Plant Gene Expression Network

The expression profile of a given gene represents the changes in expression levels and it can be established from a variety of experiments including different tissues, organs, developmental stages, and treatments. By using the wealth of publicly available RNA-seq data, we can obtain an overview of genome-wide gene expression profiles under a wide range of experimental conditions. Such gene expression profiles are particularly useful to mine a gene set having a similar expression profile. The similarity indicates that these genes may be involved in the same biological process and/or be regulated by the same transcription factor. For large-scale expression data, the gene expression network (GEN) analysis allows evaluation of the significance of the similarity in expression profiles among genes in a genome-wide manner. In order to efficiently predict the biological functions and regulatory mechanisms of expression for individual genes in GENs, we can assign various kinds of functional descriptions in GENs. This chapter introduces the types of GENs and the methods used to construct them, in addition to the database built from large-scale analysis of public datasets and the integration of existing annotation of the literature (e.g., knowledge-based) to GENs.