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5 results on '"Nurimoto, Shin"'

1. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts*

Author

Yamasaki, Chisato, Murakami, Katsuhiko, Fujii, Yasuyuki, Sato, Yoshiharu, Harada, Erimi, Takeda, Jun-ichi, Taniya, Takayuki, Sakate, Ryuichi, Kikugawa, Shingo, Shimada, Makoto, Tanino, Motohiko, Koyanagi, Kanako O., Barrero, Roberto A., Gough, Craig, Chun, Hong-Woo, Habara, Takuya, Hanaoka, Hideki, Hayakawa, Yosuke, Hilton, Phillip B., Kaneko, Yayoi, Kanno, Masako, Kawahara, Yoshihiro, Kawamura, Toshiyuki, Matsuya, Akihiro, Nagata, Naoki, Nishikata, Kensaku, Noda, Akiko Ogura, Nurimoto, Shin, Saichi, Naomi, Sakai, Hiroaki, Sanbonmatsu, Ryoko, Shiba, Rie, Suzuki, Mami, Takabayashi, Kazuhiko, Takahashi, Aiko, Tamura, Takuro, Tanaka, Masayuki, Tanaka, Susumu, Todokoro, Fusano, Yamaguchi, Kaori, Yamamoto, Naoyuki, Okido, Toshihisa, Mashima, Jun, Hashizume, Aki, Jin, Lihua, Lee, Kyung-Bum, Lin, Yi-Chueh, Nozaki, Asami, Sakai, Katsunaga, Tada, Masahito, Miyazaki, Satoru, Makino, Takashi, Ohyanagi, Hajime, Osato, Naoki, Tanaka, Nobuhiko, Suzuki, Yoshiyuki, Ikeo, Kazuho, Saitou, Naruya, Sugawara, Hideaki, OʼDonovan, Claire, Kulikova, Tamara, Whitfield, Eleanor, Halligan, Brian, Shimoyama, Mary, Twigger, Simon, Yura, Kei, Kimura, Kouichi, Yasuda, Tomohiro, Nishikawa, Tetsuo, Akiyama, Yutaka, Motono, Chie, Mukai, Yuri, Nagasaki, Hideki, Suwa, Makiko, Horton, Paul, Kikuno, Reiko, Ohara, Osamu, Lancet, Doron, Eveno, Eric, Graudens, Esther, Imbeaud, Sandrine, Anne Debily, Marie, Hayashizaki, Yoshihide, Amid, Clara, Han, Michael, Osanger, Andreas, Endo, Toshinori, Thomas, Michael A., Hirakawa, Mika, Makalowski, Wojciech, Nakao, Mitsuteru, Kim, Nam-Soon, Yoo, Hyang-Sook, De Souza, Sandro J., de Fatima Bonaldo, Maria, Niimura, Yoshihito, Kuryshev, Vladimir, Schupp, Ingo, Wiemann, Stefan, Bellgard, Matthew, Shionyu, Masafumi, Jia, Libin, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Wagner, Lukas, Zhang, Qinghua, Go, Mitiko, Minoshima, Shinsei, Ohtsubo, Masafumi, Hanada, Kousuke, Tonellato, Peter, Isogai, Takao, Zhang, Ji, Lenhard, Boris, Kim, Sangsoo, Chen, Zhu, Hinz, Ursula, Estreicher, Anne, Nakai, Kenta, Makalowska, Izabela, Hide, Winston, Tiffin, Nicola, Wilming, Laurens, Chakraborty, Ranajit, Soares, Marcelo Bento, Chiusano, Maria Luisa, Suzuki, Yutaka, Auffray, Charles, Yamaguchi-Kabata, Yumi, Itoh, Takeshi, Hishiki, Teruyoshi, Fukuchi, Satoshi, Nishikawa, Ken, Sugano, Sumio, Nomura, Nobuo, Tateno, Yoshio, Imanishi, Tadashi, and Gojobori, Takashi

Published
2008

2. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana : The Rice Annotation Project

