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

Chisato Yamasaki; Katsuhiko Murakami; Yasuyuki Fujii; Yoshiharu Sato; Erimi Harada; Jun-Ichi Takeda; Takayuki Taniya; Ryuichi Sakate; Shingo Kikugawa; Makoto Shimada; Motohiko Tanino; Kanako O. Koyanagi; Roberto A. Barrero; Craig Gough; Hong-Woo Chun; Takuya Habara; Hideki Hanaoka; Yosuke Hayakawa; Phillip B. Hilton; Yayoi Kaneko; Masako Kanno; Yoshihiro Kawahara; Toshiyuki Kawamura; Akihiro Matsuya; Naoki Nagata; Kensaku Nishikata; Akiko Ogura Noda; Shin Nurimoto; Naomi Saichi; Hiroaki Sakai; Ryoko Sanbonmatsu; Rie Shiba; Mami Suzuki; Kazuhiko Takabayashi; Aiko Takahashi; Takuro Tamura; Masayuki Tanaka; Susumu Tanaka; Fusano Todokoro; Kaori Yamaguchi; Naoyuki Yamamoto; Toshihisa Okido; Jun Mashima; Aki Hashizume; Lihua Jin; Kyung-Bum Lee; Yi-Chueh Lin; Asami Nozaki; Katsunaga Sakai; Masahito Tada; Satoru Miyazaki; Takashi Makino; Hajime Ohyanagi; Naoki Osato; Nobuhiko Tanaka; Yoshiyuki Suzuki; Kazuho Ikeo; Naruya Saitou; Hideaki Sugawara; Claire O'Donovan; Tamara Kulikova; Eleanor Whitfield; Brian Halligan; Mary Shimoyama; Simon Twigger; Kei Yura; Kouichi Kimura; Tomohiro Yasuda; Tetsuo Nishikawa; Yutaka Akiyama; Chie Motono; Yuri Mukai; Hideki Nagasaki; Makiko Suwa; Paul Horton; Reiko Kikuno; Osamu Ohara; Doron Lancet; Eric Eveno; Esther Graudens; Sandrine Imbeaud; Marie Anne Debily; Yoshihide Hayashizaki; Clara Amid; Michael Han; Andreas Osanger; Toshinori Endo; Michael A. Thomas; Mika Hirakawa; Wojciech Makalowski; Mitsuteru Nakao; Nam-Soon Kim; Hyang-Sook Yoo; Sandro J. De Souza; Maria de Fatima Bonaldo; Yoshihito Niimura; Vladimir Kuryshev; Ingo Schupp; Stefan Wiemann; Matthew Bellgard; Masafumi Shionyu; Libin Jia; Danielle Thierry-Mieg; Jean Thierry-Mieg; Lukas Wagner; Qinghua Zhang; Mitiko Go; Shinsei Minoshima; Masafumi Ohtsubo; Kousuke Hanada; Peter Tonellato; Takao Isogai; Ji Zhang; Boris Lenhard; Sangsoo Kim; Zhu Chen; Ursula Hinz; Anne Estreicher; Kenta Nakai; Izabela Makalowska; Winston Hide; Nicola Tiffin; Laurens Wilming; Ranajit Chakraborty; Marcelo Bento Soares; Maria Luisa Chiusano; Yutaka Suzuki; Charles Auffray; Yumi Yamaguchi-Kabata; Takeshi Itoh; Teruyoshi Hishiki; Satoshi Fukuchi; Ken Nishikawa; Sumio Sugano; Nobuo Nomura; Yoshio Tateno; Tadashi Imanishi; Takashi Gojobori; Genome Information Integration Project And H-Invitational 2

doi:10.1093/nar/gkm999

Back

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

Journal article

Peer reviewed

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

Chisato Yamasaki, Katsuhiko Murakami, Yasuyuki Fujii, Yoshiharu Sato, Erimi Harada, Jun-Ichi Takeda, Takayuki Taniya, Ryuichi Sakate, Shingo Kikugawa, Makoto Shimada, …

Nucleic acids research, Vol.36(suppl-1), pp.D793-D799

01/01/2008

DOI: https://doi.org/10.1093/nar/gkm999

PMCID: PMC2238988

PMID: 18089548

Abstract

Biochemistry & Molecular Biology

Life Sciences & Biomedicine

Science & Technology

Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB; http://www.h-invitational.jp/), a comprehensive annotation resource for human genes and transcripts. H-InvDB, originally developed as an integrated database of the human transcriptome based on extensive annotation of large sets of full-length cDNA (FLcDNA) clones, now provides annotation for 120 558 human mRNAs extracted from the International Nucleotide Sequence Databases (INSD), in addition to 54 978 human FLcDNAs, in the latest release H-InvDB_4.6. We mapped those human transcripts onto the human genome sequences (NCBI build 36.1) and determined 34 699 human gene clusters, which could define 34 057 (98.1%) protein-coding and 642 (1.9%) non-protein-coding loci; 858 (2.5%) transcribed loci overlapped with predicted pseudogenes. For all these transcripts and genes, we provide comprehensive annotation including gene structures, gene functions, alternative splicing variants, functional non-protein-coding RNAs, functional domains, predicted sub cellular localizations, metabolic pathways, predictions of protein 3D structure, mapping of SNPs and microsatellite repeat motifs, co-localization with orphan diseases, gene expression profiles, orthologous genes, proteinprotein interactions (PPI) and annotation for gene families. The current H-InvDB annotation resources consist of two main views: Transcript view and Locus view and eight sub-databases: the DiseaseInfo Viewer, H-ANGEL, the Clustering Viewer, G-integra, the TOPO Viewer, Evola, the PPI view and the Gene family/group.

