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1 TF and ectonucleotidase activities were measured using c
2 TF is also shown to induce signalling through activation
3 TFs that autoregulate were highly conserved between tiss
4 ssembled genome-wide binding profiles of 104 TFs in the K562 and GM12878 cell lines, which loosely mo
7 brary in three hPSC lines, we discovered 290 TFs, including 241 that were previously unreported, that
9 ssed transcription factor (TF) genes from 54 TF families, notably bHLH, MYB, ERF, MYB-related, NAC, a
14 nscription factor (TF) binding by mutating a TF binding motif, which in turn may affect the activity
16 rnatively, TF-tagging techniques, in which a TF is fused to a DNA-modifying enzyme that marks TF-bind
17 7p, Gcr1p and Gcr2p, that act together as a 'TF collective', an important but poorly characterized mo
19 d identify hundreds of differentially active TFs, yet find very little transcriptomic changes in stea
20 ional cis-eQTL SNVs are more likely to alter TF binding sites than rare SNVs in the human population.
21 ession filtering identified commonly altered TFs and coregulator genes, including well-established (e
23 on factors (TFs) at baited enhancers amplify TF binding at target enhancers, a phenomenon we term cro
25 ICAM (intercellular adhesion molecule)-1 and TF expression following TNF (tumor necrosis factor)-alph
26 evious therapeutics directly linking Dox and TF, cytotoxicity of CDT resulted from nuclear entry by D
27 and miRNA regulation pairs, their FFLs, and TF-miRNA mediated regulatory networks in two major types
30 conserved between tissues, but less so, and TFs regulate different combinations of microRNAs in a ti
35 ization operates as an antenna that attracts TF molecules in a promiscuous exchange among myriads of
36 naive TF target genes are more likely to be TFs themselves than those of formative TFs, suggesting d
40 nal regulatory module (TRM) (e.g. co-binding TFs), which helps decipher the combinatorial regulatory
41 al assays to identify and isolate biosensing TFs, and a quantum-dot Forster Resonance Energy Transfer
43 Prior studies have assumed that decoy-bound TFs are protected from degradation, and in this case dec
44 Interestingly, while protection of bound TFs from degradation slows the time-scale of fluctuation
45 in the unbound TF levels, the decay of bound TFs leads to faster fluctuations and smaller noise propa
46 etable as the "linking rate," by which bound TFs interact with Mediator components, enables our model
48 plore the mechanism of activation of PTEN by TF, the association of "membrane-associated guanylate ki
50 e-learning algorithm able to jointly combine TFs ChIP-Sequencing data and gene expression compendia t
53 ene-expression program; the ensemble of core TFs and their regulatory loops constitutes core transcri
55 Next, we determined significantly correlated TF-gene/miRNA and miRNA-gene/TF pairs with regulation di
56 n-based GRNs to accurately predict covarying TF-target relationships in natural variation data sets,
58 Furthermore, we identify Sox17 as a critical TF upregulated during the sprouting and remodeling of co
60 ratively estimates model parameters of CRMs, TF activities, and corresponding regulation on gene tran
61 tinuous-State Hidden Markov Models TF (CSHMM-TF) method which integrates probabilistic modeling of sc
63 method to directly construct a differential TF co-regulation network from paired disease-to-normal C
64 ased mixture model for monomeric and dimeric TF-binding motifs and an expectation maximization algori
68 These models allow us to characterize each TF's specificity, activity and interactions with chromat
71 Unexpectedly, nuclear expression of the EMT-TF ZEB2 in human primary melanoma has been shown to corr
72 p.Ser117HisfsTer10) in F3, the gene encoding TF, causing premature termination of TF (TFshort) in a w
74 to upregulate or activate the iPSC-enriched TFs while downregulate or silence the fibroblast-enriche
77 emonstrate that inhibition of tissue factor (TF) and the downstream coagulation proteases factor Xa a
82 rd binding the MB cell transcription factor (TF) BACH2 at the expense of the germinal center (GC) TF
83 nce variants affecting transcription factor (TF) binding at CRMs have a strong potential to influence
84 ory elements can alter transcription factor (TF) binding by mutating a TF binding motif, which in tur
85 c distances over which transcription factor (TF) binding influences gene expression is important for
86 ichment at the central transcription factor (TF) binding regions and at the flanking eRNA initiation
89 ing protein, mRNA, and transcription factor (TF) DNA-binding activity for mouse liver tissues collect
