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1.  Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana 
Nature biotechnology  2010;28(2):149-156.
Plants are essential sources of food, fiber and renewable energy. Effective methods for manipulating plant traits have important agricultural and economic consequences. 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 have measured precision greater than literature-based protein interactions (21%) for 55% of genes, and are highly predictive for diverse biological pathways. Using AraNet, we found a 10-fold enrichment in identifying early seedling development genes. By interrogating network neighborhoods, we identify At1g80710 (now Drought sensitive 1; Drs1) and At3g05090 (now Lateral root stimulator 1; Lrs1) as novel regulators of drought sensitivity and lateral root development, respectively. AraNet (http://www.functionalnet.org/aranet/) provides a global resource for plant gene function identification and genetic dissection of plant traits.
doi:10.1038/nbt.1603
PMCID: PMC2857375  PMID: 20118918

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