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

Tadashi Imanishi; Takeshi Itoh; Yutaka Suzuki; Claire O'Donovan; Satoshi Fukuchi; Kanako O Koyanagi; Roberto A Barrero; 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; Michael A Thomas; Nicola Mulder; Youla Karavidopoulou; Lihua Jin; Sangsoo Kim; Tomohiro Yasuda; Boris Lenhard; Eric Eveno; Yoshiyuki Suzuki; Chisato Yamasaki; Jun-ichi Takeda; Craig Gough; Phillip Hilton; Yasuyuki Fujii; Hiroaki Sakai; Susumu Tanaka; Clara Amid; Matthew Bellgard; Maria de Fatima Bonaldo; Hidemasa Bono; Susan K Bromberg; Anthony J Brookes; Elspeth Bruford; Piero Carninci; Claude Chelala; Christine Couillault; Sandro J. de Souza; Marie-Anne Debily; Marie-Dominique Devignes; Inna Dubchak; Toshinori Endo; Anne Estreicher; Eduardo Eyras; Kaoru Fukami-Kobayashi; Gopal R. Gopinath; Esther Graudens; Yoonsoo Hahn; Michael Han; Ze-Guang Han; Kousuke Hanada; Hideki Hanaoka; Erimi Harada; Katsuyuki Hashimoto; 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; Nobuyoshi Shimizu; Mary Shimoyama; Andrew J Simpson; Bento Soares; Charles Steward; Makiko Suwa; Mami Suzuki; Aiko Takahashi; Gen Tamiya; Hiroshi Tanaka; Todd Taylor; Joseph D Terwilliger; Per Unneberg; Vamsi Veeramachaneni; Shinya Watanabe; Laurens Wilming; Norikazu Yasuda; Hyang-Sook Yoo; Marvin Stodolsky; Wojciech Makalowski; Mitiko Go; Kenta Nakai; Toshihisa Takagi; Minoru Kanehisa; Yoshiyuki Sakaki; John Quackenbush; Yasushi Okazaki; Yoshihide Hayashizaki; Winston Hide; Ranajit Chakraborty; Ken Nishikawa; Hideaki Sugawara; Yoshio Tateno; Zhu Chen; Michio Oishi; Peter Tonellato; Rolf Apweiler; Kousaku Okubo; Lukas Wagner; Stefan Wiemann; Robert L Strausberg; Takao Isogai; Charles Auffray; Nobuo Nomura; Takashi Gojobori; Sumio Sugano; Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)

doi:10.1371/journal.pbio.0020162

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

Journal article

Open access

Peer reviewed

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

Tadashi Imanishi, Takeshi Itoh, Yutaka Suzuki, Claire O'Donovan, Satoshi Fukuchi, Kanako O Koyanagi, Roberto A Barrero, Takuro Tamura, Yumi Yamaguchi-Kabata, Motohiko Tanino, …

PLoS biology, Vol.2(6), pp.856-875

01/06/2004

DOI: https://doi.org/10.1371/journal.pbio.0020162

PMCID: 393292

PMID: 15103394

Abstract

Bioinformatics

Computational Biology

Gene Therapy

Genetics

Genomics

Homo (Human)

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. An international team has systematically validated and annotated just over 21,000 human genes using full-length cDNA, thereby providing a valuable new resource for the human genetics community

