ライフサイエンスコーパス: TF

1 TF ELISA, soluble P-selectin, d-dimer, FVIII, and C-reac

2 TF is the receptor and scaffold of coagulation proteases

3 TF knockout mutant phenotypes are consistent with model

4 TF mutations induce rippling downstream effects by simul

5 TF-SSS showed slightly higher absolute quantification.

6 TFs with winged helix-turn-helix (wHTH) motifs use an al

7 we infer the transcriptional activity of 127 TFs through analysis of RNA-seq gene expression data new

8 resulted in the assignment of motifs to 200 TFs with no SELEX-derived motifs, roughly a 50% increase

9 ered 978 TFs in 62 families, among which 404 TFs within 40 families were differentially expressed upo

10 involving 54 phenolic gene promoters and 568 TFs.

11 A total of 941 TFs are quantitatively identified, representing over 60%

12 iption factor (TF) annotation discovered 978 TFs in 62 families, among which 404 TFs within 40 famili

13 In ex vivo flowing blood, a TF-FVIIa mutant complex with impaired free FXa generatio

14 cer-associated ncRNAs that are involved in a TF-dependent regulatory network.

15 work provides detailed characterization of a TF gene cluster and advances our understanding of the tr

16 lements that contain motifs for PPARgamma, a TF that serves as a key regulator of adipogenesis.

17 inducing tumor cell proliferation through a TF-dependent mechanism, a specific effect reversed by ne

18 diction of TF binding is transferable across TFs and/or cell lines suggesting there are a set of univ

19 which promoters decode the amount of active TF into target gene expression are not well understood.

20 nts or motif predictions, and outputs active TF-gene links as well as latent TF activities.

21 mical modifications that are known to affect TF binding (such as DNA methylation) and providing incre

22 6K and TF are isoforms that are identical in their N termini bu

23 he alphavirus small membrane proteins 6K and TF have been reported to be palmitoylated and to positiv

24 Recently, the small 6K and TF proteins of alphaviruses were shown to contribute to

25 esidues in the identical N termini of 6K and TF, the four additional Cys residues in TF's unique C te

26 lts represent the first analysis of OCRs and TF-binding sites in distinct populations of postmortem h

27 ng at gene expression, chromatin states, and TF binding during the uniquely efficient Ngn2, Isl1, and

28 cies was the major difference between VS and TF group, and higher baseline diversity in TF patients.

29 gs reveal a complex network of enhancers and TFs that dynamically cooperate to restore homeostasis up

30 ld be partly reversed by addition of an anti-TF antibody.

31 easily combined with other state-of-the-art TF-DNA interaction modeling methods.

32 bility and a network of challenge-associated TFs.

33 These BEL1 TFs work in tandem with KNOTTED1-types to regulate the e

34 rent types of cancer, an association between TF(+) MVs and VTE has been observed only in pancreatic c

35 ce understanding of the relationship between TF binding, chromatin status and the regulation of gene

36 s within the graph correlate with biological TF-TF interactions.

37 by chromatin environment and promoter-bound TFs during ESC differentiation.

38 FLOWERING 1 (PEP1), two orthologous MADS-box TFs that repress flowering and confer vernalization requ

39 ed a CArG-box that is recognized by MADS-box TFs.

40 e slow kinetics of Kunitz-type inhibition by TF pathway inhibitor and preferentially activates FVIII

41 understanding diseases that are regulated by TFs.

42 k for the enhanced activation of the cardiac TF over the skeletal TF by Ca(2+) and lead to a mechanis

43 stic model for the regulation of the cardiac TF.

44 Several DREB/CBF TFs directly promote transcription of the IAA5 and IAA19

45 ted evolution of the bacteriophage lambda cI TF against two synthetic bidirectional promoters.

46 ncy of TF activity on chromatin and classify TFs by their differential capacity to alter chromatin an

47 ordered differences, which can illustrate co-TF binding affinities for motif analysis.

48 ge amount of experimental data to analyze co-TFs.

