Yasuhiro Otomo
Analysis Group
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Publication
Featured researches published by Yasuhiro Otomo.
PLOS ONE | 2007
Kouji Satoh; Koji Doi; Toshifumi Nagata; Naoki Kishimoto; Kohji Suzuki; Yasuhiro Otomo; Jun Kawai; Mari Nakamura; Tomoko Hirozane-Kishikawa; Saeko Kanagawa; Takahiro Arakawa; Juri Takahashi-Iida; Mitsuyoshi Murata; Noriko Ninomiya; Daisuke Sasaki; Shiro Fukuda; Michihira Tagami; Harumi Yamagata; Kanako Kurita; Kozue Kamiya; Mayu Yamamoto; Ari Kikuta; Takahito Bito; Nahoko Fujitsuka; Kazue Ito; Hiroyuki Kanamori; Il-Ryong Choi; Yoshiaki Nagamura; Takashi Matsumoto; Kazuo Murakami
Rice (Oryza sativa L.) is a model organism for the functional genomics of monocotyledonous plants since the genome size is considerably smaller than those of other monocotyledonous plants. Although highly accurate genome sequences of indica and japonica rice are available, additional resources such as full-length complementary DNA (FL-cDNA) sequences are also indispensable for comprehensive analyses of gene structure and function. We cross-referenced 28.5K individual loci in the rice genome defined by mapping of 578K FL-cDNA clones with the 56K loci predicted in the TIGR genome assembly. Based on the annotation status and the presence of corresponding cDNA clones, genes were classified into 23K annotated expressed (AE) genes, 33K annotated non-expressed (ANE) genes, and 5.5K non-annotated expressed (NAE) genes. We developed a 60mer oligo-array for analysis of gene expression from each locus. Analysis of gene structures and expression levels revealed that the general features of gene structure and expression of NAE and ANE genes were considerably different from those of AE genes. The results also suggested that the cloning efficiency of rice FL-cDNA is associated with the transcription activity of the corresponding genetic locus, although other factors may also have an effect. Comparison of the coverage of FL-cDNA among gene families suggested that FL-cDNA from genes encoding rice- or eukaryote-specific domains, and those involved in regulatory functions were difficult to produce in bacterial cells. Collectively, these results indicate that rice genes can be divided into distinct groups based on transcription activity and gene structure, and that the coverage bias of FL-cDNA clones exists due to the incompatibility of certain eukaryotic genes in bacteria.
DNA Research | 2003
Hisako Ooka; Kouji Satoh; Koji Doi; Toshifumi Nagata; Yasuhiro Otomo; Kazuo Murakami; Kenichi Matsubara; Naoki Osato; Jun Kawai; Piero Carninci; Yoshihide Hayashizaki; Koji Suzuki; Keiichi Kojima; Yoshinori Takahara; Koji Yamamoto; Shoshi Kikuchi
Archive | 2003
Shoshi Kikuchi; Naoki Kishimoto; Kouji Satoh; Toshifumi Nagata; Nobuyuki Kawagashira; Junshi Yazaki; Masahiro Ishikawa; Koji Doi; Jun Kawai; Yoshihide Hayashizaki; Yasuhiro Otomo; Kenichi Matsubara; Kazuo Murakami
Archive | 2002
Kouji Doi; Yoshihide Hayashizaki; Masahiro Ishikawa; Jun Kawai; Nobuyuki Kawazu; Hisashi Kikuchi; Naoki Kishimoto; Kenichi Matsubara; Kazuo Murakami; Toshibumi Nagata; Yasuhiro Otomo; Koji Sato; Jiyunji Yazaki; 浩二 佐藤; 考爾 土井; 泰裕 大友; 直己 岸本; 信之 川頭; 和雄 村上; 謙一 松原; 良英 林崎; 俊文 永田; 純 河合; 潤史 矢崎; 雅弘 石川; 尚志 菊池
Physiological Genomics | 2004
Junshi Yazaki; Zenpei Shimatani; Akiko Hashimoto; Yuko Nagata; Fumiko Fujii; Keiichi Kojima; Kohji Suzuki; Toshiki Taya; Mio Tonouchi; Charles F. Nelson; Allen Nakagawa; Yasuhiro Otomo; Kazuo Murakami; Kenichi Matsubara; Jun Kawai; Piero Carninci; Yoshihide Hayashizaki; Shoshi Kikuchi
DNA Research | 2003
Junshi Yazaki; Naoki Kishimoto; Yuko Nagata; Masahiro Ishikawa; Fumiko Fujii; Akiko Hashimoto; Kanako Shimbo; Zenpei Shimatani; Keiichi Kojima; Kouji Suzuki; Makoto Yamamoto; Sachiko Honda; Ayano Endo; Yumiko Yoshida; Yuki Sato; Keiko Takeuchi; Kazuko Toyoshima; Chikako Miyamoto; Jianzhong Wu; Takuji Sasaki; Katsumi Sakata; Kimiko Yamamoto; Koh Iba; Takahiro Oda; Yasuhiro Otomo; Kazuo Murakami; Kenichi Matsubara; Jun Kawai; Piero Carninci; Yoshihide Hayashizaki
Molecular Biology and Evolution | 2004
Toshifumi Nagata; Shigemi Iizumi; Kouji Satoh; Hisako Ooka; Jun Kawai; Piero Carninci; Yoshihide Hayashizaki; Yasuhiro Otomo; Kazuo Murakami; Kenichi Matsubara; Shoshi Kikuchi
Archive | 2005
Motonari Daito; Kazuki Nakabayashi; Yasuhiro Otomo; Masako Sonoda; Takayuki Takahata; 一樹 中林; 泰裕 大友; 元就 大東; 理子 薗田; 隆之 高畑
Archive | 2004
Shigeki Abe; Kazuki Nakabayashi; Yasuhiro Otomo; Kazuhiko Takeda; 一樹 中林; 泰裕 大友; 和彦 武田; 滋樹 阿部
Archive | 2008
Kazuhiro Ishida; Hiroyuki Kahata; Yasuhiro Otomo; Ryoko Ri; Kozo Sudo; Kenji Tanaka; Ushio Tateda; 博幸 加畑; 泰裕 大友; 潮 建田; 良子 李; 憲次 田中; 和博 石田; 浩三 須藤