cis-regulatory
Genomic cis regulatory networks in the early Ciona intestinalis embryo
... a cis-regulatory module that includes Fox binding sites (Oda-Ishii et ...this cis- regulatory element was counted with FDRs of 1% and ...
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Identification of cis-regulatory sequence variations in individual genome sequences
... improved regulatory sequence ...for cis-regulatory element detection over past ...functional regulatory regions, provid- ing the researcher with a refined search space for deter- mining the ...
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Lmx1b targeted cis regulatory modules involved in limb dorsalization
... with cis-regulatory activity (H3K27ac, H3K4me2, p300, RNAP2 and/or Med12) that overlapped Lmx1b-targeted intervals (Visel et ...to regulatory regions rather than ...
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Development of methods for combinational approaches to cis regulatory module interactions
... the regulatory logic gates are a form of transcription factor ...the regulatory systems 37 ...of cis- regulatory functionalities can ...
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Evolution of cis regulatory regions versus codifying regions
... contain cis-regulatory elements, the finding raises the possibility that introns carrying cis-regulatory modules could transpose to other genomic locations where they could exert their ...
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The search for cis -regulatory driver mutations in cancer genomes
... important cis-regulatory mutations have been identified proximally to cancer-associated ...the regulatory regions of genes involved in cancer-associated pathways has been highlighted in the published ...
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Sex-Specific Effects of Cis-Regulatory Variants in Drosophila melanogaster
... relative cis-regulatory activity could be affected by either imprinting or genetic differences between X and/or Y chromosomes (Figure 1C), one gene showed a statistically significant effect (Figure ...
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Identification and characterization of early photoreceptor cis-regulatory elements and their relation to Onecut1
... gene regulatory networks during photorecep- tor genesis, the effects on the regulatory elements described in Table 1 were tested in the flow cytometry assay ...additional cis-regulatory ...
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Identification of three new cis regulatory IRF5 polymorphisms: in vitro studies
... Additional file 1: Note S1: IRF5 haplotypes defined in previous studies and their relationship with systemic lupus erythematosus susceptibility and IRF5 expression. Note S2: RNA-seq study of the IRF5 transcriptome and ...
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The origins of the Drosophila leg revealed by the cis regulatory architecture of the Distalless gene
... dorsoventral (DV) and anteroposterior (AP) axes. In arthropods, the PD axis of the adult leg is subdivided into two broad domains, a proximal coxopodite and a distal telopodite. We show that the progressive subdivision ...
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Identification of cis-regulatory mutations generating de novo edges in personalized cancer gene regulatory networks
... a cis-GoF mutation in two or more ...by cis-GoF mutations in the prostate cancer cell lines DU-145 and PC-3 and in the colon cancer cell line HT-29 (Additional file 1: Table ...candidate ...
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OncoCis: annotation of cis regulatory mutations in cancer
... candidate cis-regulatory mutations, OncoCis was used to annotate the TERT promoter mutations, which are currently the best established example of recurrent cis-regulatory mu- tations found ...
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Cis regulatory properties of medaka synexpression groups
... the regulatory mechanisms that orchestrate their common complex expression pattern remain to be ...their regulatory properties by searching for common regulatory ...into cis-regulatory ...
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Putative cis regulatory elements in genes highly expressed in rice sperm cells
... Background: The male germ line in flowering plants is initiated within developing pollen grains via asymmetric division. The smaller cell then becomes totally encased within a much larger vegetative cell, forming a ...
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Direct regulation of knot gene expression by Ultrabithorax and the evolution of cis regulatory elements in Drosophila
... the identification of regulatory elements (Wasserman et al., 2000; Yuh et al., 2002). We attempted to use conservation to direct the further dissection of kn Mel 1-2330 to define a minimal regulatory ...
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Exact p-value calculation for heterotypic clusters of regulatory motifs and its application in computational annotation of cis-regulatory modules
... studying regulatory regions containing heterotypic clus- ters of TFBSs to distinguish genes that are regulated by given transcription factors from those that are ...on regulatory clusters in ...
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Hybrid Incompatibility Despite Pleiotropic Constraint in a Sequence-Based Bioenergetic Model of Transcription Factor Binding
... -acting regulatory factors and their cis-regulatory ...the regulatory site, and genomic back- ground size) determine the shape of the genotype–phenotype (G-P) map, and interacting allelic ...
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The ABC of the BX C: the bithorax complex explained
... In Drosophila, the bithorax complex (BX-C) controls the identity of each of the segments that contributes to the posterior two-thirds of the fly (Fig. 1, also see Box 1). It does this by regulating the expression of the ...
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Compensatory cis-trans Evolution and the Dysregulation of Gene Expression in Interspecific Hybrids of Drosophila
... major regulatory genes whose effects cascade through the regulatory network (C omai et ...of cis 3 trans interaction at individual genes, however, can be subjected to a rigorous experimental ...the ...
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bHLH dependent and independent modes of Ath5 gene regulation during retinal development
... We have identified bHLH-dependent and -independent modes of Ath5 gene regulation in Xenopus, raising the issue of how they contribute to endogenous Xath5 expression. It is possible that the distal and proximal ...
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