49 From these lists, we can find co-TFs for candidate motifs.

50 subtype-specific enhancers and their cognate TFs by integrating the magnitude of enhancer transcripti

51 ese three algorithms to obtain collaborative TF sets governing biological processes or complex traits

52 ffective way to obtain sets of collaborative TFs; each set controls a biological process or a complex

53 total phenolic (TP) and flavonoid contents (TF) decreased by about 50% at the end of the in vitro GI

54 onstrate here that transcription factor COUP-TF-interacting protein 1 (CTIP1/BCL11A; hereafter CTIP1)

55 cordingly, FVIIa mutants deficient in direct TF-dependent thrombin generation, but preserving FVIIIa

56 dentify five TFs belonging to three distinct TF families: one TCP (OsPCF2), one CPP (OsCPP5) and thre

57 on factors (TFs) belonging to three distinct TF families: one TCP (OsPCF2), one CPP (OsCPP5) and thre

58 wounding suggests cooperation with distinct TFs in different contexts.

59 Reduction of the POU domain TF Ventral veins lacking (Vvl) largely ameliorates the a

60 ich AutoAbs against cell-surface GRP78 drive TF-mediated tumor progression in an experimental model o

61 nome-wide coexpression analysis between each TF and all other genomic genes and then constructing col

62 ding sites and integrate the effects of each TF to control gene expression in specific cellular conte

63 ade on understanding and reverse-engineering TF network topologies using a range of experimental and

64 ctors/collaborators and discovering enriched TF motifs.

65 re, we assayed the binding of five essential TFs over multiple stages of embryogenesis in two distant

66 of motif-based TFBS searching for an example TF.

67 cellular traps whereas monocytes may express TF.

68 and the majority of differentially expressed TFs increased rapidly after ABA treatment.

69 We found that the extrinsic tissue factor (TF) coagulation initiation complex can selectively activ

70 Purpose Circulating tissue factor (TF) has been studied as a biomarker for predicting initi

71 Tissue factor (TF) is expressed in vascular and nonvascular tissues and

72 man ADTRP [androgen-dependent tissue factor (TF) pathway inhibitor (TFPI) regulating protein] gene in

73 s its cell-localized cofactor tissue factor (TF), which stimulates activity through membrane-dependen

74 eq data from ENCODE on transcription factor (TF) and target gene interactions.

75 Comprehensive transcription factor (TF) annotation discovered 978 TFs in 62 families, among

76 The transcription factor (TF) basic/Helix-Loop-Helix (bHLH) is important for plant

77 Transcription factor (TF) binding of cis-elements is often associated with acc

78 e wide localization of transcription factor (TF) binding or epigenetic modification events.

79 tational prediction of transcription factor (TF) binding sites in different cell types is challenging

80 (CRMs) and individual transcription factor (TF) binding sites.

81 ive enhancers, linking transcription factor (TF) binding to the molecular mechanisms controlling gene

82 sites bound by a given transcription factor (TF) can be divided according to whether they are proxima

83 ncers that require the transcription factor (TF) CDX2 to prevent the incursion of H3K27me3 from adjoi

84 tal method that allows transcription factor (TF) chromatin turnover dynamics to be measured across a

85 The presence of transcription factor (TF) DNA binding motifs correlated with specific TF activ

86 n 1 (FLI1), a critical transcription factor (TF) during megakaryocyte differentiation, is among genes

87 The T-box transcription factor (TF) Eomes is a key regulator of cell fate decisions duri

88 ave significantly more transcription factor (TF) families than animals and fungi, and plant TF famili

89 Transcription factor (TF) footprinting analysis identifies differences in the

90 s functional impact on transcription factor (TF) occupancy and enhancer activity remains poorly under

91 ng genetic variations, transcription factor (TF) occupancy, or histone modification through next gene

92 the rules that govern transcription factor (TF) occupancy.

93 of a membrane-tethered transcription factor (TF) requires both a PPI to deliver a protease proximal t

94 t the signal-dependent transcription factor (TF) STAT5 is critical for accumulation of all known ILC

95 JA)-responsive AP2/ERF transcription factor (TF), ORCA3, and its regulator, CrMYC2, play key roles in

96 dules contain multiple transcription factor (TF)-binding sites and integrate the effects of each TF t

97 btain insight into the transcription factor (TF)-dependent regulation of epiblast stem cells (EpiSCs)

98 Identifying transcription factor (TFs) cooperation controlling target gene expression is s

99 Here we examine the transcription-factor-(TF)-dependence of ncRNA expression to define enhancers a

100 n induced by aberrant transcription factors (TF) is a key feature of cancer, but its global influence

101 n chromatin marks and transcription factors (TF) that are consistent with earlier work.

