Toru Kudo
,
School of Agri., Meiji University, Kawasaki, Japan
Tomoyuki Takano
,
School of Agri., Meiji University, Kawasaki, Japan
Shin Terashima
,
School of Agri., Meiji University, Kawasaki, Japan
Masaaki Kobayashi
,
School of Agri., Meiji University, Kawasaki, Japan
Maasa Kanno
,
School of Agri., Meiji University, Kawasaki, Japan
Kyoko Morimoto
,
School of Agri., Meiji University, Kawasaki, Japan
Hiromi Kanegae
,
School of Agri., Meiji University, Kawasaki, Japan
Soichi Ozaki
,
School of Agri., Meiji University, Kawasaki, Japan
Yohei Sasaki
,
School of Agri., Meiji University, Kawasaki, Japan
Misa Saito
,
School of Agri., Meiji University, CREST, JST, Kawasaki, Kawasaki, Japan
Satomi Asano
,
School of Agri., Meiji University, Kawasaki, Japan
Koji Yokoyama
,
School of Agri., Meiji University, Kawasaki, Japan
Koichiro Aya
,
Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
Keita Suwabe
,
Mie University, Tsu, Japan
Go Suzuki
,
Osaka Kyoiku University, Kashiwara, Japan
Masao Watanabe
,
Tohoku University/Life Sciences, Sendai, Japan
Makoto Matsuoka
,
Bioscience and Biotechnology Center, Nagoya University, Nagoya, Japan
Hajime Ohyanagi
,
School of Agri., Meiji University, Kawasaki, Japan
Kentaro Yano
,
School of Agri., Meiji University, Kawasaki, Japan
Large-scale omics data from different species allow us to reveal conserved and species-specific gene functions. To provide such comprehensive information, we have maintained a web-database Plant Omics Data Center (PODC, http://bioinf.mind.meiji.ac.jp/podc/). The PODC stores information on gene expression networks (GENs) and high-quality functional annotations of genes derived from natural language processing followed by manual curations. The GEN information can be searched and visualized with an intuitive and interactive user-friendly graphical viewer in PODC. This web-tool support researcher to compare GENs among different plant species. As of October 31, 2014, PODC covers 8 plant species:
Arabidopsis thaliana,
Solanum lycopersicum,
Solanum tuberosum,
Oryza sativa,
Sorghum bicolor,
Vitis vinifera,
Medicago truncatula, and
Glycine max.Here, we introduce an example of GEN analysis in PODC. Gene expression analysis in Arabidopsis papilla cell identified candidate genes involved in reproduction (Osaka et al. 2013, Plant Cell Physiol.). Analysis of them in PODC proposed a GEN involving 5 genes related to protein quality control (PQC). These genes showed high expression levels in seed, embryo, and endosperm. One of the genes encodes a plastid localized protein disulfide isomerase (PDI), implying that PQC in plastid has a role in seed development. PODC assists us to find GENs consisted of putative orthologs of the PQC-related genes in the other species. Comparison of the GENs among the species suggested that there are three conserved GENs of PQC-related genes which act in seeds, roots, and leaves.
This work is supported by Research Funding for Computational Software Supporting Program in Meiji University.
