ライフサイエンスコーパス: transcription factor binding site

1 ted promoter regions of which one disrupts a transcription factor binding site.

2 dentified strong enrichment of a common Ets2 transcription factor-binding site.

3 traits in the human brain are located within transcription factor binding sites.

4 rvations to their functions at enhancers and transcription factor binding sites.

5 accessibility, evolutionary conservation and transcription factor binding sites.

6 a widely adopted method to identify putative transcription factor binding sites.

7 to assess the effects of variants on likely transcription factor binding sites.

8 enriched in regions of active chromatin and transcription factor binding sites.

9 ted functional TEF-1 TEC1 AbaA domain (TEAD) transcription factor binding sites.

10 es are the main techniques used to determine transcription factor binding sites.

11 -seq protocol for high resolution mapping of transcription factor binding sites.

12 ed by mutations located in the RAP1 and GCR1 transcription factor binding sites.

13 factor and development genes and enriched in transcription factor binding sites.

14 which is a cluster of evolutionary conserved transcription factor binding sites.

15 erage, with strong enrichment for particular transcription factor binding sites.

16 -induced losses of DNA methylation mapped to transcription factor binding sites.

17 ening to identify polymorphisms that disrupt transcription factor binding sites.

18 the addition of biological features such as transcription factor binding sites.

19 identify cis-regulatory modules with similar transcription factor binding sites.

20 tained a neuronal-specific enhancer and GATA transcription factor binding sites.

21 ent histone affinity and their coverage with transcription factor binding sites.

22 contains multiple activator protein 1 (AP-1) transcription factor binding sites.

23 ers show significant enrichment for NRF2/ETS transcription factor binding sites.

24 GC-boxes were shown to be functional Sp1/Sp3 transcription factor binding sites.

25 sites, promoters, functional enhancers, and transcription factor binding sites.

26 revealed several important cis-elements and transcription factor binding sites.

27 roach to identify a large proportion of true transcription factor binding sites.

28 p) compared with the average length of known transcription factor binding sites.

29 e show that active clusters are hotspots for transcription factor binding sites.

30 with accessibility of key epithelial and EMT transcription factor binding sites.

31 562 polymorphisms that modified thirty-seven transcription factor binding sites.

32 cessible sites were highly enriched for Nfib transcription factor binding sites.

33 ge chromatin domains, but also at individual transcription factor binding sites.

34 o regions of active histone modification and transcription factor binding sites.

35 occupancy are enriched in SP family and WT1 transcription factor binding sites.

36 protein sequences, transcript splicing, and transcription factor binding sites.

37 isms at the 9p21.3 locus disrupt (or create) transcription factor binding sites.

38 taining hematopoietic-specific enhancers and transcription factor-binding sites.

39 ns are enriched for novel noncoding RNAs and transcription factor-binding sites.

40 for some non-B DNA motifs was observed near transcription factor-binding sites.

41 ciprocally low levels of 5mC near but not on transcription factor-binding sites.

42 ci display very different relationships with transcription factor-binding sites.

43 ved "TGT" core promoter motif and unreported transcription factor-binding sites.

44 -wide data sets of histone modifications and transcription-factor binding sites.

45 potential of our network to discover de novo transcription-factor binding sites.

46 characterization of open chromatin peaks and transcription-factor binding sites.

47 f osteoporosis-associated genes, including 4 transcription factor binding sites, 27 histone marks, an

48 d, these data argue for a principal role for transcription factor binding sites, a prediction confirm

49 report the compilation of a large catalog of transcription factor-binding sites across Bacteria and i

50 gy to identify cancer susceptibility SNPs in transcription factor-binding sites across the whole geno

51 Given that these minimal changes in a transcription factor binding site affect latency establi

52 moters, enhancers, silencers, insulators and transcription factor binding sites; all of which play im

53 es suggest that there are many nonfunctional transcription factor binding sites along a genome.

54 entally validated cis-regulatory modules and transcription factor binding sites among the metazoa.

