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

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

Content Provider	Semantic Scholar
Author	Lee, Insuk Ambaru, Bindu Thakkar, Pranjali Marcotte, Edward M. Rhee, Seung Yon
Copyright Year	2010
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.
Starting Page	149
Ending Page	156
Page Count	8
File Format	PDF HTM / HTML
DOI	10.1038/nbt.1603
PubMed reference number	20118918
Journal	Medline
Volume Number	28
Alternate Webpage(s)	http://www.marcottelab.org/users/paper-pdfs/NatureBiotech_AraNet_2010_supplement.pdf
Alternate Webpage(s)	http://www.marcottelab.org/paper-pdfs/NatureBiotech_AraNet_2010_supplement.pdf
Alternate Webpage(s)	https://dpb.carnegiescience.edu/sites/dpb.carnegiescience.edu/files/Lee_SOM_20100106.pdf
Alternate Webpage(s)	http://www.marcottelab.org/paper-pdfs/NatureBiotech_AraNet_2010.pdf
Alternate Webpage(s)	http://www.marcottelab.org/users/paper-pdfs/NatureBiotech_AraNet_2010.pdf
Alternate Webpage(s)	https://doi.org/10.1038/nbt.1603
Journal	Nature Biotechnology
Language	English
Access Restriction	Open
Content Type	Text
Resource Type	Article

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