102 ially correlated with transcription factors (TFs) across the genome, but how these lncRNA-TF gene dup

103 Transcription factors (TFs) analysis showed that six different patterns were ob

104 de model of how plant transcription factors (TFs) and cis-regulatory elements control spatially speci

105 n regulators, such as transcription factors (TFs) and microRNAs (miRNAs), have varying regulatory tar

106 Although master transcription factors (TFs) are key to the development of specific T cell subse

107 Transcription factors (TFs) are proteins that bind to specific DNA sequences an

108 assuming activity of transcription factors (TFs) as unobserved, provide a biologically interpretable

109 Five transcription factors (TFs) belonging to three distinct TF families: one TCP (O

110 Genome-wide transcription factors (TFs) binding data has been extensively generated in the

111 Transcription factors (TFs) binding to specific DNA sequences or motifs, are el

112 in the expression of transcription factors (TFs) can influence the specification of distinct CD8(+)

113 laborative network of transcription factors (TFs) followed by decomposition and then construction of

114 Transcription factors (TFs) form a complex regulatory network within the cell t

115 tail, which activates transcription factors (TFs) glucocorticoid receptor (GR) and CREB within minute

116 upting the binding of transcription factors (TFs) in a given cellular context.

117 vity of lung-specific transcription factors (TFs) in lung carcinogenesis.

118 e coordination of key transcription factors (TFs) in multipotent progenitors that transition them awa

119 is by regulating key transcription factors (TFs) involved in triggering this process, such as the NA

120 inding specificity of transcription factors (TFs) is critical for understanding the principles of gen

121 ding specificities of transcription factors (TFs) is crucial to the study of gene expression regulati

122 s kinase') family and transcription factors (TFs) of the STAT ('signal transducer and activator of tr

123 describe a screen for transcription factors (TFs) that regulate the Aux/IAA genes.

124 of sequence-specific transcription factors (TFs) to cognate motifs.

125 Recruitment of transcription factors (TFs) to repressed genes in euchromatin is essential to a

126 lpha (e.g., Arx) cell transcription factors (TFs), and enrichment of binding motifs for these TFs in

127 hromatin remodellers, transcription factors (TFs), histone modifiers and co-factors often bind cooper

128 demonstrated that two transcription factors (TFs), Idr1 and Idr2, collaboratively regulate aspects of

129 In the 25 related transcription factors (TFs), our analysis of The Cancer Genome Atlas database (

130 is regulated by many transcription factors (TFs).

131 ression and timing of transcription factors (TFs).

132 en comparing children fed PDF with those fed TF.

133 This approach allowed us to identify five TFs belonging to three distinct TF families: one TCP (Os

134 hese patients, 805 had samples available for TF assay.

135 icular, supervised learning based models for TF-DNA interactions attempt to map sequence-level featur

136 trikingly, we find that transmitted/founder (TF) HIV-1 viruses can resist a late block that is induce

137 utants enable the organization of these four TFs and PHO1;H3 in a new gene regulatory network control

138 C stainings to quantify tumor fragmentation (TF), a measure of tumor invasiveness of lung squamous ce

139 monophosphoryl lipid A-Thomson-Friedenreich (TF) antigen conjugate was obtained to demonstrate the fe

140 ntered network with information derived from TF-centered approaches provides a foundation for a pheno

141 toAbs against cell surface-associated GRP78, TF expression/activity, and prostate cancer progression.

142 ing evidence that mutations in hematopoietic TFs are an important underlying cause for defects in pla

143 view focuses on alterations in hematopoietic TFs in the pathobiology of inherited platelet defects.

144 focal adhesion processes in tumors with high TF, supporting their increased invasive potential.

145 ntext of chromatin, our understanding of how TF-nucleosome interplay affects gene expression is highl

146 related miRNAs, CRC-related genes, and human TFs from multiple data sources.

147 ed, persistent, and specific accumulation in TF-positive BXPC-3 tumors, PET imaging using (89)Zr-Df-A

148 studies revealed no detectable difference in TF-binding affinity between ALT-836 and Df-ALT-836 in vi

149 To address the differences in TF behaviors, we developed Mocap, a method that integrat

150 d TF group, and higher baseline diversity in TF patients.

