An eight-year government supported project investigating the control of industrial plant material production processes via genetic engineering in Japan
Daisuke Shibata, Atsuhiko Shinmyo. . . . . . . 1 [PDF]
Practical network approaches and biologic interpretations of co-expression analyses in plants
Yoshiyuki Ogata, Daisuke Shibata. . . . . . . 3 [PDF]
Co-expression network analysis using DNA microarray datasets can be used to predict the functions of many plant genes. Here, we introduce recent reports for co-expression network analyses in plants and summarize practical approaches for such analyses.
DAGViz : a directed acyclic graph browser that supports analysis of Gene Ontology annotation
Kentaro Yano, Koh Aoki, Hideyuki Suzuki, Daisuke Shibata. . . . . . . 9 [PDF]
We have constructed a web-tool “DAGViz” for browsing relationships among GO terms based on directed acyclic graphs (DAGs) (http://www.pgb.kazusa.or.jp/dagviz/). By displaying all GO terms assigned to genes of interest within a single screen, DAGViz aids in the systematic grasping of gene function.
Functional genomics of the Dof transcription factor family genes in suspension-cultured cells of Arabidopsis thaliana
Yayoi Tsujimoto-Inui, Yuki Naito, Nozomu Sakurai, Hideyuki Suzuki, Ryosuke Sasaki, Hideyuki Takahashi, Namie Ohtsuki, Toshitsugu Nakano, Shuichi Yanagisawa, Daisuke Shibata, Hirofumi Uchimiya, Hideaki Shinshi, Kaoru Suzuki. . . . . . . 15 [PDF]
We examined transcriptional profiles in the Dof gene-overexpressed calli using an Arabidopsis DNA microarray analysis. Based on the results, possible involvements of the Dof genes in regulation of metabolic pathways were discussed.
Manipulation of plant metabolic pathways by transcription factors
Akira Iwase, Kyoko Matsui, Masaru Ohme-Takagi. . . . . . . 29 [PDF]This review describes the advantages of transcription factors for metabolic engineering in plants. Transcriptional activators and repressors, including the chimeric repressors, are useful tools for the genetic engineering of metabolic pathways. This report summarizes the strategies for the detection of regulators and enzyme genes involved in metabolic pathways.
Metabolic pathway engineering by plastid transformation is a powerful tool for production of compounds in higher plants
Tomohisa Hasunuma, Akihiko Kondo, Chikahiro Miyake. . . . . . . 39 [PDF]