91 fferentially expressed transcription factor (TF) genes from 54 TF families, notably bHLH, MYB, ERF, M
93 matin accessibility at transcription factor (TF) motifs in the context of Sox9(EGFP) populations, we
97 tional targets of each transcription factor (TF) requires convergent evidence from independent source
98 ile the reported short transcription factor (TF) residence times on the DNA with the high specificity
99 T cells 5 (NFAT5) is a transcription factor (TF) that mediates protection from adverse effects of hyp
101 r-binding protein beta transcription factor (TF), while the T allele did not show any interaction wit
103 se types of elements, transcription factors (TF) were identified whose binding sites were enriched or
104 g data on the role of transcription factors (TFs) - particularly the ETS and IRF families - in regula
105 , 1554 genes encoding transcription factors (TFs) and a total of 514 single nucleotide polymorphisms
106 rately predicting the transcription factors (TFs) and cofactors that drive transcriptomic differences
107 on highly researched transcription factors (TFs) and cytokines, resulting in an incomplete portrait
108 w aim to identify key transcription factors (TFs) and functional enhancers that regulate processes as
109 interactions between transcription factors (TFs) and genome-wide targets typically elude biochemical
113 mplex crosstalk among transcription factors (TFs) and their target genes, with a method able to handl
114 ize information about transcription factors (TFs) and their targets or only study these as a post-pro
115 subfamily of homeobox transcription factors (TFs) are involved in abiotic stress responses and plant
116 ied the VOZ1 and VOZ2 transcription factors (TFs) as IBI1-interacting partners, which are transcripti
118 OSINTE BRANCHED1-like transcription factors (TFs) belonging to the TEOSINTE BRANCHED1/CYCLOIDEA/PROLI
119 anscription, numerous transcription factors (TFs) bind to targets in a highly coordinated manner to c
121 recent collections of transcription factors (TFs) from the JASPAR and UniPROBE databases, methylated
125 d Stp2 are paralogous transcription factors (TFs) regulated by the Ssy1-Ptr3-Ssy5 (SPS) amino acid se
126 y, we reveal that the transcription factors (TFs) regulating cell identity contain prion-like domains
127 ple sequence-specific transcription factors (TFs) that mediate association of Tup1-Cyc8 co-repressor
128 SP activates a set of transcription factors (TFs) that orchestrate nodule organogenesis and infection
129 networks (GRNs) link transcription factors (TFs) to their target genes and represent maps of potenti
131 d various families of transcription factors (TFs) were differentially expressed in root system during
132 landscape mediated by transcription factors (TFs), we present the Human TFome, a comprehensive librar
133 ue family of bacteria transcription factors (TFs), which activate transcription in a manner distinct
137 constituted by three transcription factors (TFs): KLF15, TCF4 and NKX2-2, in Ewing sarcoma cells.
138 Here, we explored transcriptional factors (TFs) that reduce wood recalcitrance and improve sacchari
139 The primary outcome was treatment failure (TF), defined as 30-day mortality or persistent bacteremi
143 ave been proposed, ranging from the flexible TF billboard model to the stringent enhanceosome model.
147 to be TFs themselves than those of formative TFs, suggesting denser hierarchies among naive TFs.
148 Vs that bear primary or transmitted/founder (TF) Envs with modifications at Env residue 375 that enab
149 ulate key properties of transmitted/founder (TF) or primary HIV-1 isolates, such as CCR5 tropism, tie
150 that the combination of low tumor fraction (TF) and limited number of DNA fragments restricts low-di
152 is important for inferring target genes from TF chromatin immunoprecipitation followed by sequencing
154 e relevant signaling pathways and functional TFs (transcription factors) regulating these processes i
155 ings identify Med19/Med1 as a composite GATA TF interface and suggest that binary MED subunit-TF part
156 hysically interacts with the Drosophila GATA TFs, Pnr and Serpent (Srp), in vivo and in vitro through
158 2 at the expense of the germinal center (GC) TF BCL6, leading to pre-memory transcriptional reprogram
160 with COVID-19 platelet-rich plasma generated TF-bearing NETs that induced thrombotic activity of HAEC
162 Despite a common understanding that Gli TFs are utilized to convey a Hh morphogen gradient, gene
165 iding quantitative evidence that heterotypic TF interactions distinguish cell type-specific CRE activ
166 s resident in communities identified as high-TF clusters during previous population-based mapping.
