%0 Journal Article %1 Lee2010Rational %A Lee, Insuk %A Ambaru, Bindu %A Thakkar, Pranjali %A Marcotte, Edward M. %A Rhee, Seung Y. %D 2010 %I Nature Publishing Group %J Nature Biotechnology %K arabidopsis gene-networks genome-scale %N 2 %P 149--156 %R 10.1038/nbt.1603 %T Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana %U http://dx.doi.org/10.1038/nbt.1603 %V 28 %X 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.

@article{Lee2010Rational, 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.}, added-at = {2018-12-02T16:09:07.000+0100}, author = {Lee, Insuk and Ambaru, Bindu and Thakkar, Pranjali and Marcotte, Edward M. and Rhee, Seung Y.}, biburl = {https://www.bibsonomy.org/bibtex/22deafd4e294a11e84ac439b372261a06/karthikraman}, citeulike-article-id = {6609647}, citeulike-linkout-0 = {http://dx.doi.org/10.1038/nbt.1603}, citeulike-linkout-1 = {http://dx.doi.org/10.1038/nbt.1603}, citeulike-linkout-2 = {http://view.ncbi.nlm.nih.gov/pubmed/20118918}, citeulike-linkout-3 = {http://www.hubmed.org/display.cgi?uids=20118918}, day = 31, doi = {10.1038/nbt.1603}, interhash = {ed14b6c39eee1bf4b84707887f2e88ef}, intrahash = {2deafd4e294a11e84ac439b372261a06}, issn = {1087-0156}, journal = {Nature Biotechnology}, keywords = {arabidopsis gene-networks genome-scale}, month = jan, number = 2, pages = {149--156}, pmid = {20118918}, posted-at = {2010-02-03 10:07:25}, priority = {2}, publisher = {Nature Publishing Group}, timestamp = {2018-12-02T16:09:07.000+0100}, title = {Rational association of genes with traits using a genome-scale gene network for Arabidopsis thaliana}, url = {http://dx.doi.org/10.1038/nbt.1603}, volume = 28, year = 2010 }