title: Identification of immunity-related genes in Arabidopsis and cassava using genomic data.
abstract: Recent advances in genomic and post-genomic technologies have provided the opportunity to generate a previously unimaginable amount of information. However, biological knowledge is still needed to improve the understanding of complex mechanisms such as plant immune responses. Better knowledge of this process could improve crop production and management. Here, we used holistic analysis to combine our own microarray and RNA-seq data with public genomic data from Arabidopsis and cassava in order to acquire biological knowledge about the relationships between proteins encoded by immunity-related genes (IRGs) and other genes. This approach was based on a kernel method adapted for the construction of gene networks. The obtained results allowed us to propose a list of new IRGs. A putative function in the immunity pathway was predicted for the new IRGs. The analysis of networks revealed that our predicted IRGs are either well documented or recognized in previous co-expression studies. In addition to robust relationships between IRGs, there is evidence suggesting that other cellular processes may be also strongly related to immunity.
authors: Department of Statistics, Universidad Nacional de Colombia, Bogotá 111321, Colombia.
authors: Luis Guillermo
authors: LG
authors: Leal
authors: Department of Biology, Universidad Nacional de Colombia, Bogotá 111321, Colombia.
authors: Álvaro
authors: Á
authors: Perez
authors: Department of Biology, Universidad Nacional de Colombia, Bogotá 111321, Colombia.
authors: Andrés
authors: A
authors: Quintero
authors: Department of Biology, Universidad Nacional de Colombia, Bogotá 111321, Colombia.
authors: Ángela
authors: Á
authors: Bayona
authors: Department of Biology, Universidad Nacional de Colombia, Bogotá 111321, Colombia.
authors: Juan Felipe
authors: JF
authors: Ortiz
authors: Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
authors: Anju
authors: A
authors: Gangadharan
authors: Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA.
authors: David
authors: D
authors: Mackey
authors: Department of Biology, Universidad Nacional de Colombia, Bogotá 111321, Colombia.
authors: Camilo
authors: C
authors: López
authors: Department of Statistics, Universidad Nacional de Colombia, Bogotá 111321, Colombia. Electronic address: llopezk@unal.edu.co.
authors: Liliana
authors: L
authors: López-Kleine
mesh_terms: D017360:Arabidopsis / Q000235:genetics* / Q000276:immunology; D018506:Gene Expression Regulation, Plant; D053263:Gene Regulatory Networks; D018745:Genome, Plant; D023281:Genomics; D002365:Manihot / Q000235:genetics* / Q000276:immunology
keywords: Arabidopsis; Cassava; Functional gene prediction; Genomic data; Kernel canonical correlation analysis; Plant immunity