title: Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana.
abstract: We introduce a rational approach for associating genes with plant traits by combined use of a genome-scale functional network and targeted reverse genetic screening. We present a probabilistic network (AraNet) of functional associations among 19,647 (73%) genes of the reference flowering plant Arabidopsis thaliana. AraNet associations are predictive for diverse biological pathways, and outperform predictions derived only from literature-based protein interactions, achieving 21% precision for 55% of genes. AraNet prioritizes genes for limited-scale functional screening, resulting in a hit-rate tenfold greater than screens of random insertional mutants, when applied to early seedling development as a test case. By interrogating network neighborhoods, we identify AT1G80710 (now DROUGHT SENSITIVE 1; DRS1) and AT3G05090 (now LATERAL ROOT STIMULATOR 1; LRS1) as regulators of drought sensitivity and lateral root development, respectively. AraNet (http://www.functionalnet.org/aranet/) provides a resource for plant gene function identification and genetic dissection of plant traits.
authors.affiliation: Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul, Korea. insuklee@yonsei.ac.kr
authors.forename: Insuk
authors.initials: I
authors.lastname: Lee
authors.forename: Bindu
authors.initials: B
authors.lastname: Ambaru
authors.forename: Pranjali
authors.initials: P
authors.lastname: Thakkar
authors.forename: Edward M
authors.initials: EM
authors.lastname: Marcotte
authors.forename: Seung Y
authors.initials: SY
authors.lastname: Rhee
mesh_terms: D017360:Arabidopsis / Q000235:genetics*; D029681:Arabidopsis Proteins / Q000235:genetics*; D002874:Chromosome Mapping; D018745:Genome, Plant / Q000235:genetics*; D040641:Quantitative Trait Loci / Q000235:genetics*
chemical_list: D029681:Arabidopsis Proteins