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Title: Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones
Creators - without role: Tadashi Imanishi - National Institute of Advanced Industrial Science and Technology
Takeshi Itoh - National Institute of Advanced Industrial Science and Technology
Yutaka Suzuki - The University of Tokyo
Claire O'Donovan - European Bioinformatics Institute
Satoshi Fukuchi - Bank of Japan
Kanako O Koyanagi - Nara Institute of Science and Technology
Roberto A Barrero - Bank of Japan
Takuro Tamura - Japan Biological Informatics Consortium
Yumi Yamaguchi-Kabata - National Institute of Advanced Industrial Science and Technology
Motohiko Tanino - National Institute of Advanced Industrial Science and Technology
Kei Yura - Institute for Atomic Energy Research
Satoru Miyazaki - Bank of Japan
Kazuho Ikeo - National Institute of Genetics
Keiichi Homma - Bank of Japan
Arek Kasprzyk - European Bioinformatics Institute
Tetsuo Nishikawa - Hitachi
Mika Hirakawa - Kyoto University
Jean Thierry-Mieg - National Center for Biotechnology Information
Danielle Thierry-Mieg - National Center for Biotechnology Information
Jennifer Ashurst - Wellcome Sanger Institute
Libin Jia - National Institutes of Health
Mitsuteru Nakao - The University of Tokyo
Michael A Thomas - Idaho State University
Nicola Mulder - European Bioinformatics Institute
Youla Karavidopoulou - European Bioinformatics Institute
Lihua Jin - National Institute of Genetics
Sangsoo Kim - Korea Research Institute of Bioscience and Biotechnology
Tomohiro Yasuda - Hitachi
Boris Lenhard - Karolinska Institutet
Eric Eveno - Genomics
Yoshiyuki Suzuki - Bank of Japan
Chisato Yamasaki - National Institute of Advanced Industrial Science and Technology
Jun-ichi Takeda - National Institute of Advanced Industrial Science and Technology
Craig Gough - Japan Biological Informatics Consortium
Phillip Hilton - National Institute of Advanced Industrial Science and Technology
Yasuyuki Fujii - National Institute of Advanced Industrial Science and Technology
Hiroaki Sakai - Kyowa Kirin
Susumu Tanaka - National Institute of Advanced Industrial Science and Technology
Clara Amid - Institute of Bioinformatics and Systems Biology
Matthew Bellgard - Murdoch University
Maria de Fatima Bonaldo - University of Iowa
Hidemasa Bono - RIKEN Center for Integrative Medical Sciences
Susan K Bromberg - Medical College of Wisconsin
Anthony J Brookes - Karolinska Institutet
Elspeth Bruford - University College London
Piero Carninci - RIKEN
Claude Chelala - Genomics
Christine Couillault - Genomics
Sandro J. de Souza - Instituto Paulo Gontijo
Marie-Anne Debily - Genomics
Marie-Dominique Devignes - Délégation Centre-Est
Inna Dubchak - Lawrence Berkeley National Laboratory
Toshinori Endo - Tokyo Medical and Dental University
Anne Estreicher - SIB Swiss Institute of Bioinformatics
Eduardo Eyras - Wellcome Sanger Institute
Kaoru Fukami-Kobayashi - RIKEN BioResource Research Center
Gopal R. Gopinath - Cold Spring Harbor Laboratory
Esther Graudens - Genomics
Yoonsoo Hahn - Korea Research Institute of Bioscience and Biotechnology
Michael Han - Institute of Bioinformatics and Systems Biology
Ze-Guang Han - Chinese National Human Genome Center at Shanghai
Kousuke Hanada - National Institute of Genetics
Hideki Hanaoka - National Institute of Advanced Industrial Science and Technology
Erimi Harada - National Institute of Advanced Industrial Science and Technology
Katsuyuki Hashimoto - National Institute of Infectious Diseases
Ursula Hinz - SIB Swiss Institute of Bioinformatics
Momoki Hirai - The University of Tokyo
Teruyoshi Hishiki - National Institute of Advanced Industrial Science and Technology
Ian Hopkinson - University College London
Sandrine Imbeaud - Genomics
Hidetoshi Inoko - National Institute of Advanced Industrial Science and Technology
Alexander Kanapin - European Bioinformatics Institute
Yayoi Kaneko - National Institute of Advanced Industrial Science and Technology
Takeya Kasukawa - RIKEN Center for Integrative Medical Sciences
Janet Kelso - University of the Western Cape
