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

Tak Lee, Insuk Lee

Research output: Chapter in Book/Report/Conference proceedingChapter

4 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

Publication series

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

Bibliographical note

Funding Information:
This work was supported by grants from the National Research Foundation of Korea (2015R1A2A1A15055859, 2012M3A9B4 028641, 2012M3A9C7050151).

All Science Journal Classification (ASJC) codes

  • Molecular Biology
  • Genetics

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