Affymetrix gene expression update

Comprehensive integration of large-scale omics resources such as genomes, transcriptomes and metabolomes will give an insight into a broader aspect of molecular biology. To this end, we have been maintaining the OryzaExpress (gene expression and annotation database for rice), TOMATOMICS (multi-omics database for tomato), and so forth. For better understanding of plant biology in the era of NGS, now we aim to construct the NGS-derived Gene Expression Network (GEN) repository for multiple 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. With the aim of understanding 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 the gene expression stuff, their functional annotations will facilitate further biological comprehension. Currently we are trying to improve the given gene annotations with Natural Language Processing (NLP) techniques and genome-wide SNP information derived by state-of-the-art genotyping technologies (RAD-Seq, GBS, etc.). Here we introduce current status of our analyses and the web database, PODC (Plant Omics Data Center, http://bioinf.mind.meiji.ac.jp/podc/), now opened to the public providing GENs, functional annotations and additional comprehensive omics data. This work is partially supported by Resarch Funding for Computational Software Supporting Program in Meiji University.