Metrics

1 Record Views

See more details

Details

Title: The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
Creators - without role: Chisato Yamasaki - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Katsuhiko Murakami - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Yasuyuki Fujii - Okayama University
Yoshiharu Sato - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Erimi Harada - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Jun-Ichi Takeda - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Takayuki Taniya - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Ryuichi Sakate - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Shingo Kikugawa - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Makoto Shimada - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Motohiko Tanino - DNA Chip Research
Kanako O. Koyanagi - Hokkaido University
Roberto A. Barrero
Craig Gough - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Hong-Woo Chun - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Takuya Habara - Japan Biol Informat Consortium, Japan Biol Informat Res Ctr, Tokyo, Japan
Hideki Hanaoka - The University of Tokyo
Yosuke Hayakawa - Japan Biol Informat Consortium, Japan Biol Informat Res Ctr, Tokyo, Japan
Phillip B. Hilton - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Yayoi Kaneko - Mitsubishi Kagaku Inst Life Sci, Tokyo, Japan
Masako Kanno - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Yoshihiro Kawahara - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Toshiyuki Kawamura - Fujitsu Ltd, Tokyo, Japan
Akihiro Matsuya - Japan Biol Informat Consortium, Japan Biol Informat Res Ctr, Tokyo, Japan
Naoki Nagata - Japan Sci & Technol Agcy, Tokyo, Japan
Kensaku Nishikata - Japan Biol Informat Consortium, Japan Biol Informat Res Ctr, Tokyo, Japan
Akiko Ogura Noda - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Shin Nurimoto - Mitsui
Naomi Saichi - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Hiroaki Sakai - Natl Inst Agrobiol Sci, Ibaraki, Japan
Ryoko Sanbonmatsu - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Rie Shiba - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Mami Suzuki - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Kazuhiko Takabayashi
Aiko Takahashi - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Takuro Tamura - BITS Co Ltd, Shizuoka, Japan
Masayuki Tanaka - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Susumu Tanaka - Tokyo Institute of Psychiatry
Fusano Todokoro - Japan Biol Informat Consortium, Japan Biol Informat Res Ctr, Tokyo, Japan
Kaori Yamaguchi - Japan Biol Informat Consortium, Japan Biol Informat Res Ctr, Tokyo, Japan
Naoyuki Yamamoto - Japan Biol Informat Consortium, Japan Biol Informat Res Ctr, Tokyo, Japan
Toshihisa Okido - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Jun Mashima - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Aki Hashizume - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Lihua Jin - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Kyung-Bum Lee - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Yi-Chueh Lin - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Asami Nozaki - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Katsunaga Sakai - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Masahito Tada - Ctr Informat Biol, Shizuoka, Japan
Satoru Miyazaki - Tokyo Univ Sci, Chiba, Japan
Takashi Makino - Trinity College Dublin
Hajime Ohyanagi - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Naoki Osato - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Nobuhiko Tanaka - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Yoshiyuki Suzuki - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Kazuho Ikeo - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Naruya Saitou - Natl Inst Genet, Div Populat Genet, Shizuoka, Japan
Hideaki Sugawara - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Claire O'Donovan - EMBL Outstn Hinxton, European Bioinformat Inst, Cambridge, England
Tamara Kulikova - EMBL Outstn Hinxton, European Bioinformat Inst, Cambridge, England
Eleanor Whitfield - EMBL Outstn Hinxton, European Bioinformat Inst, Cambridge, England
Brian Halligan - College Station Medical Center
Mary Shimoyama - College Station Medical Center
Simon Twigger - College Station Medical Center
Kei Yura - Japan Atom Energy Agcy, Ctr Computat Sci & Engn, Kyoto, Japan
Kouichi Kimura - Hitachi
Tomohiro Yasuda - Hitachi
Tetsuo Nishikawa - Hitachi
