ライフサイエンスコーパス: gene network

1 iption factor, PU.1, a central hub in the AD gene network.

2 ighlights the complexity of the spliceosomal gene network.

3 ht the hierarchical organisation of the otic gene network.

4 stage-specific architecture of the pair-rule gene network.

5 multiple known and new targets in the p75NTR gene network.

6 ional annotations in an Arabidopsis thaliana gene network.

7 s could be traced to specific immune pathway gene networks.

8 inhibited TGF-beta, VEGFA, and inflammatory gene networks.

9 lenge to engineering sophisticated synthetic gene networks.

10 encies and non-linear dynamics that exist in gene networks.

11 were disrupted by CIE treatment in microglia gene networks.

12 s and configurations of phenotype-associated gene networks.

13 an a similar approach for joint inference of gene networks.

14 matory profile and altered NF-kappaB-related gene networks.

15 yping samples based on deregulation of their gene networks.

16 ing, gene co-expression, homology and cancer-gene networks.

17 anisms of individual genes, let alone entire gene networks.

18 th bioinformaticians who research stochastic gene networks.

19 ylation bidirectionally regulated these same gene networks.

20 ic, possibly oscillatory, data for different gene networks.

21 d, capable of discovering large co-regulated gene networks.

22 so benefits the rational design of synthetic gene networks.

23 cover redundant genes and to explore complex gene networks.

24 enin), which expressed negatively correlated gene networks.

25 n correlates with increased heterogeneity of gene networks.

26 tions and facilitate the characterization of gene networks.

27 mutations involving the deregulation of NDD-gene networks.

28 discovery of potentially causal pathways and gene networks.

29 -specific transcriptome analysis to identify gene networks activated in epidermis, cortex, and pericy

30 reveals remarkable similarities between the gene networks active during fetal and adult gammadelta T

31 we explore the transcriptional response and gene networks active in adipose tissue of rhesus macaque

32 Analysis of gene networks affected by TEADi and YAP1/TAZ knockdown i

33 Both gene network algorithms identified consensus or equivale

34 HumanNet now comprises a hierarchy of human gene networks, allowing for more flexible incorporation

35 rdant with proosteoblast and proinflammatory gene network alterations in human NOTCH1 heterozygous en

36 milies to identify significant cell-specific gene network alterations in SCZ, these studies support a

37 Pathway Analysis (IPA) was used to identify gene networks altered in the presence of S. haematobium

38 Gene network analyses showed multiple known and new targ

39 of accounting for regulatory annotations in gene network analyses.

40 Finally, gene network analysis and conditional deletion revealed

41 high-throughput screen and oxidative stress gene network analysis identified the glutathione-regulat

42 expression at the level of individual genes, gene network analysis identified two cortical and two hi

43 Further gene network analysis predicts that NMIIA and NMIIB may

44 A gene network analysis revealed putative key regulators o

45 Gene network analysis revealed that SCZ and autism spect

46 We used unbiased gene network analysis to evaluate functional convergence

47 the NS2B3 complex inhibited the antioxidant gene network and contributed to the progressive increase

48 ant dysregulation of the estrogen-responsive gene network and expression of ESR1 and ESR2 in esophage

49 toregressive prior to integrate a functional gene network and to share information between genes know

50 sion network analysis to create interspecies gene networks and assess the capacity of each stress par

51 To define the gene networks and developmental processes controlled by

52 involving temporal dysregulation of specific gene networks and morphological growth acceleration.

53 detecting disease-linked SNPs and identifies gene networks and network modules mediating the SNP effe

54 fine molecular characterization of targeted gene networks and pathway analysis.