Author

Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., Antonio, Baltazar A., Aono, Hideo, Apweiler, Rolf, Bruskiewich, Richard, Bureau, Thomas, Burr, Frances, De Oliveira, Antonio Costa, Fuks, Galina, Habara, Takuya, Haberer, Georg, Han, Bin, Harada, Erimi, Hiraki, Aiko T., Hirochika, Hirohiko, Hoen, Douglas, Hokari, Hiroki, Hosokawa, Satomi, Hsing, Yue Ie, Ikawa, Hiroshi, Ikeo, Kazuho, Imanishi, Tadashi, Ito, Yukiyo, Jaiswal, Pankaj, Kanno, Masako, Kawahara, Yoshihiro, Kawamura, Toshiyuki, Kawashima, Hiroaki, Khurana, Jitendra P., Kikuchi, Shoshi, Komatsu, Setsuko, Koyanagi, Kanako O., Kubooka, Hiromi, Lieberherr, Damien, Lin, Yao Cheng, Lonsdale, David, Matsumoto, Takashi, Matsuya, Akihiro, McCombie, W. Richard, Messing, Joachim, Miyao, Akio, Mulder, Nicola, Nagamura, Yoshiaki, Nam, Jongmin, Namiki, Nobukazu, Numa, Hisataka, Nurimoto, Shin, O'Donovan, Claire, Ohyanagi, Hajime, Okido, Toshihisa, OOta, Satoshi, Osato, Naoki, Palmer, Lance E., Quetier, Francis, Raghuvanshi, Saurabh, Saichi, Naomi, Sakai, Hiroaki, Sakai, Yasumichi, Sakata, Katsumi, Sakurai, Tetsuya, Sato, Fumihiko, Sato, Yoshiharu, Schoof, Heiko, Seki, Motoaki, Shibata, Michie, Shimizu, Yuji, Shinozaki, Kazuo, Shinso, Yuji, Singh, Nagendra K., Smith-White, Brian, Takeda, Jun Ichi, Tanino, Motohiko, Tatusova, Tatiana, Thongjuea, Supat, Todokoro, Fusano, Tsugane, Mika, Tyagi, Akhilesh K., Vanavichit, Apichart, Wang, Aihui, Wing, Rod A., Yamaguchi, Kaori, Yamamoto, Mayu, Yamamoto, Naoyuki, Yu, Yeisoo, Zhao, Qiang, Higo, Kenichi, Burr, Benjamin, Gojobori, Takashi, Sasaki, Takuji, Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., Antonio, Baltazar A., Aono, Hideo, Apweiler, Rolf, Bruskiewich, Richard, Bureau, Thomas, Burr, Frances, De Oliveira, Antonio Costa, Fuks, Galina, Habara, Takuya, Haberer, Georg, Han, Bin, Harada, Erimi, Hiraki, Aiko T., Hirochika, Hirohiko, Hoen, Douglas, Hokari, Hiroki, Hosokawa, Satomi, Hsing, Yue Ie, Ikawa, Hiroshi, Ikeo, Kazuho, Imanishi, Tadashi, Ito, Yukiyo, Jaiswal, Pankaj, Kanno, Masako, Kawahara, Yoshihiro, Kawamura, Toshiyuki, Kawashima, Hiroaki, Khurana, Jitendra P., Kikuchi, Shoshi, Komatsu, Setsuko, Koyanagi, Kanako O., Kubooka, Hiromi, Lieberherr, Damien, Lin, Yao Cheng, Lonsdale, David, Matsumoto, Takashi, Matsuya, Akihiro, McCombie, W. Richard, Messing, Joachim, Miyao, Akio, Mulder, Nicola, Nagamura, Yoshiaki, Nam, Jongmin, Namiki, Nobukazu, Numa, Hisataka, Nurimoto, Shin, O'Donovan, Claire, Ohyanagi, Hajime, Okido, Toshihisa, OOta, Satoshi, Osato, Naoki, Palmer, Lance E., Quetier, Francis, Raghuvanshi, Saurabh, Saichi, Naomi, Sakai, Hiroaki, Sakai, Yasumichi, Sakata, Katsumi, Sakurai, Tetsuya, Sato, Fumihiko, Sato, Yoshiharu, Schoof, Heiko, Seki, Motoaki, Shibata, Michie, Shimizu, Yuji, Shinozaki, Kazuo, Shinso, Yuji, Singh, Nagendra K., Smith-White, Brian, Takeda, Jun Ichi, Tanino, Motohiko, Tatusova, Tatiana, Thongjuea, Supat, Todokoro, Fusano, Tsugane, Mika, Tyagi, Akhilesh K., Vanavichit, Apichart, Wang, Aihui, Wing, Rod A., Yamaguchi, Kaori, Yamamoto, Mayu, Yamamoto, Naoyuki, Yu, Yeisoo, Zhao, Qiang, Higo, Kenichi, Burr, Benjamin, Gojobori, Takashi, and Sasaki, Takuji

Abstract

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ∼32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.

