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
- ItemWhole genome sequence of Mapuche-Huilliche Native Americans(2018) Vidal Olate, Elena Alejandra; Moyano Yugovic, Tomás Custodio; Bustos, Bernabé I.; Pérez-Palma, Eduardo; Moraga Marín, Carol Mabel; Montecinos López, Alejandro; Azócar López, Lorena Karina; Soto Wilder, Daniela Constanza; Riveras, Eleodoro; Vidal, Mabel; Genova, Alex Di; Puschel Illanes, Klaus; Nürnberg, Peter; Buch, Stephan; Hampe, Jochen; Eyheramendy Duerr, Susana; Miquel Poblete, Juan Francisco; Gutiérrez Ilabaca, Rodrigo AntonioBackground Whole human genome sequencing initiatives provide a compendium of genetic variants that help us understand population history and the basis of genetic diseases. Current data mostly focuses on Old World populations and information on the genomic structure of Native Americans, especially those from the Southern Cone is scant. Results Here we present a high-quality complete genome sequence of 11 Mapuche-Huilliche individuals (HUI) from Southern Chile (85% genomic and 98% exonic coverage at > 30X), with 96-97% high confidence calls. We found approximately 3.1x106 single nucleotide variants (SNVs) per individual and identified 403,383 (6.9%) of novel SNVs that are not included in current sequencing databases. Analyses of large-scale genomic events detected 680 copy number variants (CNVs) and 4,514 structural variants (SVs), including 398 and 1,910 novel events, respectively. Global ancestry composition of HUI genomes revealed that the cohort represents a marginally admixed population from the Southern Cone, whose genetic component is derived from early Native American ancestors. In addition, we found that HUI genomes display highly divergent and novel variants with potential functional impact that converge in ontological categories essential in cell metabolic processes. Conclusions Mapuche-Huilliche genomes contain a unique set of small- and large-scale genomic variants in functionally linked genes, which may contribute to susceptibility for the development of common complex diseases or traits in admixed Latinos and Native American populations. Our data represents an ancestral reference panel for population-based studies in Native and admixed Latin American populations