55 Differential gene expression, gene networks and pathways, transcription factors, and n

56 o, a fast and lightweight R package to infer gene networks and perform MRA from gene expression data,

57 integration, IDR facilitates the analysis of gene networks and reveals functional interactions that a

58 ty to modulate both IRF4- and MYC-controlled gene networks and ROCK inhibition could represent an att

59 d RNA-Seq to identify differentially altered gene networks and their association with PCa progression

60 We also identified several gene networks and their constituent genes that are most

61 ogical processes and discovered co-regulated gene networks and transcription factors present at disti

62 to apply in the context of complex, natural gene networks and unknown interactions.

63 te transcription of cell-identity specifying gene networks, and are critical in promoting cancer.

64 does not exploit the similarity between two gene networks, and it is thus suboptimal.

65 rated with information from genomic changes, gene networks, and master immunoregulatory genes, and th

66 tabolic engineering, the design of synthetic gene networks, and protein manufacturing.

67 f antibiotics, the construction of synthetic gene networks, and the development of many cutting-edge

68 In addition to identifying the genes, networks, and pathways involved in the pair-bondi

69 Integrative gene network approaches enable new avenues of exploratio

70 rks, and compare their performance to single gene network approaches.

71 fic atherosclerotic arterial wall regulatory gene network (AR-RGN) causal for CAD involving RNA proce

72 e protein pathways represented in this svPPA gene network are critical regulators of RNA metabolism a

73 al and positional patterns of expression and gene networks are almost entirely different.

74 ed datasets has verified that these specific gene networks are up regulated throughout the tumor prog

75 ight into the complex, dynamic modulation of gene networks as well as their impact on human disease,

76 nderstand the diverse functions of genes and gene networks, as well as help in the design of specific

77 anscripts is present in the most significant gene network associated with PTSD.

78 The activation of gene networks associated with adaptive immunity was link

79 nsus signatures were sought in 30 regulatory gene networks associated with CAD and CAD-related phenot

80 VDD induced dysregulation of gene networks associated with growth hormone and insulin

81 re accompanied by differential expression of gene networks associated with neurodevelopment in contro

82 differentially expressed genes and distinct gene networks associated with opioid abuse, specific gen

83 e involves the complex regulation of diverse gene networks associated with the physical demands of mi

84 urthermore, the changes of the co-expression gene network between diabetic and healthy donor-derived

85 present BaiHui, a brain-specific functional gene network built by probabilistically integrating expe

86 ic evidence for control of the gammadeltaT17 gene network by HEB.

87 s for zebrafish and mouse genes to construct gene networks by calculating semantic similarity between

88 These data also validate our multiscale gene networks by demonstrating how the networks intersec

89 hese results, we assessed the FOXP3 and EZH2 gene networks by RNA sequencing in isolated intestinal C

90 he timing and function of components of this gene network can account for the evolution of Citrus tho

91 Large gene networks can be dense and difficult to interpret in

92 Here, we show that synthetic gene networks can be engineered to compensate for crosst

93 However, gene network cascades can change within minutes to hours

94 mechanisms by which pioneer factors initiate gene network changes and will ultimately contribute to o

95 complexity in the evolution of developmental gene networks: changing protein-protein interactions cou

96 and adult social isolation better reproduce gene networks characteristic of human MDD.

97 iants within the network leads to changes in gene network connectivity and the emergence of a reorgan

98 In conclusion, gene network connectivity is highly informative for dise

99 Regarding cancer gene networks construction and gene function prediction,

100 m deregulation of FOXP3/EZH2-enforced T cell gene networks contributing to the underlying intestinal

101 Our data suggest that the basic gene network controlling fruit ripening is conserved in

102 volutionarily conserved and species-specific gene networks controlling glial quiescence, reactivity,

103 Transcription factors regulate gene networks controlling normal hematopoiesis and are f

104 By contrast, the gene networks coordinated by CREB in astrocytes are unkn

105 Gene network correction by the most efficacious therapeu

106 and artificial cells, where RNA produced by gene networks could fuel the assembly of nucleic acid co

107 es, suggesting UPF3B-dependent NMD regulates gene networks critical for cognition and behaviour.

