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PMID:20118918

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Citation

Lee, I, Ambaru, B, Thakkar, P, Marcotte, EM and Rhee, SY (2010) Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana. Nat. Biotechnol. 28:149-56

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.

Links

PubMed PMC2857375 Online version:10.1038/nbt.1603

Keywords

Arabidopsis/genetics; Arabidopsis Proteins/genetics; Chromosome Mapping; Genome, Plant/genetics; Quantitative Trait Loci/genetics

Significance

Annotations

Gene product Qualifier GO Term Evidence Code with/from Aspect Extension Notes Status

ARATH:Q93ZS6

acts_upstream_of_or_within

GO:0010311: lateral root formation

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

ARATH:Q9SAI7

acts_upstream_of_or_within

GO:0009737: response to abscisic acid

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete

ARATH:Q9SAI7

acts_upstream_of_or_within

GO:0009414: response to water deprivation

ECO:0000315: mutant phenotype evidence used in manual assertion

P

Seeded From UniProt

complete


See also

References

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