PlaNet: Comparative Co-Expression Network Analyses for Plants

Methods Mol Biol. 2017;1533:213-227. doi: 10.1007/978-1-4939-6658-5_12.

Abstract

Functional relations between genes can be represented as networks. These networks have been successfully used to infer gene function and to mediate transfer of functional knowledge between species. Transcriptionally coordinated or co-expressed genes tend to be functionally related, which combined with availability of transcriptomic data for multiple plant species make the co-expression networks a useful resource for the plant community. In this chapter, we describe PlaNet ( www.gene2function.de ), a database that includes comparative analyses for co-expression networks of 11 plant species. We exemplify how the tools included in PlaNet can be used to predict gene function, transfer knowledge, and discover conserved and multiplied gene modules.

Keywords: Co-expression; Comparative transcriptomics; Function prediction; Functional association; Gene modules; Gene networks; Knowledge transfer.

MeSH terms

  • Computational Biology / methods*
  • Gene Expression Profiling
  • Gene Expression Regulation, Plant*
  • Gene Ontology
  • Gene Regulatory Networks*
  • Molecular Sequence Annotation
  • Plants / genetics*
  • Software*
  • Transcriptome
  • Web Browser