55 Transcription factor binding site analysis of these regi

56 We performed a bioinformatic-based transcription factor binding site analysis on upstream p

57 Finally, using transcription factor binding site analysis, we identifie

58 This SNP maps to the transcription factor binding site and is conserved in 17

59 nes, which lies close to both a double E-box transcription factor binding site and the site of a sing

60 on-occluding nucleosome positioned between a transcription factor binding site and the TATA box regio

61 differentially expressed genes, (ii) finding transcription factor binding sites and (iii) converting

62 RPGR 5'-flanking region uncovered potential transcription factor binding sites and a CpG island.

63 dsQTLs are strongly enriched within inferred transcription factor binding sites and are frequently as

64 or enrichment within genetic pathways and of transcription factor binding sites and characterized com

65 Although some transcription factor binding sites and cis-regulatory el

66 r differentiation efficiency, transcriptome, transcription factor binding sites and DNA-methylation.

67 comparison of ChIP-Seq data sets describing transcription factor binding sites and epigenetic modifi

68 detect various epigenetic phenomena such as, transcription factor binding sites and histone modificat

69 on in regions of incomplete lineage sorting, transcription factor binding sites and human differentia

70 served strong overrepresentation of multiple transcription factor binding sites and miRNA profiles as

71 s an unbiased approach, independent of known transcription factor binding sites and motifs.

72 genes and mutations and/or appearance of new transcription factor binding sites and position of the C

73 alyses of differential chromatin patterns at transcription factor binding sites and promoters as well

74 -UTR mutations are predicted to occur within transcription factor binding sites and reporter gene ass

75 evious observations on epigenetic priming at transcription factor binding sites and suggest here that

76 ploying genomic SELEX to identify vertebrate transcription factor binding sites and target genes and

77 Here, we uncover transcription factor binding sites and target genes empl

78 ensitivity sites, modification of chromatin, transcription factor binding sites and the arrangement o

79 of coding and noncoding elements, including transcription factor binding sites and untranslated regi

80 stand how the 3' RR functions, we identified transcription factor binding sites and used chromatin im

81 genic regions were heavily enriched for AP-1 transcription factor binding sites and were frequently h

82 The rs2494737 risk A allele creates a YY1 transcription factor-binding site and abrogates the sile

83 tions are predicted to disrupt consensus ETS transcription factor-binding sites and are correlated wi

84 s, a larger number and wider distribution of transcription factor-binding sites and downstream genes

85 rs140068132 is located within several transcription factor-binding sites and electrophoretic m

86 e advantage as a consequence of the acquired transcription factor-binding sites and importantly that

87 emically active non-coding elements, such as transcription factor-binding sites and non-coding RNAs.

88 ations in developmental enhancers, validated transcription-factor-binding sites and RNA motifs.

89 ts for GTEx whole-blood eQTLs located within transcription-factor-binding-sites and DNA-hypersensitiv

90 6 bp sequence contains a putative E2F-1/DP-1 transcription factor binding site, and this transcriptio

91 to bacterial enhancers, combining a driver, transcription factor binding sites, and a poised polymer

92 iation results across populations, potential transcription factor binding sites, and analysis of phyl

93 in-DNA binding sites, depleted in permissive transcription factor binding sites, and enriched at acti

94 ormation from the GWAS Catalog, libraries of transcription factor binding sites, and genic characteri

95 equencing, nucleosome positioning/occupancy, transcription factor binding sites, and genomic sequence

96 dated enriched and depleted sites, predicted transcription factor binding sites, and highly-transcrib

97 , co-localized DNase I hypersensitive sites, transcription factor binding sites, and histone modifica

98 nucleotide mutations leading to turnover of transcription factor binding sites, and insertion of cis

99 PET does so by combining data from ChIA-PET, transcription factor binding sites, and protein interact

100 enriched in regulatory chromatin domains and transcription factor binding sites, and showed substanti

101 ions were associated with cell type-specific transcription factor binding sites, and these transcript

102 l time course, genome-wide identification of transcription factor-binding sites, and maps of chromati

103 ific genes; enrichment of cell-type-specific transcription factor binding sites; and genetic polymorp

104 The PU.1, C/EBPbeta, and Runx1 transcription factor binding sites are conserved and con

105 leotide-resolution cleavage patterns at many transcription factor binding sites are derived from intr

106 We show that FOXA2 transcription factor binding sites are enriched at lipid

107 d that genetic variants predicted to disrupt transcription factor binding sites are enriched in cis-e

108 teractions between transcription factors and transcription factor binding sites are essential activit

109 across primate species, but other postulated transcription factor binding sites are not preserved.