Paul Kersey - European Bioinformatics Institute
Reiko Kikuno - Kazusa DNA Research Institute
Kouichi Kimura - Hitachi
Bernhard Korn - Resource
Vladimir Kuryshev - German Cancer Research Center
Izabela Makalowska - Pennsylvania State University
Takashi Makino - Bank of Japan
Shuhei Mano - Tokai University
Regine Mariage-Samson - Genomics
Jun Mashima - Bank of Japan
Hideo Matsuda - Osaka University
Hans-Werner Mewes - Institute of Bioinformatics and Systems Biology
Shinsei Minoshima - Hamamatsu University School of Medicine
Keiichi Nagai - Hitachi
Hideki Nagasaki - National Institute of Advanced Industrial Science and Technology
Naoki Nagata - National Institute of Advanced Industrial Science and Technology
Rajni Nigam - Medical College of Wisconsin
Osamu Ogasawara - The University of Tokyo
Osamu Ohara - Kazusa DNA Research Institute
Masafumi Ohtsubo - Keio University
Norihiro Okada - Tokyo Institute of Technology
Toshihisa Okido - Bank of Japan
Satoshi Oota - RIKEN BioResource Research Center
Motonori Ota - Tokyo Institute of Technology
Toshio Ota - Kyowa Kirin
Tetsuji Otsuki - Taisho Pharmaceutical
Dominique Piatier-Tonneau - Genomics
Annemarie Poustka - Molecular Genome Analysis, German Cancer Research Center-DKFZ
Shuang-Xi Ren - Chinese National Human Genome Center at Shanghai
Naruya Saitou - National Institute of Genetics
Katsunaga Sakai - National Institute of Genetics
Shigetaka Sakamoto - National Institute of Genetics
Ryuichi Sakate - The University of Tokyo
Ingo Schupp - Molecular Genome Analysis, German Cancer Research Center-DKFZ
Florence Servant - Wellcome Trust
Stephen Sherry - National Center for Biotechnology Information
Rie Shiba - Japan Biological Informatics Consortium
Nobuyoshi Shimizu - Keio University
Mary Shimoyama - Medical College of Wisconsin
Andrew J Simpson - Ludwig Institute of Cancer Research
Bento Soares - University of Iowa
Charles Steward - Wellcome Sanger Institute
Makiko Suwa - Computational Biology Research Center, National Institute of Advanced Industrial Science and Technology
Mami Suzuki - National Institute of Genetics
Aiko Takahashi - Japan Biological Informatics Consortium
Gen Tamiya - Tokai University
Hiroshi Tanaka - Tokyo Medical and Dental University
Todd Taylor - Genomic
Joseph D Terwilliger - Columbia University
Per Unneberg - Department of Biotechnology
Vamsi Veeramachaneni - Pennsylvania State University
Shinya Watanabe - Tokyo University of Science
Laurens Wilming - Wellcome Sanger Institute
Norikazu Yasuda - Japan Biological Informatics Consortium
Hyang-Sook Yoo - Korea Research Institute of Bioscience and Biotechnology
Marvin Stodolsky - Office of Biological and Environmental Research
Wojciech Makalowski - Pennsylvania State University
Mitiko Go - Nagahama Institute of Bio-Science and Technology
Kenta Nakai - Tokyo University of Science
Toshihisa Takagi - Tokyo University of Science
Minoru Kanehisa - Kyoto University
Yoshiyuki Sakaki - Tokyo University of Science
John Quackenbush - Genomic
Yasushi Okazaki - Genomic
Yoshihide Hayashizaki - Genomic
Winston Hide - University of the Western Cape
Ranajit Chakraborty - University of Cincinnati
Ken Nishikawa - National Institute of Genetics
Hideaki Sugawara - National Institute of Genetics
Yoshio Tateno - National Institute of Genetics
Zhu Chen - Chinese National Human Genome Center at Shanghai
Michio Oishi - Kazusa DNA Research Institute
Peter Tonellato - PointOne Systems
Rolf Apweiler - Wellcome Trust
Kousaku Okubo - National Institute of Genetics
Lukas Wagner - National Center for Biotechnology Information
Stefan Wiemann - Molecular Genome Analysis, German Cancer Research Center-DKFZ
Robert L Strausberg - National Institutes of Health
Takao Isogai - University of Tsukuba
Charles Auffray - Genomics
Nobuo Nomura - Genomics
Takashi Gojobori - National Institute of Genetics
Sumio Sugano - Tokyo University of Science
Lawrence Berkeley National Lab. (LBNL), Berkeley, CA (United States)
Publication Details: PLoS biology, Vol.2(6), pp.856-875
Publisher: Public Library of Science
Identifiers: 9943764608331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article