Step-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data

Simple item page
dc.catalogadorjlo
dc.contributor.authorContreras López, Orlando
dc.contributor.authorMoyano, Tomás C.
dc.contributor.authorSoto, Daniela C.
dc.contributor.authorGutiérrez, Rodrigo A.
dc.date.accessioned2024-01-29T17:48:28Z
dc.date.available2024-01-29T17:48:28Z
dc.date.issued2018
dc.description.abstractThe rapid increase in the availability of transcriptomics data generated by RNA sequencing represents both a challenge and an opportunity for biologists without bioinformatics training. The challenge is handling, integrating, and interpreting these data sets. The opportunity is to use this information to generate testable hypothesis to understand molecular mechanisms controlling gene expression and biological processes (Fig. 1). A successful strategy to generate tractable hypotheses from transcriptomics data has been to build undirected network graphs based on patterns of gene co-expression. Many examples of new hypothesis derived from network analyses can be found in the literature, spanning different organisms including plants and specific fields such as root developmental biology. In order to make the process of constructing a gene co-expression network more accessible to biologists, here we provide step-by-step instructions using published RNA-seq experimental data obtained from a public database. Similar strategies have been used in previous studies to advance root developmental biology. This guide includes basic instructions for the operation of widely used open source platforms such as Bio-Linux, R, and Cytoscape. Even though the data we used in this example was obtained from Arabidopsis thaliana, the workflow developed in this guide can be easily adapted to work with RNA-seq data from any organism.
dc.fuente.origenORCID-ene24
dc.identifier.doi10.1007/978-1-4939-7747-5_21
dc.identifier.isbn978-1-4939-7746-8
dc.identifier.urihttp://dx.doi.org/10.1007/978-1-4939-7747-5_21
dc.identifier.urihttps://repositorio.uc.cl/handle/11534/81012
dc.information.autorucFacultad de Ciencias Biológicas; Contreras López, Luis Orlando; 0000-0002-4048-6637; 149770
dc.information.autorucFacultad de Ciencias Biológicas; Moyano Yugovic, Tomás Custodio; S/I; 149778
dc.information.autorucFacultad de Ciencias Biológicas; Gutiérrez Ilabaca, Rodrigo Antonio; 0000-0002-5961-5005; 86782
dc.language.isoen
dc.nota.accesoContenido parcial
dc.publisherHumana Press
dc.relation.ispartofRoot Development 
dc.rightsacceso restringido
dc.subjectRNA-seq
dc.subjectGene co-expression network
dc.subjectDifferential gene expression
dc.subjectDESeq2
dc.subjectCytoscape
dc.subject.ddc570
dc.subject.deweyBiologíaes_ES
dc.titleStep-by-Step Construction of Gene Co-expression Networks from High-Throughput Arabidopsis RNA Sequencing Data
dc.typecapítulo de libro
sipa.codpersvinculados149770
sipa.codpersvinculados149778
sipa.codpersvinculados86782
sipa.trazabilidadORCID;2024-01-15
Files
Collections
Capítulos de libros