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Publicly available microarray-based transcriptome data on plants are remarkably valuable in terms of abundance and variation of samples, particularly for Oryza sativa (rice) and Arabidopsis thaliana (Arabidopsis). Here, we introduce the web database PlantExpress (http://plantomics.mind.meiji.ac.jp/PlantExpress/) as a platform for gene expression network (GEN) analysis with the public microarray data of rice and Arabidopsis. PlantExpress has two functional modes. The single-species mode is specialized for GEN analysis within one of the species, while the cross-species mode is optimized for comparative GEN analysis between the species. The single-species mode for rice is the new version of OryzaExpress, which we have maintained since 2006. The single-species mode for Arabidopsis, named ArthaExpress, was newly developed. PlantExpress stores data obtained from three microarrays, the Affymetrix Rice Genome Array, the Agilent Rice Gene Expression 4x44K Microarray, and the Affymetrix Arabidopsis ATH1 Genome Array, with respective totals of 2,678, 1,206, and 10,940 samples. This database employs a ‘MyList’ function with which users may save lists of arbitrary genes and samples (experimental conditions) to use in analyses. In cross-species mode, the MyList function allows performing comparative GEN analysis between rice and Arabidopsis. In addition, the gene lists saved in MyList can be directly exported to the PODC database, which provides information and a platform for comparative GEN analysis based on RNA-seq data and knowledge-based functional annotation of plant genes. PlantExpress will facilitate understanding the biological functions of plant genes.

Analysis of a gene expression network (GEN), which is constructed based on similarity of gene expression profiles, is a widely used approach to gain clues for new biological insights. The recent abundant availability of transcriptome data in public databases is enabling GEN analysis under various experimental conditions, and even comparative GEN analysis across species. To provide a platform to gain biological insights from public transcriptome data, valuable databases have been created and maintained. This chapter introduces the web database OryzaExpress, providing omics information on Oryza sativa (rice). The integrated database Plant Omics Data Center, supporting a wide variety of plant species, is also described to compare omics information among multiple plant species.

Comprehensive integration of large-scale omics resources such as genomes, transcriptomes and metabolomes will provide deeper insights into broader aspects of molecular biology. For better understanding of plant biology, we aim to construct a next-generation sequencing (NGS)-derived gene expression network (GEN) repository for a broad range of plant species. So far we have incorporated information about 745 high-quality mRNA sequencing (mRNA-Seq) samples from eight plant species (Arabidopsis thaliana, Oryza sativa, Solanum lycopersicum, Sorghum bicolor, Vitis vinifera, Solanum tuberosum, Medicago truncatula and Glycine max) from the public short read archive, digitally profiled the entire set of gene expression profiles, and drawn GENs by using correspondence analysis (CA) to take advantage of gene expression similarities. In order to understand the evolutionary significance of the GENs from multiple species, they were linked according to the orthology of each node (gene) among species. In addition to other gene expression information, functional annotation of the genes will facilitate biological comprehension. Currently we are improving the given gene annotations with natural language processing (NLP) techniques and manual curation. Here we introduce the current status of our analyses and the web database, PODC (Plant Omics Data Center; http://bioinf.mind.meiji.ac.jp/podc/), now open to the public, providing GENs, functional annotations and additional comprehensive omics resources., (© The Author 2014. Published by Oxford University Press on behalf of Japanese Society of Plant Physiologists.)