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 20 of 130 for “"Transcription factor binding"”.
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Recording Transcription Factor Binding During Development
… application of a novel method for mapping the binding sites of transcription factors using transposons to insert into the genome near to where the factors are bound. The method, named "Calling Cards", offers an alternative to chromatin immunoprecipitation (ChIP) methods and furthermore has the …
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Investigation of transcription factor binding at distal regulatory elements
… looping. Enhancers typically contain clusters of transcription factor binding sites, and TF recruitment to them is thought to play a key role in transcriptional control. In this thesis I have addressed two issues regarding gene regulation by enhancers. First, with recent genome-wide enhancer …
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Computation identification of transcription factor binding using DNase-seq
… profiles to facilitate the identification of transcription factor (TF) binding sites. Through the use of machine learning techniques, PIQ identified binding sites for >700 TFs from one DNase-seq experiment with accuracy comparable to ChIP-seq for motif-associated TFs (median AUC=0.93 across …
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Whole genome regulatory variant evaluation for transcription factor binding
… cell. For example these variants can alter the binding of the transcription factors (TF). In this thesis we present Whole-genome regulAtory Variant Evaluation (WAVE), a computational method that models the TF binding ChIP-seq signal solely from DNA sequence and predicts genetic a variant's …
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Anthraquinone-peptide conjugates as inhibitors of DNA transcription factor binding.
… (AP-1)~ a collective term referring to dimeric transcription factors involved in mediating long term responses to signals that regulate growth control and development~ were designed and synthesised in this study. Truncated peptide sequences of 5-7 residues containing the highly conserved …
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Transcription Factor Binding Dynamics and Spatial Co-localization In Human Genome
Transcription factor (TF) binding has been studied extensively in relation to binding site affinity and chromosome modifications; however, the relationship between genome spatial organisation and transcription factor binding is not well studied. Using the recently available high resolution Hi-C …
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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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Predicting enhancer regions and transcription factor binding sites in D. melanogaster
… and D. melanogaster genomes. The genome- wide binding locations of all known transcription factors as well as of other DNA- binding proteins are currently being mapped within the context of this project [8]. The large quantity of new data that is becoming available through the modENCODE project …
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Integrating Epigenetic Priors For Improving Computational Identification of Transcription Factor Binding Sites
Transcription factors and histone modifications play critical roles in tissue-specific gene expression. Identifying binding sites is key in understanding the regulatory interactions of gene expression. Nave computational approaches uses solely DNA sequence data to construct models known as Position …
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The Mapping of Transcription Factor Binding Sites in the Turkey Prolactin Gene
… not occur in the turkey in vivo. The mapping of transcription factor binding sites in the tPRL 5'-flanking region is the first step toward the identification and isolation of factors that bind to and regulate transcription of the PRL gene.
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Novel Sequence-Based Method for Identifying Transcription Factor Binding Sites in Prokaryotic Genomes
… sequence data in order to determine prokaryotic transcription factor binding specificities. The prototypical prokaryotic transcription factor: TF) contains a helix–turn–helix: HTH) fold and bind DNA as homodimers, leading to their palindromic motif specificities. The connection …
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Zero-Inflated Models to Identify Transcription Factor Binding Sites in ChIP-seq Experiments
<p>It is essential to determine the protein-DNA binding sites to understand many biological processes. A transcription factor is a particular type of protein that binds to DNA and controls gene regulation in living organisms. Chromatin immunoprecipitation followed by highthroughput sequencing …
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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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Quantifying the functional and evolutionary relationships among sequences, transcription factor binding and gene expression
… relationship between regulatory sequences, transcription factor (TF) binding and gene expression. Many studies have discussed how TFs recognize their DNA binding sites. However, it is not well understood how the various factors that influence TF-DNA binding alter the cascade of gene …
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A regulatory role for repeated decoy transcription factor binding sites in target gene expression
… studies reveal that many intergenic TRs contain transcription factor (TF) binding sites and that several TRs of TF binding sites indeed influence gene expression. A possible mechanism is that TRs serve as TF decoys, competing with a promoter for TF binding. We utilized a synthetic system in …
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Estimating transcription factor binding properties in human cell lines using statistical methods and genomics datasets
Site specific transcription factors recognise and bind DNA motifs to regulate gene expression. Therefore, it is important to understand how and where they interact with the genome. Besides DNA sequence, chromatin accessibility, CpG methylation and cooperative binding with other transcription …
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Tracing the evolution of lineage-specific transcription factor binding sites in a birth-death framework
… evolution of lineage-specific traits. Although transcription factor binding events show substantial variation across species, most computational approaches to study regulatory elements focus primarily upon highly conserved sites, and rely heavily upon multiple sequence alignments. However, …
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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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Simultaneous computational discovery of DNA regulatory motifs and transcription factor binding constraints at high spatial resolution
… resolution and accuracy in resolving proximal binding events when comparing with existing methods. Second, I present the k-mer set motif (KSM) representation and the k-mer motif alignment and clustering (KMAC) method which discovers DNA-binding motifs from ChIP-Seq derived sequences. I …
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