168 he genomic binding profiles of different Hox TFs, even among the posterior group paralogs that share
169 the differential abilities of posterior Hox TFs to bind to previously inaccessible chromatin drive p
171 imilar DNA-binding motifs of the various HOX TFs contrast with the wide-range of HOX-dependent geneti
172 changes rather than quantitative changes in TF gene expression are more likely associated with chang
176 In this study, we extensively investigated TF and miRNA regulation pairs, their FFLs, and TF-miRNA
177 To address how interactions between four key TFs contribute to cis-regulation in mouse ESCs, we assay
179 the subnetworks regulated by the B-lymphoid TF Ebf1 and T-lymphoid TF Gata3 revealed a surprising ro
180 ted by the B-lymphoid TF Ebf1 and T-lymphoid TF Gata3 revealed a surprising role in common activation
181 s fused to a DNA-modifying enzyme that marks TF-binding events across the genome as they occur, do no
185 ed the Continuous-State Hidden Markov Models TF (CSHMM-TF) method which integrates probabilistic mode
187 t activation and platelet-dependent monocyte TF expression, which were associated with COVID-19 sever
194 TFs, including closure of neurodevelopmental TF binding sites and increased expression and binding ca
197 Specifically, we used TFs, miRNAs and non-TF genes to form feed-forward loops (FFLs) using genomic
198 ions through increasing the accessibility of TF motifs NR1H4 and OLIG (OLIGI and OLIG2), respectively
199 e study identified unique characteristics of TF viruses thus prompting further investigation into vir
200 lationship between the gain or disruption of TF (transcription factor)-binding motifs, inferred from
205 udy is the first systematic investigation of TF and miRNA regulation and their co-regulation in two m
206 ng signal analyses reveal co-localization of TF binding sites based on inferred cis-regulatory module
208 mic techniques have uncovered a multitude of TF binding sites in ESCs, yet a major challenge lies in
209 or unique applications, such as recording of TF occupancy over time and cell type specificity through
213 ynamics emerging from nonspecific binding of TFs and highlights the dual role of decoys as attenuator
214 to two cell lines with a rich collection of TFs and identify combinatorial binding patterns that sho
217 ize the binding and expression of a group of TFs, Tye7p, Gcr1p and Gcr2p, that act together as a 'TF
218 Homodimerization or heterodimerization of TFs are required for DNA binding and the association int
219 provide a resource for the identification of TFs which regulate the dynamical properties of human gen
222 iew is focused on the ever-growing number of TFs whose effects on ageing are evolutionarily conserved
225 tial legitimate transcriptional responses of TFs to OSKM reprogramming were also observed in the repr
227 el and infers context-specific CRMs based on TF-gene binding events and gene expression data for a pa
228 somatic mutations have different effects on TF binding sites from different TF families on a cancer-
232 isease-associated repeat expansions in other TFs (HOXA13, RUNX2, and TBP) were similarly found to alt
233 ing site accessibility change for many other TFs, including closure of neurodevelopmental TF binding
234 man cells, including interactions with other TFs, and propose that Bhlhe40 is a central mediator of b
235 o the BHJ film top surface, changes the PBDB-TF/Y6 vertical phase separation and intermixing, and red
236 trate how a single sequence-specific pioneer TF can synergize with remodelers to activate sets of gen
238 e developed a footprinting method to predict TF footprints in active chromatin elements (TRACE) to im
239 h-dependent SBF/MBF clustering and predicted TF dynamics that were confirmed in live cell PALM experi
240 ll lines were exposed to recombinant-TF (rec-TF), or activated using a PAR2-agonist peptide and the p
241 In contrast, continuous exposure to rec-TF up to 14 days, resulted in lower PTEN antigen levels,
242 Seven cell lines were exposed to recombinant-TF (rec-TF), or activated using a PAR2-agonist peptide a
247 pression signature based on over-represented TFs correlated with poor survival and unfavorable progno
248 oss the genome as they occur, do not require TF-specific antibodies and offer the potential for uniqu
253 show utility in defining cell type-specific TF profiles and recording and integrating TF-binding eve
256 ognizes partial binding sites display stable TF-DNA interactions similar to those observed in complex
257 nterface and suggest that binary MED subunit-TF partnerships are probably oversimplified models.
259 Applied to gene sets derived from targeted TF perturbation experiments, Lisa boosted the performanc
260 stablished the proof of concept of targeting TF as a new target in CAR-NK immunotherapy for effective
261 argets captured in root cells using temporal TF perturbation account for 50% of NLP7-regulated genes
262 ightly better than PPM models for 314 tested TFs (or their DNA-binding domains) from four families (b
265 uch difference in replicative fitness of the TF viruses in cultures treated with and without IFN-alph
268 and experimental evidence for a role of the TFs NURR1 and ERR1 in modulating the expression pattern
270 ally, we analyzed expression levels of these TFs in dorsolateral prefrontal cortex (DLPFC) of SCZ pat
275 ments suggest that the nucleosome barrier to TF binding is modulated by dynamic nucleosome unwrapping
281 compare three methods for determining total (TF) and total soluble fluorides (TSF) in 5 child formula
285 finity decoys, noise in the level of unbound TF always monotonically decreases to the Poisson limit w
286 he time-scale of fluctuations in the unbound TF levels, the decay of bound TFs leads to faster fluctu
287 gs overexpressing previously uncharacterized TF genes increased total glucan hydrolysis on average co
290 ded catalogs of putative open regions, where TFs can recognize their motifs and regulate gene express
291 Yet, how the DNA sequence determines which TF complex forms at any given site is poorly understood.
293 ficient mixing and spatial separation, while TF-labeled semiconductor quantum dots serve as bright fl
294 AP1-IRF composite elements (AICEs) and with TF PU.1 at Ets-IRF composite elements (EICEs), it is unc
297 Since IRF8 and IRF4 can each interact with TF BATF3 at AP1-IRF composite elements (AICEs) and with
299 resolved 'trans-omic' datasets together with TF binding profiles and chromatin conformation data to i
300 haliana zinc finger transcription factor (ZF-TF), S-nitrosothiol (SNO) Regulated 1 (SRG1), is a centr