110 regulated during stresses and stress-related transcription factor binding sites are prevalent in thei

111 ow transcriptional enhancers and constituent transcription factor binding sites are used in both ance

112 the downregulation of genes containing HIC1 transcription factor binding sites as early as 4 days po

113 enes and showed increased DNA methylation at transcription factor binding sites associated with diffe

114 er regions, being anti-correlated focally at transcription factor-binding sites but positively correl

115 e describe versatile genome-wide analysis of transcription-factor binding sites by combining directed

116 We have previously shown that SNPs within transcription factor binding sites can affect transcript

117 ed broad epigenetic programming of selective transcription factor binding sites coincident with the d

118 n their homotypic analogs and favor specific transcription factor binding site combinations, mimickin

119 r regions was more efficient for identifying transcription factor binding sites compared to sequencin

120 The CONserved transcription FACtor binding site (CONFAC) software pack

121 on that introduces a glucocorticoid receptor transcription factor binding site, confirmed via oligonu

122 dence for positive selection of mutations in transcription factor binding sites, consistent with thes

123 We used this model to analyze the transcription factor binding site content of promoters e

124 Epigenetic changes at transcription factor binding sites correlated significan

125 jects, and identified the presence of common transcription factor binding sites corresponding to gluc

126 or co-localized with known liver-associated transcription factor binding sites, demonstrating the va

127 address this question, we collect ancestral transcription factor binding sites disrupted by an indiv

128 major role in identifying and ranking genes, transcription factor binding sites, DNA methylation regi

129 enables analysis of nucleosome positioning, transcription factor-binding sites, DNA methylation site

130 This analysis identifies three transcription factor binding sites (E-box motifs, along

131 Transcription factor-binding sites (eg, the c-myc-bindin

132 gene ontology enrichment analysis, motifs of transcription factor binding sites enriched in superenha

133 Transcription factor binding site enrichment analysis ve

134 related gene expression patterns and similar transcription factor binding site enrichments in promote

135 e modification states, methylation patterns, transcription factor binding sites, eQTL and higher-orde

136 s and found enrichment for key hematopoietic transcription factor binding sites, especially E2A.

137 ies' such as biological processes, pathways, transcription factor binding sites, etc., one property a

138 that activation of genes associated with the transcription factor binding site for the nuclear factor

139 Transcription factor binding sites for p53, MEF2A and E2

140 a canonical TATA box (-38/-32), and putative transcription factor binding sites for Sp1, EGR1, ZBP-89

141 en the enhancer cassettes contain additional transcription factor binding sites for TetR, a bacterial

142 ' untranslated region that contains specific transcription factor-binding sites for ARABIDOPSIS THALI

143 In the same region, sexalleles contain transcription factor-binding sites for DNA BINDING WITH

144 is successful in extracting known composite transcription factor binding sites from real datasets.

145 To characterize transcription factor binding site function on a large sc

146 es public data on gene expression, pathways, transcription factor binding sites, gene and protein seq

147 ded predictive models of how combinations of transcription factor binding sites generate specific lev

148 ns revealed the presence of several putative transcription factor binding sites generated by the dupl

149 The genome-wide map of these transcription factor binding sites has been termed the c

150 variants in CCCTC-binding factor (CTCF) and transcription factor binding sites have been mechanistic

151 We find that, on average, transcription factor binding sites have experienced some

152 g over splice sites and surrounding putative transcription factor binding sites highlights the regula

153 ccessfully used for genome-wide profiling of transcription factor binding sites, histone modification

