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

Nature Protocols volume 6, pages 1429–1442 (2011)Cite this article

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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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Figure 1: Overview of the method of using AraNet to discover gene function.
Figure 2: A report from a 'Find new members of a pathway' search showing an analysis of query genes (e.
Figure 3: An example of ROC analysis of predictive power of query genes for the 'Find new members of a pathway' search in AraNet.
Figure 4: An example list of candidate pathway genes from a 'Find new members of a pathway' search.
Figure 5: An example of a network layout view page in a new web browser window.
Figure 6: The 'Infer function from network neighbors' search.
Figure 7: A report from a 'Find new members of a pathway' search.
Figure 8: Functional gene set enrichment analysis (e.

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Acknowledgements

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.).

AUTHOR CONTRIBUTIONS

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.

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Authors and Affiliations

  1. Department of Biotechnology, College of Life Science and Biotechnology, Yonsei University, Seoul, Korea

    Sohyun Hwang & Insuk Lee

  2. Department of Plant Biology, Carnegie Institution for Science, Stanford, California, USA

    Seung Y Rhee

  3. Center for Systems and Synthetic Biology, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA

    Edward M Marcotte

  4. Department of Chemistry and Biochemistry, Institute for Cellular and Molecular Biology, University of Texas at Austin, Austin, Texas, USA

    Edward M Marcotte

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  1. Sohyun Hwang
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  2. Seung Y Rhee
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Contributions

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.

Corresponding authors

Correspondence to Seung Y Rhee, Edward M Marcotte or Insuk Lee.

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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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