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.
Results
Showing 1 to 20 of 60 for “"Transcription Factor (TF)"”.
-
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 …
-
Analysis of the PROM algorithm as a tool to generate genome-scale metabolic-regulatory networks
… which accurately predict growth phenotypes of transcriptional regulatory mutants under various conditions. E. coli, M. tuberculosis and S. cerevisase were used as model organisms. We showed that PROM could be successfully applied to model less complex systems (E. coli and M. tuberculosis) but …
-
A Cancer-Specific Study On The Differentially Expressed Protein-Protein Interactions of Fumarate Hydratase
… the significantly expressed genes with a transcription factor (TF). Our results have allowed us to construct a network that presents our findings. Most importantly, it has revealed the significant role played by the HIF3a TF in FH-deficient cells. While HIF3a is less understood compared to …
-
On the Diversity of Eukaryotic Transcription Factor Specificities
Transcription factor (TF) DNA-binding specificities (motifs) are often conserved between species, and many TFs have conserved functions over long evolutionary distances. As a consequence, changes in gene expression are largely attributed to evolution of cis-regulatory DNA sequences rather than …
-
Dissecting Transcriptional Regulatory Networks with Systems Biology Approaches
… is focused on understanding these mechanisms of transcriptional regulation using systems biology approaches. Transcription regulatory networks play an important role in mediating external stimuli and coordinating responses to changing environments. Different methods that infer regulatory …
-
Entropy-based machine learning algorithms applied to genomics and pattern recognition
Transcription factors (TF) are proteins that interact with DNA to regulate the transcription of DNA to RNA and play key roles in both healthy and cancerous cells. Thus, gaining a deeper understanding of the biological factors underlying transcription factor (TF) binding specificity is important for …
-
Role of DNA replication timing in gene expression and chromatin organisation
… genome duplication are associated with altered transcription and chromatin organisation, it is still unknown whether DNA replication timing (RT) is a cause or a consequence of cellular fate changes. During my thesis I used a conditional system to perturb DNA RT in a single cell cycle in budding …
-
The NuRD complex regulates chromatin dynamics driving exit from naïve pluripotency
… ESCs to dissect its role in the regulation of transcription factor (TF) binding dynamics, chromatin accessibility, genome organisation and ultimately gene expression in naive pluripotency through to lineage specification. Single-molecule tracking of pluripotency-associated TFs in live mouse …
-
Non-Parametric Analyses of the Regulatory Roles of LINE-1 Retrotransposons during Motor Neuron Differentiation
… in a biological process of interest, e.g. transcription factor (TF) binding, from functional data modalities such as ChIP-seq and ChIA-PET. Results: First, I present a non-parametric, k-mer based method that overcomes analysis ambiguities introduced by short read multimapping and the …
-
EPIGENETIC AND FUNCTIONAL ASSESSMENT OF ENHANCEROPATHIES ACROSS HUMAN MODELS: FOCUS ON GABRIELE-DE VRIES SYNDROME
Yin Yang 1 (YY1) is a ubiquitous zinc finger transcription factor (TF) that occupies active enhancers and promoters contributing to physical interactions between these regions via DNA looping. Increasing evidence shows that disruption of non-coding regions such as enhancers is prevalent across …
-
The Role of the Transcription Factor CEBPA in Regulating Lung Alveolar Type 2 Cell Fate In Vivo
… investigations reveal the critical role of the transcription factor (TF) CEBPA, specific to lung alveolar type 2 (AT2) cells, in modulating AT2 cell plasticity within the mouse lung. We demonstrate that CEBPA constrains AT2 cell plasticity by promoting the AT2 differentiation program and …
-
TCF4 Is a Key Mediator of Cell Identity and Oncogenesis in Neuroblastoma
… (MES) cell state. Super-enhancer-associated transcription factor (TF) networks define cell identities in neuroblastoma (NB). Dysregulation of these TFs contributes to the initiation and maintenance of NB by enforcing early developmental identity states. We report the bHLH transcription factor …
-
Characterisation of Nuclear EnvelopeAssociated Proteins (NEAP) in Arabidopsis thaliana
… Transfer), which confirmed interactions with the transcription factor (TF) AtbZIP18. AtNEAP specific antibodies generated during this study were used to confirm expression in vivo. Altogether, results indicated that AtNEAPs are part of the nucleoskeleton, with a role in anchoring TFs at the INM to …
-
Nucleosome repositioning in glioblastoma
… in relation to other features, such as transcription factor (TF) binding, ALU repeats and histone modification changes. I show that the relationship between TF binding and nucleosome positioning in brain tissues, as well as cell-free DNA (cfDNA) from peripheral blood, is a highly …
-
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 …
-
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 …
-
Control of Inflammation Using Drug Delivery Strategies in in vitro Models
… communication at the cellular level is transcription factor (TF) NF-κB. Under normal conditions, NF-κB is bound to an inhibitor in the cytoplasm. In a chronic disease state, NF-κB is overactive and found in the unbound form, resulting in increased production of inflammatory signals. </p> …
-
Evolution-Inspired Design of Bacterial Biosensors
… propose a novel workflow for the prediction of transcription factor (TF) operator sites based on a modified phylogenetic footprinting framework. We increase operator prediction accuracy from 45% to 83% when compared to leading methods and use this framework to predict operator sites for …
-
Nuclear proteomics and transcription factor profiling in Chlamydomonas reinhardtii
The transcriptional regulation of the cellular mechanisms involves many different components and different levels of control which together contribute to fine tune the response of cells to different environmental stimuli. In some responses, diverse signaling pathways can be controlled …
-
Discovery of a DNA-binding Consensus and Potential Genomic Regulatory Binding Sites for the Thermus thermophilus HB8 Transcriptional Regulator TTHA1359
<p>Transcription factor (TF) proteins act as molecular mechanisms that modulate the initiation of the first step in the expression of genes, gene transcription. Currently, knowledge of the DNA-binding specificities and genes regulated by many TFs, including those of well-studied model organisms …
Page 1 of 3