108 igenetic silencing of oncogenic TBXT, alters gene networks critical to survival, and represents a pot

109 Moreover, analysis of the gene network derived from APOE varepsilon3/4 patient ind

110 Cellular genes and gene networks differentially expressed during virus infe

111 dentify small molecules that broadly correct gene networks dysregulated in a human induced pluripoten

112 Gene networks dysregulated in PMD included inflammatory

113 for the TXTL community interested either in gene network engineering or in biomanufacturing beyond t

114 We identify topologically replicable gene networks enriched for diverse immune functions incl

115 Gene networks enriched for myeloid cells were anticorrel

116 genes, cis regulation, and the structure of gene networks, epigenetics, and novel genes.

117 cting variations in the function of the DAT1 gene network (ePRS-DAT1) in the prefrontal cortex and ex

118 The resulting gene network exhibits reduced crosstalk in the sensing o

119 nes into the existing ectopic mineralization gene network expands the current knowledge on the comple

120 sgnesR (Stochastic Gene Network Expression Simulator in R) is an R package

121 provide a rational basis for targeting this gene network for radiosensitization.

122 ct virtual cell-lineage maps and provisional gene networks for 41 neural subtypes that comprise the l

123 ork analysis identified separate coexpressed gene networks for acylsugar metabolism (including six tr

124 eated adherent cell transcriptome identified gene networks for T cells, DNA damage and replication, a

125 data permitted development of comprehensive gene networks for two major breeding traits, flowering t

126 acean ancestor could account for the similar gene networks found in the glandular and respiratory org

127 Gene networks found only in NAFC-exposed fish suggest NA

128 The numerous cellular genes and gene networks found to be differentially expressed durin

129 ped a web server that efficiently constructs gene networks from expression data.

130 Reconstructions of gene networks from gene expression data greatly facilita

131 and versatile approach to detect oscillatory gene networks from snapshot single-cell data addressing

132 el members of gene groups, assess how well a gene network groups known sets of genes, and determines

133 Human gene networks have proven useful in many aspects of dise

134 We previously developed a human functional gene network, HumanNet, by integrating diverse types of

135 nfluenced by regulatory genetic variants and gene networks, identify novel splice-altering variants m

136 us, and a lack of knowledge of the conserved gene networks-if any-that are under its control.

137 transcriptional activity of STAT3-regulated gene networks implicated in cell proliferation and migra

138 d robust evidence for abnormal expression of gene networks important for the regulation and implement

139 to promoters revealed an extended microglia gene network in AD.

140 cistrome, implicating a myeloid PU.1 target gene network in AD.

141 Here, we show decision-making by a bistable gene network in artificial cells with constant protein t

142 egulation of key lncRNAs affecting important gene network in key cancer pathways associated with pert

143 mplex as a key regulator of the self-renewal gene network in organ of Corti progenitor cells.

144 by the fine regulation of the Zn homeostasis gene network in roots of A. thaliana.

145 f PD pathology, perturbs a circadian/mitotic gene network in striatal neurons.

146 systems genetics to identify a pro-fibrotic gene network in the diseased heart and show that this ne

147 We use the gap gene network in the early fly embryo as an example to sh

148 ely benchmarked it to infer context-specific gene networks in 39 human tumor and 27 normal tissue dat

149 s a pivotal role in the regulation of global gene networks in a cell type-dependent manner and is ind

150 letion in mouse, the complexity of imprinted gene networks in brain nor the molecular basis of system

151 ntial for cellular reprogramming, and rewire gene networks in cancer cells.

152 However, a robust map of immune-related gene networks in circulating human cells, their interact

153 Recent studies have highlighted the role of gene networks in disease biology.

154 al mechanism whereby cocaine alters specific gene networks in dlPFC neurons.

155 Our analyses revealed distinct immunity gene networks in each cell type.

156 e release of selective constraint on somatic gene networks in embryogenesis, thus leading to accelera

157 pitulate the transcriptional organization of gene networks in human MDD.

