Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

Sohyun Hwang; Seung Y. Rhee; Edward M. Marcotte; Insuk Lee

doi:10.1038/nprot.2011.372

Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

Sohyun Hwang, Seung Y. Rhee, Edward M. Marcotte, Insuk Lee

Research output: Contribution to journal › Article › peer-review

38 Citations (Scopus)

Abstract

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.

Original language	English
Pages (from-to)	1429-1442
Number of pages	14
Journal	Nature Protocols
Volume	6
Issue number	9
DOIs	https://doi.org/10.1038/nprot.2011.372
Publication status	Published - 2011 Sep

Bibliographical note

Funding Information:
acknowleDGMents 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.).

All Science Journal Classification (ASJC) codes

Biochemistry, Genetics and Molecular Biology(all)

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10.1038/nprot.2011.372

Cite this

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abstract = "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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Systematic prediction of gene function in Arabidopsis thaliana using a probabilistic functional gene network

Abstract

Bibliographical note

All Science Journal Classification (ASJC) codes

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