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Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones

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Title: Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Authors: Imanishi, Tadashi Browse this author
Itoh, Takeshi Browse this author
Suzuki, Yutaka Browse this author
O'Donovan, Claire Browse this author
Fukuchi, Satoshi Browse this author
Koyanagi, Kanako O. Browse this author
Barrero, Roberto A. Browse this author
Tamura, Takuro Browse this author
Yamaguchi-Kabata, Yumi Browse this author
Tanino, Motohiko Browse this author
Yura, Kei Browse this author
Miyazaki, Satoru Browse this author
Ikeo, Kazuho Browse this author
Homma, Keiichi Browse this author
Kasprzyk, Arek Browse this author
Nishikawa, Tetsuo Browse this author
Hirakawa, Mika Browse this author
Thierry-Mieg, Jean Browse this author
Thierry-Mieg, Danielle Browse this author
Ashurst, Jennifer Browse this author
Jia, Libin Browse this author
Nakao, Mitsuteru Browse this author
Thomas, Michael A. Browse this author
Mulder, Nicola Browse this author
Karavidopoulou, Youla Browse this author
Jin, Lihua Browse this author
Kim, Sangsoo Browse this author
Yasuda, Tomohiro Browse this author
Lenhard, Boris Browse this author
Eveno, Eric Browse this author
Suzuki, Yoshiyuki Browse this author
Yamasaki, Chisato Browse this author
Takeda, Jun-ichi Browse this author
Gough, Craig Browse this author
Hilton, Phillip Browse this author
Fujii, Yasuyuki Browse this author
Sakai, Hiroaki Browse this author
Tanaka, Susumu Browse this author
Amid, Clara Browse this author
Bellgard, Matthew Browse this author
Bonaldo, Maria de Fatima Browse this author
Bono, Hidemasa Browse this author
Bromberg, Susan K. Browse this author
Brookes, Anthony J. Browse this author
Bruford, Elspeth Browse this author
Carninci, Piero Browse this author
Chelala, Claude Browse this author
Couillault, Christine Browse this author
Souza, Sandro J. de Browse this author
Debily, Marie-Anne Browse this author
Devignes, Marie-Dominique Browse this author
Dubchak, Inna Browse this author
Endo, Toshinori Browse this author
Estreicher, Anne Browse this author
Eyras, Eduardo Browse this author
Fukami-Kobayashi, Kaoru Browse this author
R. Gopinath, Gopal Browse this author
Graudens, Esther Browse this author
Hahn, Yoonsoo Browse this author
Han, Michael Browse this author
Han, Ze-Guang Browse this author
Hanada, Kousuke Browse this author
Hanaoka, Hideki Browse this author
Harada, Erimi Browse this author
Hashimoto, Katsuyuki Browse this author
Hinz, Ursula Browse this author
Hirai, Momoki Browse this author
Hishiki, Teruyoshi Browse this author
Hopkinson, Ian Browse this author
Imbeaud, Sandrine Browse this author
Inoko, Hidetoshi Browse this author
Kanapin, Alexander Browse this author
Kaneko, Yayoi Browse this author
Kasukawa, Takeya Browse this author
Kelso, Janet Browse this author
Kersey, Paul Browse this author
Kikuno, Reiko Browse this author
Kimura, Kouichi Browse this author
Korn, Bernhard Browse this author
Kuryshev, Vladimir Browse this author
Makalowska, Izabela Browse this author
Makino, Takashi Browse this author
Mano, Shuhei Browse this author
Mariage-Samson, Regine Browse this author
Mashima, Jun Browse this author
Matsuda, Hideo Browse this author
Mewes, Hans-Werner Browse this author
Minoshima, Shinsei Browse this author
Nagai, Keiichi Browse this author
Nagasaki, Hideki Browse this author
Nagata, Naoki Browse this author
Nigam, Rajni Browse this author
Ogasawara, Osamu Browse this author
Ohara, Osamu Browse this author
Ohtsubo, Masafumi Browse this author
Okada, Norihiro Browse this author
Okido, Toshihisa Browse this author
Oota, Satoshi Browse this author
Ota, Motonori Browse this author
Ota, Toshio Browse this author
Otsuki, Tetsuji Browse this author
Piatier-Tonneau, Dominique Browse this author
Poustka, Annemarie Browse this author
Ren, Shuang-Xi Browse this author
Saitou, Naruya Browse this author
Sakai, Katsunaga Browse this author
Sakamoto, Shigetaka Browse this author
Sakate, Ryuichi Browse this author
Schupp, Ingo Browse this author
Servant, Florence Browse this author
Sherry, Stephen Browse this author
Shiba, Rie Browse this author
Shimizu, Nobuyoshi Browse this author
Shimoyama, Mary Browse this author
Simpson, Andrew J. Browse this author
Soares, Bento Browse this author
Steward, Charles Browse this author
Suwa, Makiko Browse this author