158 ed transcriptional regulators and downstream gene networks in human T(reg) cells that could be target

159 d a novel role for miR-92 and its associated gene networks in immunosuppression.

160 Gene networks in living cells can change depending on va

161 pes, the damaging effect of the variants and gene networks in order to identify loci-trait associatio

162 ndings demonstrate novel [Ca(2+) ] regulated gene networks in podocytes deepening our understanding o

163 first-generation model, built from existing gene networks in Saccharomyces, captures most known auto

164 eliable and scalable approach to investigate gene networks in the diverse P. fluorescens group.

165 of global reprogramming of the inflammatory gene networks in the innate immune cells are poorly unde

166 iptome level, DEHP significantly upregulated gene networks in the intestine associated with helper T

167 We have previously reconstructed gene networks in the striatum of a population of (C57BL/

168 es for specific tumor subpopulation-enriched gene networks in tumorigenesis.

169 These gene networks included immunity, inflammatory response,

170 iR-96, compared to the reverse, identified a gene network including several RARgamma target genes (e.

171 Arabidopsis this process is controlled by a gene network, including components of the signalling pat

172 ytokine stimulation, which revealed distinct gene networks individually regulated by FOXP3 and PRDM1,

173 Gene network inference and master regulator analysis (MR

174 p53 controls transcription of a wide-ranging gene network involved in apoptosis, cell cycle arrest, D

175 ed that defense responses were aggravated by gene networks involved in hypersensitive responses (PAR1

176 lls, providing a better understanding of the gene networks involved in immune regulation.

177 Cytokine activation of cells induces gene networks involved in inflammation and immunity.

178 jective was to identify individual genes and gene networks involved in metabolizing fenbendazole (FBZ

179 estigations into the mechanisms of genes and gene networks involved in the vulnerability to, and cons

180 cer growth; however, the specific downstream gene networks involved in their activity are not complet

181 with hippocampal sclerosis tissue as well as gene networks involving neuronal and glial mechanisms th

182 Learning the underlying details of a gene network is a major challenge in cellular and synthe

183 enesis pathway requires that the appropriate gene network is activated and the antagonist network is

184 Importantly, the WWP2-regulated pro-fibrotic gene network is conserved across different cardiac disea

185 Computer simulations suggest that this gene network is sufficient to spontaneously polarise the

186 Identifying the differential changes in gene networks is very important to understand molecular

187 rable approach would be clearly to infer two gene networks jointly, which can yield improved estimate

188 At the gene network level, distinct genetic paths were used to

189 rturbed sleep and affective functions at the gene network level.

190 that introduce compensatory crosstalk at the gene network level.

191 ence that WIN site inhibitors act to repress gene networks linked to protein synthesis homeostasis.

192 s implicate that dysregulation of functional gene networks may be involved in the emergence of non-mo

193 isease architectures, but the information in gene networks may be subsumed by regulatory annotations,

194 tion mechanisms, and analysis of coexpressed gene networks may help to clarify SCZ molecular basis.

195 ing proinflammatory and steroid biosynthetic gene networks, may represent biomarkers and molecular ta

196 Here we took advantage of a trans-regulated gene network (MMnet, macrophage multinucleation network)

197 me points of gene expression data along with gene network modeling to identify transcription factors

198 es extract a detailed description of how the gene network modulates the genetic effects on phenotypes

199 In this study, we focus on finding gene-gene network modules which are functionally similar in n

200 nomic data types, including gene expression, gene network, mutation data, and contains a two-stage pr

201 Using Citrus, we characterize a gene network necessary for thorn development.

202 e show that Myc transcriptionally controls a gene network of subcellular mitochondrial trafficking th

203 RACIPE was further applied to a proposed 22-gene network of the Epithelial-to-Mesenchymal Transition

204 We further created an integrated regulatory gene network of the salt response in P. euphratica by co

205 acetylation enhancer enrichment dynamics and gene networks of coregulation.

