AraNet

A network biology server for Arabidopsis thaliana and other non-model plant species

Tak Lee, In suk Lee

Research output: Chapter in Book/Report/Conference proceedingChapter

2 Citations (Scopus)

Abstract

Functional gene networks link genes based on their functional relatedness, which is inferred from various complementary biological datasets. Gene networks comprising vast amounts of data can be used to predict which genes are associated with complex traits. Decades of studies in plant biology using the model organism Arabidopsis thaliana have generated large amounts of information, enabling the development of a system-level molecular network. AraNet (currently version 2) is a genome-scale functional gene network for Arabidopsis thaliana, constructed by integrating 19 types of genomics data and can be explored through a web-server (http://www.inetbio.org/aranet) to identify candidate genes for traits of interest. AraNet provides two alternative search paths for users to identify candidate genes and functions. The web server also exploits ortholog relationships between plant species and projects the genes of 28 other plant species (as of April, 2016) into the network of Arabidopsis genes. This allows researchers to use AraNet to predict genes/functions of not only Arabidopsis but also other non-model plants by expanding the functional knowledge of Arabidopsis. Here, we present a detailed description of how to search the AraNet network and interpret the search results to study plant gene functions and their associations with complex phenotypes.

Original languageEnglish
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages225-238
Number of pages14
DOIs
Publication statusPublished - 2017 Jan 1

Publication series

NameMethods in Molecular Biology
Volume1629
ISSN (Print)1064-3745

Fingerprint

Arabidopsis
Gene Regulatory Networks
Genes
Plant Genes
Genomics
Research Personnel
Genome
Phenotype

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

Cite this

Lee, T., & Lee, I. S. (2017). AraNet: A network biology server for Arabidopsis thaliana and other non-model plant species. In Methods in Molecular Biology (pp. 225-238). (Methods in Molecular Biology; Vol. 1629). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7125-1_15
Lee, Tak ; Lee, In suk. / AraNet : A network biology server for Arabidopsis thaliana and other non-model plant species. Methods in Molecular Biology. Humana Press Inc., 2017. pp. 225-238 (Methods in Molecular Biology).
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Lee, T & Lee, IS 2017, AraNet: A network biology server for Arabidopsis thaliana and other non-model plant species. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1629, Humana Press Inc., pp. 225-238. https://doi.org/10.1007/978-1-4939-7125-1_15

AraNet : A network biology server for Arabidopsis thaliana and other non-model plant species. / Lee, Tak; Lee, In suk.

Methods in Molecular Biology. Humana Press Inc., 2017. p. 225-238 (Methods in Molecular Biology; Vol. 1629).

Research output: Chapter in Book/Report/Conference proceedingChapter

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Lee T, Lee IS. AraNet: A network biology server for Arabidopsis thaliana and other non-model plant species. In Methods in Molecular Biology. Humana Press Inc. 2017. p. 225-238. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-7125-1_15