Plant Omics Data Center and CATchUP: web databases for effective gene mining utilizing public RNA-Seq-based transcriptome data

Abstract

Analysis using transcriptome data deposited in public repositories can advance scientific research and crop breeding with minimal extra effort and cost. To provide platforms for quick and easy gene mining from publicly available RNA sequencing (RNA-Seq) data of model and crop plants, we are maintaining two web databases: the Plant Omics Data Center (PODC, http://plantomics.mind.meiji.ac.jp/podc) and CATchUP (http://plantomics.mind.meiji.ac.jp/CATchUP). This chapter presents their functionality, summarizes their stored information and demonstrates a typical workflow using the databases, focusing on Medicago truncatula.