Integrative annotation of 21,037 human genes validated by full-length cDNA clones.

Tadashi Imanishi 1 Takeshi Itoh Yutaka Suzuki Claire O'Donovan Satoshi Fukuchi O. Koyanagi Kanako A. Barrero Roberto Takuro Tamura Yumi Yamaguchi-Kabata Motohiko Tanino Kei Yura Satoru Miyazaki Kazuho Ikeo Keiichi Homma Arek Kasprzyk Tetsuo Nishikawa Mika Hirakawa Jean Thierry-Mieg Danielle Thierry-Mieg Jennifer Ashurst Libin Jia Mitsuteru Nakao A. Thomas, Michael Nicola Mulder Youla Karavidopoulou Lihua Jin Sangsoo Kim Tomohiro Yasuda Boris Lenhard Eric Eveno 2 Yoshiyuki Suzuki Jun-Ichi Takeda Craig Gough Phillip Hilton Yasuyuki Fujii Hiroaki Sakai Susumu Tanaka Clara Amid Matthew Bellgard, Maria de Fatima Bonaldo Hidemasa Bono K. Bromberg Susan J. Brookes Anthony Elspeth Bruford Piero Carninci Claude Chelala Christine Couillault J. de Souza Sandro Marie-Anne Debily Marie-Dominique Devignes 1 Inna Dubchak Toshinori Endo Anne Estreicher Eduardo Eyras Kaoru Fukami-Kobayashi R. Gopinath Gopal Esther Graudens Yoonsoo Hahn Ze-Guang Han Michael Han Kousuke Hanada Hideki Hanaoka Erimi Harada Katsuyuki Hashimoto Chisato Yamasaki Ursula Hinz Momoki Hirai Teruyoshi Hishiki Ian Hopkinson Sandrine Imbeaud Hidetoshi Inoko Alexander Kanapin Yayoi Kaneko Takeya Kasukawa Janet Kelso Paul Kersey Reiko Kikuno Kouichi Kimura Bernhard Korn Vladimir Kuryshev Izabela Makalowska Takashi Makino Shuhei Mano Regine Mariage-Samson Jun Mashima Hideo Matsuda Hans-Werner Mewes Shinsei Minoshima Keiichi Nagai Hideki Nagasaki Naoki Nagata Rajni Nigam Osamu Ogasawara Osamu Ohara Masafumi Ohtsubo Norihiro Okada Toshihisa Okido Satoshi Oota Motonori Ota Toshio Ota Tetsuji Otsuki Dominique Piatier-Tonneau Annemarie Poustka Shuang-Xi Ren Naruya Saitou Katsunaga Sakai Shigetaka Sakamoto Ryuichi Sakate Ingo Schupp Florence Servant Stephen Sherry Rie Shiba Sumio Sugano 3
1 ORPAILLEUR - Knowledge representation, reasonning
INRIA Lorraine, LORIA - Laboratoire Lorrain de Recherche en Informatique et ses Applications
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 non-protein-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.
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Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, et al.. Integrative annotation of 21,037 human genes validated by full-length cDNA clones.. PLoS Biology, Public Library of Science, 2004, 2 (6), pp.856-875. ⟨inria-00099938⟩

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