Published
2007

3. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana

Author

Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., Antonio, Baltazar A., Aono, Hideo, Apweiler, Rolf, Bruskiewich, Richard, Bureau, Thomas, Burr, Frances, Costa de Oliveira, Antonio, Fuks, Galina, Habara, Takuya, Haberer, Georg, Han, Bin, Harada, Erimi, Hiraki, Aiko T., Hirochika, Hirohiko, Hoen, Douglas, Hokari, Hiroki, Hosokawa, Satomi, Hsing, Yue, Ikawa, Hiroshi, Ikeo, Kazuho, Imanishi, Tadashi, Ito, Yukiyo, Jaiswal, Pankaj, Kanno, Masako, Kawahara, Yosihiro, Kawamura, Toshiyuki, Kawashima, Hiroaki, Khurana, Jitendra P., Kikuchi, Shoshi, Komatsu, Setsuko, Koyanagi, Kanako O., Kubooka, Hiromi, McCombie, W. Richard, Messing, Joachim, Miyao, Akio, Mulder, Nicola, Nagamura, Yoshiaki, Nam, Jongmin, Namiki, Nobukazu, Numa, Hisataka, Nurimoto, Shin, O'Donovan, Claire, Ohyanagi, Hajimi, Liberherr, Damien, Lin, Yao-Cheng, Lonsdale, David, Matsumoto, Takashi, Matsuya, Akihiro, Okido, Toshihisa, OOta, Satoshi, Osato, Naoki, Palmer, Lance E., Quetier, Francis, Raghuvanshi, Surabh, Saichi, Naomi, Sakai, Hiroaki, Sakai, Yasumichi, Sakata, Katsumi, Sakurai, Tetsuya, Sato, Fumihiko, Sato, Yoshiharu, Schoof, Heiko, Seki, Motoaki, Shibata, Katsumi, Shibata, Michie, Shimizu, Yuji, Shinozaki, Kazuo, Shinso, Yuji, Singh, Nagendra K., Smith-White, Brian, Takeda, Jun-ichi, Tanino, Motohiko, Tatusova, Tatiana, Thongjuea, Supat, Todokoro, Fusano, Tsugane, Mika, Tyagi, Akhilesh K., Vanavichit, Apichart, Wang, Aihui, Wing, Rod A., Yamaguchi, Kaori, Yamamoto, Mayu, Yamamoto, Naoyuki, Yu, Yeisoo, Zhang, Hao, Zhao, Qiang, Higo, Kenichi, Burr, Benjamin, Gojobori, Takashi, Saski, Takuji, Itoh, Takeshi, Tanaka, Tsuyoshi, Barrero, Roberto A., Yamasaki, Chisato, Fujii, Yasuyuki, Hilton, Phillip B., Antonio, Baltazar A., Aono, Hideo, Apweiler, Rolf, Bruskiewich, Richard, Bureau, Thomas, Burr, Frances, Costa de Oliveira, Antonio, Fuks, Galina, Habara, Takuya, Haberer, Georg, Han, Bin, Harada, Erimi, Hiraki, Aiko T., Hirochika, Hirohiko, Hoen, Douglas, Hokari, Hiroki, Hosokawa, Satomi, Hsing, Yue, Ikawa, Hiroshi, Ikeo, Kazuho, Imanishi, Tadashi, Ito, Yukiyo, Jaiswal, Pankaj, Kanno, Masako, Kawahara, Yosihiro, Kawamura, Toshiyuki, Kawashima, Hiroaki, Khurana, Jitendra P., Kikuchi, Shoshi, Komatsu, Setsuko, Koyanagi, Kanako O., Kubooka, Hiromi, McCombie, W. Richard, Messing, Joachim, Miyao, Akio, Mulder, Nicola, Nagamura, Yoshiaki, Nam, Jongmin, Namiki, Nobukazu, Numa, Hisataka, Nurimoto, Shin, O'Donovan, Claire, Ohyanagi, Hajimi, Liberherr, Damien, Lin, Yao-Cheng, Lonsdale, David, Matsumoto, Takashi, Matsuya, Akihiro, Okido, Toshihisa, OOta, Satoshi, Osato, Naoki, Palmer, Lance E., Quetier, Francis, Raghuvanshi, Surabh, Saichi, Naomi, Sakai, Hiroaki, Sakai, Yasumichi, Sakata, Katsumi, Sakurai, Tetsuya, Sato, Fumihiko, Sato, Yoshiharu, Schoof, Heiko, Seki, Motoaki, Shibata, Katsumi, Shibata, Michie, Shimizu, Yuji, Shinozaki, Kazuo, Shinso, Yuji, Singh, Nagendra K., Smith-White, Brian, Takeda, Jun-ichi, Tanino, Motohiko, Tatusova, Tatiana, Thongjuea, Supat, Todokoro, Fusano, Tsugane, Mika, Tyagi, Akhilesh K., Vanavichit, Apichart, Wang, Aihui, Wing, Rod A., Yamaguchi, Kaori, Yamamoto, Mayu, Yamamoto, Naoyuki, Yu, Yeisoo, Zhang, Hao, Zhao, Qiang, Higo, Kenichi, Burr, Benjamin, Gojobori, Takashi, and Saski, Takuji

