Plant Omics Data Center: Updates on the Versatile Web Repository for Interspecies Gene Expression Networks

With the aim of giving an insight into a broader aspect of molecular biology, we have been maintaining some plant omics databases, the OryzaExpress (gene expression and annotation database for rice), TOMATOMICS (multi-omics database for tomato), and so forth. Each of them comprehensively integrates the large-scale omics resources such as genomes, transcriptomes and metabolomes. For better understanding of plant biology in the era of NGS, now we aim to construct and maintain the NGS-derived Gene Expression Network (GEN) database, the PODC (Plant Omics Data Center, http://bioinf.mind.meiji.ac.jp/podc/) for a broad range of plant species. So far we have collected more than 1,000 mRNA-Seq samples of five plant species (Arabidopsis thaliana, Oryza sariva, Solanum lycopersicum, Sorghum bicolor and Vitis vinifera) from the public short read archive, digitally profiled the entire gene expression profiles, and drawn GENs by taking advantage of the Corresponding Analysis with gene expression similarities. In order to understand the evolutionary significance of the GENs among multiple species, they were linked according to the orthology of each node (gene) among species. In addition to the gene expression data, their functional annotations will facilitate further biological comprehension. Currently we are improving the gene annotations with Natural Language Processing (NLP) techniques, enhancing the user interface of the database and integrating genome-wide SNP information derived by RAD-Seq, etc. Here we introduce recent updates on the PODC, providing GENs, functional annotations and additional comprehensive omics data. This work is partially supported by Research Funding for Computational Software Supporting Program in Meiji University.