric hindrance.",AZD1775:"Wee1 kinase inhibitor.",BRM014:"ATPase inhibitor.",C16:"WIN site inhibitor.",C3:"WIN (WDR5 interaction) site blockade, leading to WDR5 displacement from chromatin and decreased expression of WDR5-bound genes.",C60:"Lytic activating compound of EBV.",Celastrol:"A compound derived from traditional Chinese medicine that has potent anti-inflammatory, tumor-inhibitory and obesity-controlling effects.","CHX (Cycloheximide)":"Protein translation inhibitor.",Cisplatin:"Anticancer drug that forms cisplatin-DNA adducts, obstructing DNA synthesis and transcription.",DC3000:"Pseudomonas syringae pv. tomato DC3000 (PstDC3000) is an important plant pathogen that infects tomatoes and Arabidopsis.","Dex (dexamethasone)":"Synthetic glucocorticoid, glucocorticoid receptor agonist.","DHT (5alpha-dihydrotestosterone)":"Androgen receptor (AR) agonist.","Dina (Dinaciclib)":"A more potent broad spectrum CDK inhibitor.","DOX (Doxycycline)":"Tet-Off system silences gene expression via tetracycline or derivatives like doxycycline, Tet-On system activates gene expression with doxycycline.","DRB (5,6-dichloro-1-beta-d-ribofuranosyl-benzimidazole)":"RNA polymerase II elongation inhibitor.",dTAG:"The degradation tag system.",Duvelisib:"A drug used in leukemia or lymphoma therapy, blocks PI3Kδ activity.","E2 (estrogen hormone)":"Can bind to estrogen receptor alpha (ERα) and beta (ERβ), inducing their translocation from the cytosol to the nucleus, where they bind to specific estrogen response elements (EREs) and regulate gene expression.","ENRI (ENRI media)":"Epidermal growth factor, Noggin, R-spondin, Wnt inhibitor IWP2 media.","Flavopiridol (Flavo)":"Cyclin-dependent kinase (CDK) inhibitor, preferentially inhibits Cdk9 activity at low concentrations.","GC-1 (3,5-dimethyl-4-(4'-hydroxy-3'-isopropylbenzyl)-phenoxy acetic acid)":"Thyroid hormone receptor β agonist.",GDC0068:"AKT inhibitor.",GLKD:"Germline knockdown.",GSK2879552:"LSD1 inhibitor.",IBET151:"Selective inhibitor of BET (bromodomain and extra terminal domain) protein binding to acetylated histones.","ICI 182780":"ERα and ERβ antagonist.",Ibrutinib:"PI3Kδ inhibitor.",Idelalisib:"PI3Kδ inhibitor.","IL4 (Interleukin 4)":"Activates STAT6 transcription factor in macrophages.",INCB059872:"LSD1 inhibitor.",JQ1:"Potent and selective inhibitor of the BRD4 signaling pathway.","KL-1/2":"Super elongation complex (SEC) inhibitors.","Kdo2 lipid A (KLA)":"TLR4 agonist.",LBH589:"HDAC inhibitor.",LIF:"Leukemia inhibitory factor.","LG100268 (LG268)":"RXR agonist.",LNA:"Locked Nucleic Acid.","LPS (Lipopolysaccharides)":"Activates the TLR4 signaling pathway.","LPS/anti IgD-dextran":"Induces immunoglobulin heavy chain class switch recombination (CSR) to Sγ3, Sγ2b, and Sγ2a.","LPS + IL4":"stimulate antibody class switch recombination (CSR) between Eμ, Sμ, Sγ1, and the 3′RR",Menadione:"Oxidative stress inducer.",MS40:"A cereblon (CRBN)-recruiting proteolysis targeting chimera (PROTAC) of WDR5.",MS417:"Bromodomain and extra-terminal domain (BET) inhibitor.","NaB (Sodium butyrate)":"Potent HDAC inhibitor.",Nocodazole:"Reversibly interferes with microtubule polymerization, widely used to induce mitotic arrest.","NO2-OA (electrophilic fatty acid-derivative