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

Tadashi Imanishi; 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; 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; 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

Journal Articles PLoS Biology Year : 2004

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

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Tadashi Imanishi

Function : Author

Knowledge representation, reasonning

Takeshi Itoh

Function : Author

Yutaka Suzuki

Function : Author

Claire O'Donovan

Function : Author

Satoshi Fukuchi

Function : Author

O. Koyanagi Kanako

Function : Author

A. Barrero Roberto

Function : Author

Takuro Tamura

Function : Author

Yumi Yamaguchi-Kabata

Function : Author

Motohiko Tanino

Function : Author

Kei Yura

Function : Author

Satoru Miyazaki

Function : Author

Kazuho Ikeo

Function : Author

Keiichi Homma

Function : Author

Arek Kasprzyk

Function : Author

Tetsuo Nishikawa

Function : Author

Mika Hirakawa

Function : Author

Jean Thierry-Mieg

Function : Author

Danielle Thierry-Mieg

Function : Author

Jennifer Ashurst

Function : Author

Libin Jia

Function : Author

Mitsuteru Nakao

Function : Author

A. Thomas, Michael

Function : Author

Nicola Mulder

Function : Author
PersonId : 766533
ORCID : 0000-0003-4905-0941
IdRef : 11755765X

Youla Karavidopoulou

Function : Author

Lihua Jin

Function : Author

Sangsoo Kim

Function : Author

Tomohiro Yasuda

Function : Author

Boris Lenhard

Function : Author

Eric Eveno

Function : Author
PersonId : 174723
IdHAL : eric-eveno
ORCID : 0000-0002-7282-280X

Genexpress

Yoshiyuki Suzuki

Function : Author

Jun-Ichi Takeda

Function : Author

Craig Gough

Function : Author

Phillip Hilton

Function : Author

Yasuyuki Fujii

Function : Author

Hiroaki Sakai

Function : Author

Susumu Tanaka

Function : Author

Clara Amid

Function : Author

Matthew Bellgard,

Function : Author

Maria de Fatima Bonaldo

Function : Author

Hidemasa Bono

Function : Author

K. Bromberg Susan

Function : Author

J. Brookes Anthony

Function : Author

Elspeth Bruford

Function : Author

Piero Carninci

Function : Author

Claude Chelala

Function : Author

Christine Couillault

Function : Author

J. de Souza Sandro

Function : Author

Marie-Anne Debily

Function : Author

Marie-Dominique Devignes

Function : Author
PersonId : 742369
IdHAL : mddevignes
ORCID : 0000-0002-0399-8713
IdRef : 134215001

Knowledge representation, reasonning

Inna Dubchak

Function : Author

Toshinori Endo

Function : Author

Anne Estreicher

Function : Author

Eduardo Eyras

Function : Author

Kaoru Fukami-Kobayashi

Function : Author

R. Gopinath Gopal

Function : Author

Esther Graudens

Function : Author

Yoonsoo Hahn

Function : Author

Ze-Guang Han

Function : Author

Michael Han

Function : Author

Kousuke Hanada

Function : Author

Hideki Hanaoka

Function : Author

Erimi Harada

Function : Author

Katsuyuki Hashimoto

Function : Author

Chisato Yamasaki

Function : Author

Ursula Hinz

Function : Author

Momoki Hirai

Function : Author

Teruyoshi Hishiki

Function : Author

Ian Hopkinson

Function : Author

Sandrine Imbeaud

Function : Author
PersonId : 1162373
IdHAL : sandrine-imbeaud
ORCID : 0000-0001-8439-6732

Hidetoshi Inoko

Function : Author

Alexander Kanapin

Function : Author

Yayoi Kaneko

Function : Author

Takeya Kasukawa

Function : Author

Janet Kelso

Function : Author

Paul Kersey

Function : Author

Reiko Kikuno

Function : Author

Kouichi Kimura

Function : Author

Bernhard Korn

Function : Author

Vladimir Kuryshev

Function : Author

Izabela Makalowska

Function : Author

Takashi Makino

Function : Author

Shuhei Mano

Function : Author

Regine Mariage-Samson

Function : Author

Jun Mashima

Function : Author

Hideo Matsuda

Function : Author

Hans-Werner Mewes

Function : Author

Shinsei Minoshima

Function : Author

Keiichi Nagai

Function : Author

Hideki Nagasaki

Function : Author

Naoki Nagata

Function : Author

Rajni Nigam

Function : Author

Osamu Ogasawara

Function : Author

Osamu Ohara

Function : Author

Masafumi Ohtsubo

Function : Author

Norihiro Okada

Function : Author

Toshihisa Okido

Function : Author

Satoshi Oota

Function : Author

Motonori Ota

Function : Author

Toshio Ota

Function : Author

Tetsuji Otsuki

Function : Author

Dominique Piatier-Tonneau

Function : Author

Annemarie Poustka

Function : Author

Shuang-Xi Ren

Function : Author

Naruya Saitou

Function : Author

Katsunaga Sakai

Function : Author

Shigetaka Sakamoto

Function : Author

Ryuichi Sakate

Function : Author

Ingo Schupp

Function : Author

Florence Servant

Function : Author

Stephen Sherry

Function : Author

Rie Shiba

Function : Author

Sumio Sugano

Function : Author

The University of Tokyo

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.

Keywords

transcriptome humain full-length cdna human transcriptome annotation cdna complet

Domains

Other [cs.OH]

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A04-R-517.pdf (2.03 Mo)

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Submitted on : Tuesday, September 26, 2006-10:12:26 AM

Last modification on : Friday, March 24, 2023-2:52:48 PM

Long-term archiving on: Friday, November 25, 2016-12:17:16 PM

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inria-00099938 , version 1 (26-09-2006)

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HAL Id : inria-00099938 , version 1

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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, 2004, 2 (6), pp.856-875. ⟨inria-00099938⟩

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

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