RiceFREND: a platform for retrieving coexpressed gene networks in rice

Abstract

Similarity of gene expression across a wide range of biological conditions can be efficiently used in characterization of gene function. We have constructed a rice gene coexpression database, RiceFREND (http://ricefrend.dna.affrc.go.jp/), to identify gene modules with similar expression profiles and provide a platform for more accurate prediction of gene functions. Coexpression analysis of 27 201 genes was performed against 815 microarray data derived from expression profiling of various organs and tissues at different developmental stages, mature organs throughout the growth from transplanting until harvesting in the field and plant hormone treatment conditions, using a single microarray platform. The database is provided with two search options, namely, ‘single guide gene search’ and ‘multiple guide gene search’ to efficiently retrieve information on coexpressed genes. A user-friendly web interface facilitates visualization and interpretation of gene coexpression networks in HyperTree, Cytoscape Web and Graphviz formats. In addition, analysis tools for identification of enriched Gene Ontology terms and cis-elements provide clue for better prediction of biological functions associated with the coexpressed genes. These features allow users to clarify gene functions and gene regulatory networks that could lead to a more thorough understanding of many complex agronomic traits.

Polyploidy enhances F1 pollen sterility loci interactions that increase meiosis abnormalities and pollen sterility in autotetraploid rice

“…To determine predicted gene functions and gene regulatory networks of differentially down-regulated genes that were putatively associated with IPE, coexpression analysis was performed using the RiceFREND database (http:// ricefrend.dna.affrc.go.jp/; Stuart et al, 2003;Sato et al, 2013). To determine the potential functional relevance of the down-regulated genes that are involved in meiosis or expressed at specific stages of meiosis, the PlantCARE database (http://bioinformatics.psb.ugent.be/webtools/plantcare/html/) was used to search for transcriptional cis-elements.…”

Global transcriptome profile of rice root in response to essential macronutrient deficiency

“…2). 18 The upregulated genes under -N condition showed significant enrichment of the GO terms corresponding to transport of cellular component, namely, "oligopeptide transport," "amino acid transport," "lipid transport," "peptide transport," "amine transport" and "organic acid transport," implying that -N treatment affected various cellular metabolic pathways. It has been known that N-deficiency lead to drastic modification of root system architecture and increase of root biomass resulting in decrease of shoot-root ratio.…”

“…GO enrichment test was performed against terms of biological process using the option available in the gene co-expression database RiceFREND. 18 The statistical enriched terms with FDR below 0.05 are highlighted in yellow. to characterize the molecular genetic basis for efficient utilization of essential macronutrients in rice.…”

Genomic survey and gene expression analysis of the VDAC gene family in rice

“…go.jp/), which uses the gene expression data of RiceXPro. The co-expressed gene network in Cytoscape Web and Mutual Rank (MR) list was obtained using a multiple guide gene search in RiceFREND (Sato et al, 2013a).…”