Yutaka Akiyama - Natl Inst Adv Ind Sci & Technol, Computat Biol Res Ctr, Tokyo, Japan
Chie Motono - Natl Inst Adv Ind Sci & Technol, Computat Biol Res Ctr, Tokyo, Japan
Yuri Mukai - Natl Inst Adv Ind Sci & Technol, Computat Biol Res Ctr, Tokyo, Japan
Hideki Nagasaki - Natl Inst Adv Ind Sci & Technol, Computat Biol Res Ctr, Tokyo, Japan
Makiko Suwa - Natl Inst Adv Ind Sci & Technol, Computat Biol Res Ctr, Tokyo, Japan
Paul Horton - Natl Inst Adv Ind Sci & Technol, Computat Biol Res Ctr, Tokyo, Japan
Reiko Kikuno - Kazusa DNA Research Institute
Osamu Ohara - Kazusa DNA Research Institute
Doron Lancet - Weizmann Inst Sci, Dept Mol Genet, IL-76100 Rehovot, Israel
Eric Eveno - CNRS, Villejuif, France
Esther Graudens - CNRS, Villejuif, France
Sandrine Imbeaud - CNRS, Villejuif, France
Marie Anne Debily - CNRS, Villejuif, France
Yoshihide Hayashizaki - RIKEN
Clara Amid - GSF, Natl Res Ctr Environm & Hlth, Inst Bioinformat, Neuherberg, Germany
Michael Han - GSF, Natl Res Ctr Environm & Hlth, Inst Bioinformat, Neuherberg, Germany
Andreas Osanger - GSF, Natl Res Ctr Environm & Hlth, Inst Bioinformat, Neuherberg, Germany
Toshinori Endo - Hokkaido University
Michael A. Thomas - Idaho State University
Mika Hirakawa - Kyoto University
Wojciech Makalowski - University of Münster
Mitsuteru Nakao - Kazusa DNA Research Institute
Nam-Soon Kim - Korea Res Inst Biosci & Biotechnol, Taejon, South Korea
Hyang-Sook Yoo - Korea Res Inst Biosci & Biotechnol, Taejon, South Korea
Sandro J. De Souza - Ludwig Inst Canc Res, Sao Paulo, Brazil
Maria de Fatima Bonaldo - University of Iowa
Yoshihito Niimura - College Station Medical Center
Vladimir Kuryshev - Heidelberg
Ingo Schupp - Heidelberg
Stefan Wiemann - Heidelberg
Matthew Bellgard - Murdoch University
Masafumi Shionyu - BIO
Libin Jia - Natl Inst Hlth, Natl Canc Inst, Baltimore, MD USA
Danielle Thierry-Mieg - College Station Medical Center
Jean Thierry-Mieg - College Station Medical Center
Lukas Wagner - College Station Medical Center
Qinghua Zhang - Sino French Lab Lif Sci & Genom, Shanghai, Peoples R China
Mitiko Go - Ochanomizu University
Shinsei Minoshima - Hamamatsu University
Masafumi Ohtsubo - Hamamatsu University
Kousuke Hanada - RIKEN
Peter Tonellato - Harvard University
Takao Isogai
Ji Zhang - Chinese Acad Sci, Shanghai Inst Biol Sci, Shanghai, Peoples R China
Boris Lenhard - Karolinska Institutet
Sangsoo Kim - Soongsil University
Zhu Chen - Shanghai Jiao Tong University
Ursula Hinz - Swiss Ins Bioinformat, Geneva, Switzerland
Anne Estreicher - Swiss Ins Bioinformat, Geneva, Switzerland
Kenta Nakai - The University of Tokyo
Izabela Makalowska - Pennsylvania State University
Winston Hide - University of the Western Cape
Nicola Tiffin - University of the Western Cape
Laurens Wilming - Well Trust Sanger Inst, Cambridge, England
Ranajit Chakraborty - University of Cincinnati
Marcelo Bento Soares - Northwestern Univ, Feinberg Sch med, Childrens Mem Res Ctr, Evanston, IL 60208 USA
Maria Luisa Chiusano - University of Naples Federico II
Yutaka Suzuki - The University of Tokyo
Charles Auffray
Yumi Yamaguchi-Kabata - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Takeshi Itoh - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Teruyoshi Hishiki - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Satoshi Fukuchi - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Ken Nishikawa - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Sumio Sugano - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Nobuo Nomura - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Yoshio Tateno - Natl Inst Genet, DNA Data Bank, Shizuoka, Japan
Tadashi Imanishi - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Takashi Gojobori - Natl Inst Adv Ind Sci & Technol, Biol Informat Res Ctr, Tokyo, Japan
Genome Information Integration Project And H-Invitational 2
Publication Details: Nucleic acids research, Vol.36(suppl-1), pp.D793-D799
Publisher: Oxford Univ Press
Number of pages: 7
Grant note: R01 HL064541; P50 HL054998 / NHLBI NIH HHS; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Heart Lung & Blood Institute (NHLBI) 077198 / Wellcome Trust; European Commission R01HL064541 / NATIONAL HEART, LUNG, AND BLOOD INSTITUTE; United States Department of Health & Human Services; National Institutes of Health (NIH) - USA; NIH National Heart Lung & Blood Institute (NHLBI)
Identifiers: 9944128808331
Academic Unit: King Abdullah University of Science & Technology
Language: English
Resource Type: Journal article