154 This data helps illuminate transcription factor-binding sites, histone marks, chrom

155 Computational approaches to transcription factor binding site identification have be

156 This novel transcription factor binding site identification protoco

157 uding rs12194974 (G>A), an SNP in a putative transcription factor binding site in the LIN28B promoter

158 te-specific deletion or mutation of an HES-1 transcription factor binding site in this region also ab

159 ting data define accurate maps of functional transcription factor binding sites in both enhancers at

160 ilico modeling to nominate several candidate transcription factor binding sites in both Ogt (i.e. the

161 r gene regulation and that contains multiple transcription factor binding sites in close proximity.

162 Here, we report a genome-wide map of 827,000 transcription factor binding sites in human lymphoblasto

163 erformance of the YGP1 promoter by modifying transcription factor binding sites in its upstream activ

164 comparison of EBNA3 binding sites with known transcription factor binding sites in LCL GM12878 reveal

165 Most of the other transcription factor binding sites in LCR HS2 or in the

166 r(2), a web-based system for the analysis of transcription factor binding sites in multiple genomes.

167 t a general algorithm that allow to identify transcription factor binding sites in one newly sequence

168 and Integrated Discovery (DAVID) analysis of transcription factor binding sites in palmitate-modified

169 cale PWM scores and estimate the strength of transcription factor binding sites in quantitative studi

170 nally, we identified distinct enrichments of transcription factor binding sites in rods and cones, re

171 ion/mutation analysis revealed that multiple transcription factor binding sites in the +286/+690 regi

172 a result of mutations that abolish essential transcription factor binding sites in the limb-specific

173 nt Nfe2l2 and other mitochondrial biogenesis transcription factor binding sites in the promoter regio

174 specific and dependent on the repertoire of transcription factor binding sites in the promoters of l

175 nome coordinates of evolutionarily conserved transcription factor binding sites in the proximal promo

176 its transcriptional activity, and identified transcription factor binding sites in the proximal promo

177 depends on the presence of functional GATA-2 transcription factor binding sites in the UL144 promoter

178 oRNAs important for this switch and putative transcription factor binding sites in their promoters.

179 ights of this issue are six databases of the transcription factor binding sites in various organisms

180 We proposed to search for transcription factor binding sites in vector spaces.

181 feasibility of small-molecule targeting of a transcription factor-binding site in Mediator as a novel

182 reported duplication or deletion of diverse transcription factor-binding sites in the viral promoter

183 rmatics analysis identified over-represented transcription factor-binding sites in this network of co

184 ed the presence of DNaseI hypersensitive and transcription factors binding sites in these regions.

185 uced genes and is associated with intestinal transcription factor binding sites, including those for

186 romo 3.0.2 online tool for the prediction of transcription factor binding sites indicated the presenc

187 r distinctive regulatory chromatin marks and transcription factor binding sites indicative of active

188 lude differentially methylated CpGs/regions, transcription factor binding sites, interacting chromati

189 When a transcription factor binding site is located within a nu

190 Prediction of transcription factor binding sites is an important chall

191 Identifying the locations of transcription factor binding sites is critical for under

192 uence consisting of neighboring ETS and AP-1 transcription factor binding sites is enriched near cell

193 Identification of transcription factor binding sites is necessary for deci

194 ter nucleosomes that do not directly occlude transcription factor binding sites is not obvious.

195 Genome-wide prediction of transcription factor binding sites is notoriously diffic

196 1-dependent ADH2 promoter, or just the major transcription factor binding site, is sufficient to conf

197 a novel c-maf (required for IL-4 expression) transcription factor binding site just upstream of the d

198 or 1 with an IFN-responsive sequence element transcription factor binding site located in the first p

199 an excess of human-specific substitutions in transcription factor binding sites located within human

200 Synthetic restoration of a single transcription factor binding site lost in the snake line

201 tures (e.g. single nucleotide polymorphisms, transcription factor binding sites, methylation peaks, e

202 ome datasets identifies associations between transcription factor binding sites, methylation, nucleot