206 The gene networks of EMT, angiogenesis, immune-suppression a

207 etworks and identified metastasis-correlated gene networks of immune-suppression, epithelial-mesenchy

208 ression regulation are vital for engineering gene networks of increasing scales and complexity with b

209 suppression of certain regulatory genes and gene networks, our study demonstrates how chromatin remo

210 or organ samples, but most of the functional gene networks overlapped.

211 s biology approach to delineate upper-airway gene network patterns underlying asthma exacerbation phe

212 at a gene network similar to the insect wing gene network (preWGN) operates both in the crustacean te

213 ltering the activity of AR-RGN, a regulatory gene network promoting foam cell formation and risk of C

214 parental expression patterns, co-expression gene network properties, and genomic loci responsible fo

215 , transcription, protein domain content, and gene network properties.

216 servation in the developmental processes and gene networks regulated by LEC1 in two dicotyledonous pl

217 h bioinformatics pipelines to identify novel gene networks regulated by particular epigenetic modific

218 Interrogation of the gene networks regulated by PRH and Notch3 reveals that u

219 Pathway analysis identified gene networks regulating stem cell pluripotency, Wnt sig

220 ene expression RNA-seq datasets, to identify gene network regulatory modules associated with GBM.

221 Both affected a functional gene network related to cell death and survival.

222 nes were downregulated and co-expressed in a gene network related to immune cell functions.

223 THC altered functional gene networks related to cell morphogenesis, dendritic d

224 nalyses revealed an effect of cell ageing on gene networks related to neurogenesis, telomere maintena

225 , less conserved, and less well connected in gene networks relative to GM genes.

226 Functional gene networks, representing how likely two genes work in

227 This gene network repurposing strategy can be extended to oth

228 Charting a temporal path in gene networks requires linking early transcription facto

229 l types; dysregulation of cell-type-specific gene networks results in birth defects, which affect 5%

230 d failing and non-failing cardiac regulatory gene networks, revealing important regulators and cardia

231 Developmental dynamics in Boolean models of gene networks self-organize, either into point attractor

232 existing algorithms can be used to infer two gene networks separately from gene expression data under

233 ctional analyses in Parhyale, we show that a gene network similar to the insect wing gene network (pr

234 ion initiation is common to and preserved in gene network structure with the ASD cortical transcripto

235 plement subnetwork identified by multi-scale gene network studies of postmortem human AD brain.

236 g interest in combining gene expression with gene networks such as protein-protein interaction (PPI)

237 clones had greater activation of EMT-related gene networks than parental Suit2 cells, and forced over

238 We discovered a perturbed gene network that includes highly expressed genes during

239 alyses of brain tissue, we identified an A2M gene network that includes regulator of calcineurin (RCA

240 how that CHD7 fine-tunes the expression of a gene network that is critical for cardiac NCC developmen

241 from brains of resilient mice to identify a gene network that is unique to resilience.

242 indings identify heterochronic dynamics of a gene network that, while established earlier in developm

243 aring the coherence of molecular-interaction gene networks that accounts for the network size and sha

244 In an effort to uncover gene networks that are associated with the Sw-7 resistan

245 aster circuits: virus-encoded autoregulatory gene networks that autonomously control viral expression

246 ver, the prevalence of the structures within gene networks that drive these dynamical behaviours, suc

247 scriptomic findings of miR-128 in regulating gene networks that govern membrane excitability.

248 bioinformatic analysis identified two novel gene networks that may underlie normal MEC function.