151 he role of 12/15-lipoxygenase (12/15-LOX) in TF expression.

152 and TF, the four additional Cys residues in TF's unique C terminus, or all nine Cys residues in TF.

153 ique C terminus, or all nine Cys residues in TF.

154 t humoral immunity may play a direct role in TF in long-term antiretroviral-experienced patients and

155 In addition, we incorporated TF binding sites identified via large-scale in vitro ass

156 an neural progenitors and (ii) incorporating TF conditional expression in a developmental-based proto

157 edented capabilities to visualize individual TF molecules, to track single transcription sites, and t

158 or product of human 15-LOXs 1 and 2, induced TF expression and activity in a time-dependent manner in

159 model and extend it to multiple interacting TFs, and build an agent-based simulation of multiple TFs

160 about how combinatorial complexity among JAZ-TF interactions maintains control over myriad aspects of

161 nd shoot compared with models based on known TF binding motifs.

162 tputs active TF-gene links as well as latent TF activities.

163 er transcription, TF mRNA expression levels, TF motif P-values, and enrichment of H3K4me1 and H3K27ac

164 TFs) across the genome, but how these lncRNA-TF gene duplexes regulate tissue development and homeost

165 ncreatic cancer cell lines with high and low TF expression levels, respectively.

166 thm to partition the graph while maintaining TF-cluster and cluster-cluster interactions.

167 of the genomic binding regions of five major TFs.

168 Recently, ChIP-seq in mapping TF provides a large amount of experimental data to analy

169 C reduced expression of the Treg cell master TF Foxp3 and induced TH2 differentiation even under iTre

170 Mean and median TF levels were 72.5 pg/mL and 50.3 pg/mL, respectively (

171 y sequences give rise to nucleosome-mediated TF collaborations that quantitatively account for the re

172 with thin film solid phase microextraction (TF-SPME) and liquid chromatography tandem mass spectrome

173 Moreover, TF activity was confirmed in the centrifuged fractions.

174 Moreover, TF suppression with neutralizing antibodies blocked 15(S

175 build an agent-based simulation of multiple TFs to investigate the dynamics of such coupled systems.

176 We have identified and validated multiple TFs influencing asthma treatment response.

177 es with the N-terminal Cys residues mutated, TF is much less efficiently localized to the plasma memb

178 in triggering this process, such as the NAC TF ORESARA1 (ORE1).

179 ressed energy-related and neurodevelopmental TF genes.

180 g S phase entry inhibited recruitment of new TFs to DNA and significantly blocked cell differentiatio

181 TransDetect was used to identify novel TF modules regulating the expression of Arabidopsis (Ara

182 nses to 265 compounds, we uncovered numerous TFs whose activity interacts with anticancer drugs.

183 Phenotypic and genetic analyses of TF mutants enable the organization of these four TFs and

184 Analysis of TF BSs in these lineages thus distinguishes widely conse

185 We evaluated the association of TF, clinical risk factors, and other biomarkers measured

186 strate the impact of limited availability of TF resource on the regulation of noise in gene expressio

187 r transcription can illuminate components of TF-dependent gene regulatory networks.

188 pronounced differences in the dependency of TF activity on chromatin and classify TFs by their diffe

189 between FVIIa and the soluble ectodomain of TF (sTF) was engineered by introduction of a nonperturbi

190 al reality and allow for fast exploration of TF clustering and regulatory dynamics.

191 posits that TF off rates are independent of TF concentration in solution.

192 Although elevated levels of TF(+) MVs have been observed in patients with different

193 esigned promoters at six different levels of TF.

194 We develop and apply a physical model of TF-chromatin competitive binding using chemical reaction

195 tions and XRC data into predictive models of TF binding and compared their performance.

196 f mouse-specific TEs that encode a module of TF-binding sites in mouse embryonic stem cells (ESCs).