203 peak-calling, aims to find the locations of transcription factor binding sites, modified histones or

204 h there are tools for ab initio discovery of transcription factor-binding sites, most do not provide

205 Naive Bayes classifiers using transcription factor binding site motifs accurately pred

206 Based on both enrichment for transcription factor binding site motifs and co-occupanc

207 ation, are used to predict CRMs: clusters of transcription factor binding site motifs, non-coding DNA

208 Finally, analysis of transcription factor-binding site motifs of differential

209 anscription start site containing three SP-1 transcription factor-binding sites; mutation of these VE

210 oding changes (n = 13), direct disruption of transcription-factor binding sites (n = 3), and tissue-s

211 entative protein components of each of these transcription factor binding sites, namely c-Jun, STAT3,

212 ed chromatin accessibility and likelihood of transcription factor binding site occupancy by HSPC regu

213 < 1e-05) CpGs are significantly enriched for transcription factor binding sites of EBF1, EP300, and C

214 py number, spacing, combination and order of transcription factor binding sites on gene expression.

215 to promote tumorigenesis, such as disrupting transcription factor-binding sites or functions of non-c

216 Within these CRMs many transcription factor-binding sites, particularly the hot

217 t genes, mammalian interspersed repeats, and transcription factor-binding sites (PcG/MIR/TFBS), was a

218 Transcription factor binding site polymorphisms are corr

219 are highly enriched for erroneously inferred transcription factor binding sites, positions of nucleos

220 plified integrative energy function improved transcription factor binding site prediction accuracy an

221 a simplified integrative energy function for transcription factor binding site prediction.

222 st fragment-based method for structure-based transcription factor binding sites prediction.

223 gion analysis of these genes revealed common transcription factor binding sites, providing insight in

224 aging had neighboring sequences enriched for transcription-factor binding sites related to immune mod

225 2 might be located in an enhancer region and transcription factor binding sites, respectively.

226 sequences resulting in lower noise and more transcription factor binding sites resulting in higher n

227 ntains information about regulatory regions, transcription factor binding sites, RNA binding sites, r

228 olycomb response elements, chromatin states, transcription factor binding sites, RNA polymerase II re

229 ents an alternative mechanism for regulating transcription factor-binding site selection that could a

230 mputational analysis that revealed potential transcription factor binding sites shared by the majorit

231 Focal regions of low methylation linked to transcription-factor-binding sites shed light on differe

232 A search for transcription factor binding sites showed that 93% of th

233 al selection has profoundly influenced human transcription factor binding sites since the divergence

234 ifferences impact small sequence motifs like transcription factor binding sites such as estrogen resp

235 inct positioning, length, and enrichment for transcription factor binding sites suggest these CNSs pl

236 , and that they are particularly enriched in transcription factor binding sites, suggesting that many

237 In addition, transcription factor binding sites surrounding the assoc

238 ets and clusters of evolutionarily conserved transcription factor binding sites, taking advantage of

239 ound for specific promoter elements, such as transcription-factor binding sites, TATA-like elements,

240 ral selection in non-coding regions [such as transcription-factor binding sites (TF-binding sites) an

241 Transcription factor binding site (TFBS) analysis confir

242 In addition, transcription factor binding site (TFBS) analysis was pe

243 nbound DNA after ChIP, is designed to reveal transcription factor binding site (TFBS) boundaries with

244 recently indicated the likely importance of transcription factor binding site (TFBS) copies in effec

245 been successfully applied to the problem of transcription factor binding site (TFBS) motif discovery

246 matrix (PWM) is a useful representation of a transcription factor binding site (TFBS) sequence patter

247 We also suggest one mechanism, transcription factor binding site (TFBS) turnover, which

248 of genome regularities as well as to improve transcription factor binding sites (TFBS) and gene regul

249 with a complexity assessment of co-occurring transcription factor binding sites (TFBS) can identify c

250 Common putative transcription factor binding sites (TFBS) found at these

251 d through conservation of the composition of transcription factor binding sites (TFBS) in a regulator

252 erformed computational analysis of consensus transcription factor binding sites (TFBS) in the genes o

253 r activity in cell lines and define possible transcription factor binding sites (TFBS).