Abstract

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is ~32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.

Published
2007

4. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts

Author

Yamasaki, Chisato, Murakami, Katsuhiko, Fujii, Yasuyuki, Sato, Yoshiharu, Harada, Erimi, Takeda, Jun-Ichi, Taniya, Takayuki, Sakate, Ryuichi, Kikugawa, Shingo, Shimada, Makoto, Tanino, Motohiko, Koyanagi, Kanako O., Barrero, Roberto A., Gough, Craig, Chun, Hong-Woo, Habara, Takuya, Hanaoka, Hideki, Hayakawa, Yosuke, Hilton, Phillip B., Kaneko, Yayoi, Kanno, Masako, Kawahara, Yoshihiro, Kawamura, Toshiyuki, Matsuya, Akihiro, Nagata, Naoki, Nishikata, Kensaku, Noda, Akiko Ogura, Nurimoto, Shin, Saichi, Naomi, Sakai, Hiroaki, Sanbonmatsu, Ryoko, Shiba, Rie, Suzuki, Mami, Takabayashi, Kazuhiko, Takahashi, Aiko, Tamura, Takuro, Tanaka, Masayuki, Tanaka, Susumu, Todokoro, Fusano, Yamaguchi, Kaori, Yamamoto, Naoyuki, Okido, Toshihisa, Mashima, Jun, Hashizume, Aki, Jin, Lihua, Lee, Kyung-Bum, Lin, Yi-Chueh, Nozaki, Asami, Sakai, Katsunaga, Tada, Masahito, Miyazaki, Satoru, Makino, Takashi, Ohyanagi, Hajime, Osato, Naoki, Tanaka, Nobuhiko, Suzuki, Yoshiyuki, Ikeo, Kazuho, Saitou, Naruya, Sugawara, Hideaki, O Donovan, Claire, Kulikova, Tamara, Whitfield, Eleanor, Halligan, Brian, Shimoyama, Mary, Twigger, Simon, Yura, Kei, Kimura, Kouichi, Yasuda, Tomohiro, Nishikawa, Tetsuo, Akiyama, Yutaka, Motono, Chie, Mukai, Yuri, Nagasaki, Hideki, Suwa, Makiko, Horton, Paul, Kikuno, Reiko, Ohara, Osamu, Lancet, Doron, Eveno, Eric, Graudens, Esther, Imbeaud, Sandrine, Debily, Marie Anne, Hayashizaki, Yoshihide, Amid, Clara, Han, Michael, Osanger, Andreas, Endo, Toshinori, Thomas, Michael A., Hirakawa, Mika, Makalowski, Wojciech, Nakao, Mitsuteru, Kim, Nam-Soon, Yoo, Hyang-Sook, Souza, Sandro J., Bonaldo, Maria Fatima, Niimura, Yoshihito, Kuryshev, Vladimir, Schupp, Ingo, Wiemann, Stefan, Bellgard, Matthew, Shionyu, Masafumi, Jia, Libin, Thierry-Mieg, Danielle, Thierry-Mieg, Jean, Wagner, Lukas, Zhang, Qinghua, Go, Mitiko, Minoshima, Shinsei, Ohtsubo, Masafumi, Hanada, Kousuke, Tonellato, Peter, Isogai, Takao, Zhang, Ji, Lenhard, Boris, Kim, Sangsoo, Chen, Zhu, Hinz, Ursula, Estreicher, Anne, Nakai, Kenta, Makalowska, Izabela, Winston Hide, Tiffin, Nicola, Wilming, Laurens, Chakraborty, Ranajit, Soares, Marcelo Bento, Chiusano, Maria Luisa, Suzuki, Yutaka, Auffray, Charles, Yamaguchi-Kabata, Yumi, Itoh, Takeshi, Hishiki, Teruyoshi, Fukuchi, Satoshi, Nishikawa, Ken, Sugano, Sumio, Nomura, Nobuo, Tateno, Yoshio, Imanishi, Tadashi, Gojobori, Takashi, and Genome Information Integration Project And, H. Invitational

5. Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana.

Author

Itoh T, Tanaka T, Barrero RA, Yamasaki C, Fujii Y, Hilton PB, Antonio BA, Aono H, Apweiler R, Bruskiewich R, Bureau T, Burr F, Costa de Oliveira A, Fuks G, Habara T, Haberer G, Han B, Harada E, Hiraki AT, Hirochika H, Hoen D, Hokari H, Hosokawa S, Hsing YI, Ikawa H, Ikeo K, Imanishi T, Ito Y, Jaiswal P, Kanno M, Kawahara Y, Kawamura T, Kawashima H, Khurana JP, Kikuchi S, Komatsu S, Koyanagi KO, Kubooka H, Lieberherr D, Lin YC, Lonsdale D, Matsumoto T, Matsuya A, McCombie WR, Messing J, Miyao A, Mulder N, Nagamura Y, Nam J, Namiki N, Numa H, Nurimoto S, O'Donovan C, Ohyanagi H, Okido T, Oota S, Osato N, Palmer LE, Quetier F, Raghuvanshi S, Saichi N, Sakai H, Sakai Y, Sakata K, Sakurai T, Sato F, Sato Y, Schoof H, Seki M, Shibata M, Shimizu Y, Shinozaki K, Shinso Y, Singh NK, Smith-White B, Takeda J, Tanino M, Tatusova T, Thongjuea S, Todokoro F, Tsugane M, Tyagi AK, Vanavichit A, Wang A, Wing RA, Yamaguchi K, Yamamoto M, Yamamoto N, Yu Y, Zhang H, Zhao Q, Higo K, Burr B, Gojobori T, and Sasaki T

Subjects
Arabidopsis Proteins genetics, Codon genetics, DNA, Complementary genetics, DNA, Plant genetics, Databases, Protein, Evolution, Molecular, Genetic Variation, Mutagenesis, Insertional, Open Reading Frames, Plant Proteins genetics, RNA, Messenger genetics, RNA, Plant genetics, RNA, Transfer genetics, Species Specificity, Arabidopsis genetics, Genome, Plant, Oryza genetics
Abstract

We present here the annotation of the complete genome of rice Oryza sativa L. ssp. japonica cultivar Nipponbare. All functional annotations for proteins and non-protein-coding RNA (npRNA) candidates were manually curated. Functions were identified or inferred in 19,969 (70%) of the proteins, and 131 possible npRNAs (including 58 antisense transcripts) were found. Almost 5000 annotated protein-coding genes were found to be disrupted in insertional mutant lines, which will accelerate future experimental validation of the annotations. The rice loci were determined by using cDNA sequences obtained from rice and other representative cereals. Our conservative estimate based on these loci and an extrapolation suggested that the gene number of rice is approximately 32,000, which is smaller than previous estimates. We conducted comparative analyses between rice and Arabidopsis thaliana and found that both genomes possessed several lineage-specific genes, which might account for the observed differences between these species, while they had similar sets of predicted functional domains among the protein sequences. A system to control translational efficiency seems to be conserved across large evolutionary distances. Moreover, the evolutionary process of protein-coding genes was examined. Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene.

Published
2007
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