197 rminus of TF modulates the palmitoylation of TF at the N terminus, and palmitoylated TF is preferenti

198 eighboring binding sites for a local pool of TF molecules explains this behavior and accurately predi

199 s prediction of TF binding.The prediction of TF binding is transferable across TFs and/or cell lines

200 sequence information improves prediction of TF binding.The prediction of TF binding is transferable

201 the last round of MDA and the prevalence of TF among children aged 1 to 9 years and the prevalence o

202 Moreover, nascent FXa product of TF-FVIIa can transiently escape the slow kinetics of Kun

203 To exploit these properties of TF, a covalent complex between FVIIa and the soluble ect

204 Patients in the highest quartile of TF experienced the greatest VTE recurrence (> 64.6 pg/mL

205 etween such structures and the regulation of TF binding to cis-regulatory elements remains to be eluc

206 effect is most likely due to the release of TF-bearing EVs of different dimensions, which are releas

207 We propose a model where the C terminus of TF modulates the palmitoylation of TF at the N terminus,

208 tive SMAD2/3 could enhance multiple types of TF-based cell identity conversion and therefore be a pow

209 Two types of TF-SPME passive samplers, including a retracted thin fil

210 ents) confirmed the poor prognostic value of TF using a similar human-based score on hematoxylin-eosi

211 k architecture and insufficient variation of TF mRNA level.

212 itive interactions among specific classes of TFs, with both spatially constrained and flexible gramma

213 We reveal a combinatorial code of TFs, cell surface molecules, and determinants of neurona

214 The gene is regulated by a combination of TFs in close proximity.

215 icts some potentially useful combinations of TFs.

216 the observation of equivalent expression of TFs among differentially fated precursor cells suggests

217 B within minutes and increases expression of TFs C/EBPbeta, C/EBPdelta, KLF4, and Krox20 within hours

218 as a linear combination of the expression of TFs.

219 rements of the specificities for hundreds of TFs.

220 ediates and facilitate the identification of TFs with previously unappreciated roles in CD8(+) T cell

221 This study provides a landscape of TFs in mouse tissues that can be used to elucidate trans

222 then constructing collaborative networks of TFs but only one algorithm, called Triple-Link Algorithm

223 ta-guided methodology identifies a number of TFs previously validated for reprogramming and/or natura

224 mechanism assisting in the local removal of TFs from their binding sites and does not necessarily re

225 ), for building collaborative subnetworks of TFs by identifying the fully-linked triple-node seeds fr

226 e SMAD2/3 also markedly enhances three other TF-mediated direct reprogramming conversions, from B cel

227 make the identification of targets of other TFs difficult, including network architecture and insuff

228 n of TF at the N terminus, and palmitoylated TF is preferentially trafficked to the plasma membrane f

229 s) and whole sections (WS: n = 99 patients), TF was associated with poor prognosis and increased risk

230 sites may be a key feature of other pioneer TFs operating at intractable genomic loci.

231 ) families than animals and fungi, and plant TF families tend to contain more genes; these expansions

232 Somatic and pluripotency TFs modulate reprogramming efficiency when overexpressed

233 rocess and require OS and other pluripotency TFs.

234 ytes, platelets, and tissue factor-positive (TF(+)) microvesicles (MVs) are all potential factors tha

235 odels have been used successfully to predict TF binding specificities, we found that including DNA sh

236 d an algorithm, TransDetect, able to predict TF combinations controlling the expression level of a gi

237 ks, identifying putative targets, predicting TF responsive enhancers, revealing potential cofactors/c

238 ane localization, which effectively prevents TF from participating in budding or being incorporated i

239 dent membrane perturbations to prothrombotic TF activation on myeloid cells.

240 bound by ZIC2 and OTX2 prominently regulate TF genes in EpiSCs.

241 y by attractor states of a master regulatory TF network.

242 NFIB and YBX1 are both risk TF associated with progression of ESR1-negative disease.

243 hat members of two opposing clusters of risk TFs associated with ESR1-positive and -negative breast c

244 rates chromatin accessibility, motif scores, TF footprints, CpG/GC content, evolutionary conservation

245 e the mapping between promoter DNA sequence, TF concentration, and gene expression output, we have co

246 xplaining these observations, enhancers show TF-dependent binding of the H3K27 demethylase KDM6A.

247 Here we take the single TF model and extend it to multiple interacting TFs, and

248 is correlated high tumor uptake with in situ TF expression.

