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Nat Biotechnol. 2010 Feb;28(2):149-56. doi: 10.1038/nbt.1603. Epub 2010 Jan 31.

Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana.

Author information

1
Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seodaemun-gu, Seoul, Korea. insuklee@yonsei.ac.kr

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.

PMID:
20118918
PMCID:
PMC2857375
DOI:
10.1038/nbt.1603
[Indexed for MEDLINE]
Free PMC Article
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