Browsing by Author "Vidal Olate, Elena Alejandra"
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- ItemA systems view of nitrogen nutrient and metabolite responses in Arabidopsis(2008) Vidal Olate, Elena Alejandra; Gutiérrez Ilabaca, Rodrigo Antonio
- ItemConstructing Simple Biological Networks for Understanding Complex High-Throughput Data in Plants(Springer, 2015) Vidal Olate, Elena Alejandra; Contreras López, Luis Orlando; Gutiérrez Ilabaca, Rodrigo Antonio; Moyano Yugovic, Tomás Custodio; Stepanova, Anna N.Technological advances in the last decade have enabled biologists to produce increasing amounts of information for the transcriptome, proteome, interactome, and other -omics data sets in many model organisms. A major challenge is integration and biological interpretation of these massive data sets in order to generate testable hypotheses about gene regulatory networks or molecular mechanisms that govern system behaviors. Constructing gene networks requires bioinformatics skills to adequately manage, integrate, analyze and productively use the data to generate biological insights. In this chapter, we provide detailed methods for users without prior knowledge of bioinformatics to construct gene networks and derive hypotheses that can be experimentally verified. Step-by-step instructions for acquiring, integrating, analyzing, and visualizing genome-wide data are provided for two widely used open source platforms, R and Cytoscape platforms. The examples provided are based on Arabidopsis data, but the protocols presented should be readily applicable to any organism for which similar data can be obtained.
- ItemGene networks for nitrogen sensing, signaling, and response in Arabidopsis thaliana(2010) Vidal Olate, Elena Alejandra; Tamayo Godoy, Karem Patricia; Gutiérrez Ilabaca, Rodrigo Antonio
- ItemIntegrated RNA-seq and sRNA-seq analysis identifies novel nitrate-responsive genes in Arabidopsis thaliana roots(2013) Vidal Olate, Elena Alejandra; Moyano Yugovic, Tomás Custodio; Gutiérrez Ilabaca, Rodrigo Antonio
- ItemIntegration of local and systemic signaling pathways for plant N responses(2012) Alvarez Herrera, José Miguel; Vidal Olate, Elena Alejandra; Gutiérrez Ilabaca, Rodrigo Antonio
- ItemNitrate regulation of AFB3 and NAC4 gene expression in Arabidopsis roots depends on NRT1.1 nitrate transport function(2014) Vidal Olate, Elena Alejandra; Alvarez Herrera, José Miguel; Gutiérrez Ilabaca, Rodrigo Antonio
- ItemNitrate-responsive miR393/AFB3 regulatory module controls root system architecture in Arabidopsis thaliana(2010) Vidal Olate, Elena Alejandra; Araus Caramori, Viviana; Gutiérrez Ilabaca, Rodrigo Antonio
- ItemNitrogen control of developmental phase transitions in Arabidopsis thaliana(2014) Vidal Olate, Elena Alejandra; Moyano Yugovic, Tomás Custodio; Canales Carrasco, Javier; Gutiérrez Ilabaca, Rodrigo Antonio
- ItemSMZ/SNZ and gibberellin signaling are required for nitrate-elicited delay of flowering time in Arabidopsis thaliana(2018) Gras, D. E.; Vidal Olate, Elena Alejandra; Undurraga, S. F.; Riveras Hernández, Eleodoro Javier; Moreno, S.; Domínguez Figueroa, J.; Alabadi, D.; Blazquez, M. A.; Medina, J.; Gutiérrez Ilabaca, Rodrigo Antonio
- ItemSystems approach identifies TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response of Arabidopsis thaliana roots(2014) Alvarez, J.; Riveras Hernández, Eleodoro Javier; Vidal Olate, Elena Alejandra; Gras, Diana; Contreras, O.; Tamayo, K.; Aceituno, F.; Gómez, Isabel; Ruffel, S.; Lejay, L.; Jordana, X.; Gutiérrez Ilabaca, Rodrigo Antonio
- ItemSystems approaches map regulatory networks downstream of the auxin receptor AFB3 in the nitrate response of Arabidopsis thaliana roots(2013) Vidal Olate, Elena Alejandra; Moyano, T.; Riveras Hernández, Eleodoro Javier; Contreras López, O.; Gutiérrez Ilabaca, Rodrigo Antonio