254 For every possible transcription factor-binding site (TFBS)-putatively regu

255 trand separation - was the best predictor of transcription factor-binding sites (TFBS) followed by fe

256 activity in apes involves epistasis between transcription factor binding sites (TFBSs) ancestral to

257 nificantly, we developed a method to predict transcription factor binding sites (TFBSs) and their cog

258 Transcription factor binding sites (TFBSs) are most comm

259 Transcription factor binding sites (TFBSs) are the funct

260 Accurate annotation of transcription factor binding sites (TFBSs) at genome sca

261 greatly improved the reliability with which transcription factor binding sites (TFBSs) can be identi

262 : The ability to efficiently investigate transcription factor binding sites (TFBSs) genome-wide i

263 Typical approaches for predicting transcription factor binding sites (TFBSs) involve use o

264 Binding of transcription factors to transcription factor binding sites (TFBSs) is key to the

265 Some transcription factor binding sites (TFBSs) near the tran

266 and made it possible to map the positions of transcription factor binding sites (TFBSs) with high pre

267 r, non-coding DNA binding sequences, such as transcription factor binding sites (TFBSs), are frequent

268 erentially affected CpGs in or near specific transcription factor binding sites (TFBSs), implicating

269 Gene promoters typically contain multiple transcription factor binding sites (TFBSs), which may va

270 (ChIP-Seq) methods that provide genome-wide transcription factor binding sites (TFBSs).

271 ions between transcription factors (TFs) and transcription factor binding sites (TFBSs, also known as

272 lications of BIRD-predicted DH in predicting transcription factor-binding sites (TFBSs), turning publ

273 s have fewer nucleosome-depleted regions and transcription factor-binding sites than monovalent regio

274 This approach identified SNPs in specific transcription factor binding sites that are located near

275 Finally, we identify transcription factor binding sites that are overrepresen

276 lly through mechanisms other than changes in transcription factor-binding sites that drive patterning

277 We also identify transcription factor-binding sites that may drive these

278 y biological parameters: the strength of the transcription factor binding sites, the concentration of

279 s and their dense clusters ('epicentres') of transcription factor binding sites undergo remodelling u

280 ic single nucleotide variants within or near transcription factor binding sites upstream of key genes

281 d a structure-based method for prediction of transcription factor binding sites using an integrative

282 The presence of putative WRKY transcription factor binding sites (W-boxes) in the prom

283 s containing patterns from 12 liver-specific transcription factor binding sites was assayed in mice a

284 ranscription initiation clusters with mapped transcription factor binding sites, we define 2361 trans

285 nsensus sequence motifs containing predicted transcription factor binding sites were enriched in geno

286 group target genes; developmentally related transcription factor binding sites were overrepresented

287 nd destabilized nucleosomes, for example, at transcription factor binding sites where nucleosomes com

288 ensitive sites that frequently coincide with transcription factor binding sites, whereas broader doma

289 lly, we provided direct comparison of likely transcription factor binding sites, which are useful to

290 ore promoter regions, including Sp1 and TATA transcription factor binding sites, which increased the

291 to identify predictive combinations of short transcription factor-binding sites, which determine the

292 ulatory elements, particularly enhancers and transcription-factor-binding sites, which allow identifi

293 Ultimately, the comprehensive mapping of transcription factor binding sites will identify feature

294 tterns in terms of computationally predicted transcription factor binding sites with singular value d

295 onsiderable effort is focused on identifying transcription factor binding sites, with the goal of pre

296 n the PWS-IC in brain cells, then identified transcription factor binding sites within a subset of th

297 upancy at heterochromatic regions but TFIIIC transcription factor binding sites within boundary eleme

298 repressors, like Su(H), and organization of transcription factor binding sites within cis-regulatory

299 e potential to improve prediction of precise transcription factor binding sites within regions identi

300 Further examination revealed potential transcription factor-binding sites within rs4972593 and