249 urbNet, a statistical framework for learning gene networks that modulate the influence of genetic var

250 ntA were very different, suggesting that the gene networks that pattern a wing have diverged consider

251 , transient (lasting <24 hours) induction of gene networks that promote lipolysis and adipogenesis in

252 ne model annotations, expression atlases and gene networks that provide information about putative fu

253 Germ-cell transcription factors control gene networks that regulate oocyte differentiation and p

254 about the global transcriptomic programs or gene networks that regulate these gateway progenitors in

255 e not been shown before, expanding the clock gene networks that require LUX function.

256 s where they interact, and the communicating gene networks that they engage in cancer.

257 also discovered differentially co-expressed gene networks that were functionally associated with per

258 tion-seq analyses of NRSF targets identified gene networks that, in addition to Crh, likely contribut

259 For each gene network, the network connectivity annotation was st

260 ches to the model-driven design of synthetic gene networks, the fast and portable sensing of compound

261 of interactions between genes yield distinct gene networks, there is the need to integrate different

262 For each gene network, these pathway+network annotations were str

263 We show that cis-regulatory elements and the gene networks they regulate direct the formation and fun

264 to identify and validate specific regulatory gene networks through which ART drugs may promote CAD.

265 This process often results in genes network through which a certain biological mechani

266 ted a computer-assisted inspection of a drug-gene network to in silico repurpose drugs that work like

267 s data from public databases and linked this gene network to postsynaptic dopamine signaling in the s

268 of perturbation from genetic variants to the gene network to the phenotype network along with the net

269 g the fundamental contributions of genes and gene networks to bacterial physiology and human health.

270 as used the engineered assembly of synthetic gene networks to create a wide range of functions in bio

271 amework that integrates multi-omics data and gene networks to infer risk genes in GWAS loci.

272 l- and chronologic model of cardioprotective gene networks to prevent left ventricular (LV) adverse r

273 PFC-NAcc gene network topological analyses, following cocaine exp

274 Gene network transitions in embryos and other fate-chang

275 d radioresistant properties of cancer cells, gene networks triggering the HIF-1-mediated reprogrammin

276 roGAdNet) inference, that jointly infers two gene networks under different conditions and then identi

277 -induced constraints on the growth-promoting gene networks under the control of Hippo-Yorkie signalin

278 These findings enabled identification of a gene network underlying AF; our experimental and analyti

279 explore this organelle organization and the gene network underlying it.

280 We identify key regulators of sex-specific gene networks underlying MDD and confirm their sex-speci

281 o simulate gene expression data from a given gene network using the stochastic simulation algorithm (

282 Moreover, derepression of this gene network was associated with RUNX1 DNA binding and t

283 Using a cell-free gene network we programmed molecular interactions that c

284 ed pathway-trait pairs, for each of the four gene networks, we constructed pathway+network annotation

285 Next, for each of four published gene networks, we constructed probabilistic annotations

286 To permit high-throughput analysis of gene networks, we have implemented a set of very efficie

287 These anatomy-based gene networks were semantic networks, as they were const

288 tly dysregulated genes within the functional gene network which capture three distinct biological pro

289 lves a small, and not completely defined two-gene network which governs a potentially bi-stable switc

290 The Arabidopsis circadian oscillator is a gene network which orchestrates rhythmic expression acro

291 nd gain-of-function datasets reveals complex gene networks which control drug response and illustrate

292 ressed a hepatocyte nuclear factor 4A-driven gene network, which was down-regulated in mouse hepatocy

293 vides a valuable tool for finding changes in gene networks, which may aid the discovery of gene-gene

294 activate markedly distinct lineage-specific gene networks while turning off or rewiring pluripotency

295 teraction counts within a phenotype-specific gene network, while the external degree distribution cou

296 in T(reg) cell function, coregulates another gene network with SATB1 and is important for T(reg) cell

297 est that our methods can be used to identify gene networks with dysregulated pairwise interactions, a

298 We integrated these anatomy-based gene networks with mouse and zebrafish PPI networks retr

299 Evaluating gene networks with respect to known biology is a common

300 c and comparative analysis of the p63 target gene network within the integrated framework of the tran