Suzuki, Mami Browse this author
Takahashi, Aiko Browse this author
Tamiya, Gen Browse this author
Tanaka, Hiroshi Browse this author
Taylor, Todd Browse this author
Terwilliger, Joseph D. Browse this author
Unneberg, Per Browse this author
Veeramachaneni, Vamsi Browse this author
Watanabe, Shinya Browse this author
Wilming, Laurens Browse this author
Yasuda, Norikazu Browse this author
Yoo, Hyang-Sook Browse this author
Stodolsky, Marvin Browse this author
Makalowski, Wojciech Browse this author
Go, Mitiko Browse this author
Nakai, Kenta Browse this author
Takagi, Toshihisa Browse this author
Kanehisa, Minoru Browse this author
Sakaki, Yoshiyuki Browse this author
Quackenbush, John Browse this author
Okazaki, Yasushi Browse this author
Hayashizaki, Yoshihide Browse this author
Hide, Winston Browse this author
Chakraborty, Ranajit Browse this author
Nishikawa, Ken Browse this author
Sugawara, Hideaki Browse this author
Tateno, Yoshio Browse this author
Chen, Zhu Browse this author
Oishi, Michio Browse this author
Tonellato, Peter Browse this author
Apweiler, Rolf Browse this author
Okubo, Kousaku Browse this author
Wagner, Lukas Browse this author
Wiemann, Stefan Browse this author
Strausberg, Robert L. Browse this author
Isogai, Takao Browse this author
Auffray, Charles Browse this author
Nomura, Nobuo Browse this author
Gojobori, Takashi Browse this author
Sugano, Sumio Browse this author
Issue Date: Jun-2004
Publisher: Public Library of Science
Journal Title: PLoS Biology
Volume: 2
Issue: 6
Start Page: 856
End Page: 875
Publisher DOI: 10.1371/journal.pbio.0020162
Abstract: The human genome sequence defines our inherent biological potential; the realization of the biology encoded therein requires knowledge of the function of each gene. Currently, our knowledge in this area is still limited. Several lines of investigation have been used to elucidate the structure and function of the genes in the human genome. Even so, gene prediction remains a difficult task, as the varieties of transcripts of a gene may vary to a great extent. We thus performed an exhaustive integrative characterization of 41,118 full-length cDNAs that capture the gene transcripts as complete functional cassettes, providing an unequivocal report of structural and functional diversity at the gene level. Our international collaboration has validated 21,037 human gene candidates by analysis of high-quality full-length cDNA clones through curation using unified criteria. This led to the identification of 5,155 new gene candidates. It also manifested the most reliable way to control the quality of the cDNA clones. We have developed a human gene database, called the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/). It provides the following: integrative annotation of human genes, description of gene structures, details of novel alternative splicing isoforms, non-protein-coding RNAs, functional domains, subcellular localizations, metabolic pathways, predictions of protein three-dimensional structure, mapping of known single nucleotide polymorphisms (SNPs), identification of polymorphic microsatellite repeats within human genes, and comparative results with mouse full-length cDNAs. The H-InvDB analysis has shown that up to 4% of the human genome sequence (National Center for Biotechnology Information build 34 assembly) may contain misassembled or missing regions. We found that 6.5% of the human gene candidates(1,377 loci) did not have a good protein-coding open reading frame, of which 296 loci are strong candidates for nonprotein-coding RNA genes. In addition, among 72,027 uniquely mapped SNPs and insertions/deletions localized within human genes, 13,215 nonsynonymous SNPs, 315 nonsense SNPs, and 452 indels occurred in coding regions. Together with 25 polymorphic microsatellite repeats present in coding regions, they may alter protein structure, causing phenotypic effects or resulting in disease. The H-InvDB platform represents a substantial contribution to resources needed for the exploration of human biology and pathology.
Rights: http://creativecommons.org/licenses/by/3.0/
Type: article
URI: http://hdl.handle.net/2115/50044
Appears in Collections:情報科学院・情報科学研究院 (Graduate School of Information Science and Technology / Faculty of Information Science and Technology) > 雑誌発表論文等 (Peer-reviewed Journal Articles, etc)

Submitter: 遠藤 俊徳

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