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Full-Text Articles in Genetics and Genomics
Discovery And Validation Of Information Theory-Based Transcription Factor And Cofactor Binding Site Motifs., Ruipeng Lu, Eliseos J Mucaki, Peter K Rogan
Discovery And Validation Of Information Theory-Based Transcription Factor And Cofactor Binding Site Motifs., Ruipeng Lu, Eliseos J Mucaki, Peter K Rogan
Biochemistry Publications
Data from ChIP-seq experiments can derive the genome-wide binding specificities of transcription factors (TFs) and other regulatory proteins. We analyzed 765 ENCODE ChIP-seq peak datasets of 207 human TFs with a novel motif discovery pipeline based on recursive, thresholded entropy minimization. This approach, while obviating the need to compensate for skewed nucleotide composition, distinguishes true binding motifs from noise, quantifies the strengths of individual binding sites based on computed affinity and detects adjacent cofactor binding sites that coordinate with the targets of primary, immunoprecipitated TFs. We obtained contiguous and bipartite information theory-based position weight matrices (iPWMs) for 93 sequence-specific TFs, …
Inheritance, Differential Expression, And Candidate Gene Analyses For Avr2 In Phytophthora Sojae, Chelsea S. Ishmael
Inheritance, Differential Expression, And Candidate Gene Analyses For Avr2 In Phytophthora Sojae, Chelsea S. Ishmael
Electronic Thesis and Dissertation Repository
Phytophthora sojae is an oomycete responsible for seed, root and stem rot of soybean plants. Managing this disease relies on growing soybean cultivars with race-specific resistance (Rps) genes that deliver complete host immunity in the presence of corresponding pathogen avirulence (Avr) effector proteins. The aims of this study were to characterize virulence towards Rps2 among different P. sojae strains, track the inheritance of this trait, and attempt to identify an Avr2 gene. Fifteen P. sojae strains were tested for virulence towards Rps2 and crosses were performed between selected virulent and avirulent strains to follow the inheritance of virulence. …
Associations Between Hypothalamic-Pituitary-Adrenal Axis System Gene Variants And Cortisol Reactivity In Preschoolers: Main Effects And Gene-Environment Interactions, Haroon I. Sheikh
Electronic Thesis and Dissertation Repository
Exposure to stressful events during early development has consistently been shown to produce long lasting effects on the hypothalamic-pituitary-adrenal (HPA) axis, which may increase vulnerability to mood and anxiety disorders. Recently reported genetic association studies indicate that these disorders may be influenced, in part, by gene-environment interactions (GxE) involving polymorphisms within the corticotrophin-releasing hormone and monoaminergic system genes. However, little is known about how genetic variants and life stress work to shape children’s neuroendocrine reactivity and emerging symptoms. Therefore, the aim of this thesis is to examine main effects of candidate genes and GxE on the neuroendocrine stress response and …