Global ETD Search
Search theses and dissertations gathered from participating repositories worldwide. Every result links back to the library that holds it. No account is needed.
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Showing 1 to 17 of 17 for “"Transcription Factor Binding Site"”.
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Systematic determination of a transcription factor/binding site functional interaction landscape
… and internal signals is central to survival. Transcription factors are a major class of regulatory proteins that specifically bind DNA to modulate the expression of targeted genes. While they have been extensively studied, major questions remain about the protein-DNA interaction underlying …
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De Novo Transcription Factor Binding Site Discovery: A Machine Learning And Model Selection Approach
… simple models for the positional distribution of transcription factor binding sites (TFBS) to the problem of TFBS discovery. As alternate measures of positional specificity, log-likelihood ratios for the three models are calculated and treated as features to classify TFBSs as biologically relevant …
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Extraction and identification of frequent sequential patterns in transcription factor binding site organization of enhancers
… has created vast arrays of data correlating binding sites and regulatory elements with genome regions. There has been great interest in developing new computational approaches that leverage these annotations in order to better understand the layout and organization of eukaryotic genomes and …
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Mitochondrial respiratory defects induces claudin 1 expression via ROS-mediated HSF1 activation
… most effectively induced Cln-1 expression at transcriptional level, accompanied by increase in mitochondrial ROS production. Treatment of H2O2 directly induced Cln-1 expression, implying that Cln-1 induction was mediated by mitochondrial ROS. Interestingly, Cln-1 promoter region (-2700bp ~ …
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Duplication is a prominent mechanism of recent gene birth in Caenorhabditis elegans
… a highly proliferative transposon harbouring a transcription factor binding site (TFBS) and use it to address the question of transposon co-option in this model organism. Finally, using this dataset, I show that tandem gene duplication is a prominent gene birth mechanism, whereas horizontal gene …
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Characterization of lin-42/period transcriptional regulation by the Ikaros/hunchback-family transcription factor ZTF-16 in Caenorhabditis elegans
… has shown that ZTF-16 is a regulator of lin-42 transcription. The lin-42 locus encodes three isoforms, and we have characterized lin-42 isoform specific regulation by ZTF-16 through phenotypic assays and analysis of transcriptional reporter strains. Our data show that ZTF-16 regulates the cyclic …
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cis-Regulation in the Mammalian Rod Photoreceptor
<p>Transcription factors regulate the expression level of target genes by binding to <italic>cis</italic>-regulatory elements (CREs) present in gene promoters. The goal of my thesis research is to define the sequence components of CREs that determine transcriptional output. In order to accomplish …
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ASMT gene polymorphisms are associated with Autism Spectrum Disorder (ASD) symptom severity in a South African population
… study found novel SNPs, and a SNP in a putative transcription factor binding site not previously associated with ASD. The associations found between SNPs and ASD endophenotypes, together with the positions of the SNPs, suggest a potential link between ASMT polymorphisms and ASD symptom severity. …
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A Missing link between lipid metabolism, inflammation and apoptosis: Phospholipase A2-activating protein (PLAA)
… We compared plaa high and plaa low cells for transcriptional profiling and their responses to TNF-¦Á stimulation. Overexpression of the plaa gene induced the expression of the proinflammatory cytokine IL-32 and reduced the expression of annexin A4 (a PLA2 inhibitor) and clusterin. We …
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Regulation of the HCMV UL98 Promoter by Cooperation of the Cyclic AMP Response Element and Gamma Interferon Response Element
… for UL98 promoter activation by IE proteins. Site-directed mutations generated in two cellular transcription factor binding sites resulted in a drastic reduction in promoter activation. A mutation in the cyclic AND response element (CRE) (−82 to −75) resulted in a 70% loss of promoter …
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Identification of Deleterious and Disease Alleles in a General Population and Preterm Labor Patients
… genome-wide association studies and the transcriptional regulatory network. However, even in protein-coding regions, it is not well understood how often and by what mechanism deleterious alleles disrupting strong sequence conservation can become common in population frequency and affect …
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Polony sequencing : DNA sequencing technology and a computational analysis reveals chromosomal domains of gene expression
… that in certain regions of the genome a single transcription factor binding site may regulate several genes. It is also shown that evolution may take advantage of this phenomenon by keeping genes with similar functions in adjacent positions along the chromosomes. The techniques that are …
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A knowledgebase of stress reponsive gene regulatory elements in arabidopsis Thaliana
… stress. Their gene products are linked to DNA transcription and its consequent translation into a response product. However, whilst these genes play a significant role in manufacturing responses to stressful stimuli, transcription factors coordinate access to these genes, specifically by …
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A Combined Motif Discovery Method
… problem in the bioinformatics is to find the binding sites for regulatory motifs. This is a challenging problem that leads us to a platform to apply a variety of data mining methods. In the efforts described here, a combined motif discovery method that uses mutual information and Gibbs …
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Applying integrative computational models to study the evolution of gene regulation
… algorithm for de novo prediction of transcription factor binding site motifs in multiple species. The algorithm, named ""GibbsModule"", uses three information sources to improve the prediction power, which are 1)co-expressed genes sharing the same set of motifs; 2)binding sites …
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Computational Prediction of Functional Elements through Comparative Genomics
… elements, such as protein coding genes, transcriptional regulatory sequences, and non-coding RNA genes. This dissertation research has been focused on two grand challenges of genomics: (i) to decode cis-regulatory modules (CRMs), non-coding DNA sequences controlling gene expression; and …
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In vivo and in vitro regulation of plasminogen activator inhibitor type-1
… analyzed by gel retardation to investigate the transcription factors that bound to these regions. The functional data taken together with the DNA binding data supported the hypothesis that the response of the PAl-1 promoter to TGFP was mediated by two conserved regions of the promoter and 5' …