249 observed based on the expression of the six TFs families (AP2/ERF, NAC, MYB, MYB-related, bZIP and W

250 tivation of the cardiac TF over the skeletal TF by Ca(2+) and lead to a mechanistic model for the reg

251 recruiting Hdac1, and repressing the somatic TF Fra1.

252 de by inducing the redistribution of somatic TFs away from somatic enhancers to sites elsewhere engag

253 DNA binding motifs correlated with specific TF activity during temporal MeJA-induced transcriptional

254 We show that lung-specific TFs become preferentially inactivated in lung cancer and

255 s enhancers together with cell-type-specific TFs by collaboratively binding to nucleosomal enhancers

256 N and BAF coordinate with cell-type-specific TFs to select enhancer repertoires that enable different

257 ggest that recruitment of lineage-specifying TFs occurs soon after replication and is facilitated by

258 r data indicate transient rather than stable TF-cofactors chromatin interactions at response elements

259 capable of associating known motifs to such TFs will avoid tremendous experimental efforts and enabl

260 In this issue, Hau et al. show that the TALE TF MEIS recruits the histone modifier PARP1/ARTD1 at pro

261 We illustrate that TF-dependent enhancer transcription can illuminate compo

262 tion of bimolecular interactions posits that TF off rates are independent of TF concentration in solu

263 We show that TF sharing enhances noise in mRNA distribution across an

264 The TF BACH2 is essential for T and B lymphocytes and is ass

265 th factor-beta (TGF-beta), we identified the TF musculin (MSC) as being critical for the development

266 data position STAT5 as a central node in the TF network that instructs ILC development, homeostasis,

267 TFPI is the TF pathway inhibitor that is involved in coagulation.

268 argets representing the core function of the TF from those that were recruited later in evolution.

269 MSC interrupted binding of the TF GATA-3 to the locus encoding TH2-cell-related cytokin

270 he structural basis for the crosstalk of the TF-FVIIa complex with integrin trafficking and suggest a

271 e structural positions on the surface of the TF.

272 After pressure overload, the TF genes in Module 1 were up-regulated before the occurr

273 Our analyses revealed that the TF genes up-regulated at the early stages likely initiat

274 viral replication analyses suggest that the TF protein is critical for neurological disease.

275 is of the whole dataset pointed out that the TF system at reduced thickness could be adopted up to 60

276 motif TFBS searching, demonstrating that the TF-TF connections within the graph correlate with biolog

277 To better understand the TF-related mechanisms in atherosclerosis, here we invest

278 Among the TFs with the most localized contributions, we identified

279 such as specific sequences recognized by the TFs and evolutionary conservation, as well as cell type-

280 ely identified, representing over 60% of the TFs in the mouse genome.

281 Analysis of subnetworks surrounding the TFs ORA47, RAP2.6L, MYB59, and ANAC055, using transcript

282 In order to unveil the TFs regulating NHX1 gene expression, which is known to b

283 These TFs were confirmed to interact between themselves and wi

284 , and enrichment of binding motifs for these TFs in alphaTC1/betaTC6 cis-regulatory elements.

285 Mutations involving these TFs affect diverse aspects of megakaryocyte biology, and

286 p-regulated in Hasawi, indicating that these TFs may be associated with the salt and drought stress t

287 25 kb region by independently tethering this TF without coincidental ETS1 binding.

288 Thus, TF synergistically primes FIXa-dependent thrombin genera

289 algorithm is comparable but not superior to TF-SSS, warranting further investigations of algorithm o

290 resent a method to associate known motifs to TFs (MATLAB code is available in Supplementary Materials

291 ing the magnitude of enhancer transcription, TF mRNA expression levels, TF motif P-values, and enrich

292 Two TFs having different thickness and one FP were compared

293 Thus, a previously unrecognized TF-initiated pathway directly yielding FVIIIa-FIXa intri

294 We use TF co-occurrence to construct a filtered, normalized adj

295 ng binding sites interact competitively when TF is limiting but otherwise act additively.

296 Mutants in which TF is not palmitoylated display drastically reduced plas

297 While genome-wide TF ORFeome clone collections are increasingly available,

298 In vitro, FXa stably associated with TF-FVIIa activates FVIII, but not FV.

299 bining existing pharmacogenomic markers with TF activities often improves the stratification of cell

300 s of which transcripts corresponding to WRKY TFs were the most abundant (14.14%).