AraNet is a functional gene network for the reference plant Arabidopsis and has been constructed in order to identify new genes associated with plant traits. It is highly predictive for diverse biological pathways and can be used to prioritize genes for functional screens. Moreover, AraNet provides a web-based tool with which plant biologists can efficiently discover novel functions of Arabidopsis genes (http://www.functionalnet.org/aranet/). This protocol explains how to conduct network-based prediction of gene functions using AraNet and how to interpret the prediction results. Functional discovery in plant biology is facilitated by combining candidate prioritization by AraNet with focused experimental tests.
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This work was supported by the National Research Foundation of Korea grant funded by the Korean government (no. 20100017649); Pohang Iron and Steel Company (POSCO) TJ Park Science Fellowship (to I.L.); grants from the National Science Foundation, National Institutes of Health, Welch (F1515) and Packard Foundations (to E.M.M.); the Carnegie Institution for Science; and a grant from the National Science Foundation (to S.Y.R.).
I.L., E.M.M., S.Y.R. and S.H. conceived the protocol. S.H. constructed the current version of the AraNet web application and wrote the protocol. I.L., E.M.M. and S.Y.R. edited the protocol.
The authors declare no competing financial interests.
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Hwang, S., Rhee, S., Marcotte, E. et al. Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network. Nat Protoc 6, 1429–1442 (2011). https://doi.org/10.1038/nprot.2011.372
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