nitro-oleic acid)":"NRF2 activator","Nutlin (Nutlin-3)":"Binds to the hydrophobic pocket in MDM2 required for p53 binding, acting as a competitive inhibitor.",NVP2:"CDK9 inhibitor.","oxPAPC (Oxidized 1-palmitoyl-2-arachidonoyl-sn-glycero-3-phosphorylcholine)":"Protects barrier function and activates the Nuclear factor erythroid 2-Related Factor 2 (NRF2) pathway.","PAA (phosphonoacetic acid)":"DNA replication inhibitor.","Palbo (Palbociclib, PD-0332991)":"CDK4/6 inhibitor.","PE (phenylephrine)":"α-adrenergic receptor agonist.","PHA (PHA767491)":"CDK9 inhibitor.","Phosphonoformic acid (PFA)":"An HCMV replication inhibitor that prevents the transcription of late genes.",PJ34:"PARP inhibitor.","PMA/ionomycin":"PMA activates protein kinase C, while ionomycin is a calcium ionophore, and stimulation with these compounds bypasses the T cell membrane receptor complex and will lead to activation of several intracellular signaling pathways, resulting in T cell activation and production of a variety of cytokines.",R1881:"Androgen.","RA (retinoic acid)":"Binding and activating retinoic acid receptor",RankL:"Eeceptor activator of nuclear factor κB ligand.",RGFP966:"HDAC3 selective inhibitor.","Rosiglitazone (RSG or Rosi)":"PPARγ agonist",Sarkosyl:"Contributes to pause-release, particularly in promoter-proximal regions of coding genes and enhancers.",RANKL:"Receptor activator of NF-κB ligand.",Romidepsin:"Histone deacetylase inhibitor.","SPI-21":"Spt5-Pol II inhibitor.","STI-571":"Abl kinase inhibitor.","Tamoxifen (Tam)":"A drug that c

1ompetitively inhibits the binding of estrogen to its receptor.",TamR:"Tamoxifen-resistant cell.","TFF1p-KO":"TFF1 promoter deletion.","Thapsigargin (THAP)":"ER stressor.",THZ1:"CDK7 inhibitor.",THZ531:"CDK12 and CDK13 inhibitor.","TNFα (Tumor Necrosis Factor Alpha)":"A master cytokine that mediates inflammatory responses and innate immunity. Major pathways activated by TNFα include caspases, NF-κB, and mitogen-activated protein kinases (MAP kinases).","Trichostatin A (TSA)":"HDAC inhibitor.",triptolide:'Inhibits the initiation of transcription by preventing the formation of the "transcription bubble".',Trp:"A covalent TFIIH subunit XPB inhibitor, which can block transcription initiation.","VTP-50469":"Menin-MLL inhibitor, which selectively disrupts the interaction between Menin and MLL1 and leads to a loss of MLL1 binding from a subset of its targets, which in turn also show decreased gene expression.","WENRC (WENRC media)":"Wnt, epidermal growth factor, Noggin, R-spondin, Chir media.",ZT:"Zeitgeber time","α-amanitin":"Traps the conformation of RNAPII, preventing nucleotide incorporation and transcript translocation.","γSI (γ-secretase inhibitor)":"can inhibit the cleavage of notch receptor and thus inhibit the notch pathway."});return(I,x)=>{const r=a("el-descriptions-item"),c=a("el-descriptions");return e(),n("div",T,[D,t("div",C,[P,m(c,{column:1,border:""},{default:o(()=>[(e(!0),n(b,null,g(s.value,(d,l)=>(e(),u(r,{label:l,"label-class-name":"my-label","class-name":"my-content"},{default:o(()=>[t("span",{class:"info",innerHTML:d},null,8,S)]),_:2},1032,["label"]))),256))]),_:1})])])}}});const _=A(w,[["__scopeId","data-v-1349485a"]]);export{_ as default};