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

C. Yamasaki; K. Murakami; Y. Fujii; Y. Sato; E. Harada; J-I Takeda; T. Taniya; R. Sakate; S. Kikugawa; M. Shimada; M. Tanino; K.O. Koyanagi; R.A. Barrero; C. Gough; H-W Chun; T. Habara; H. Hanaoka; Y. Hayakawa; P.B. Hilton; Y. Kaneko; M. Kanno; Y. Kawahara; T. Kawamura; A. Matsuya; N. Nagata; K. Nishikata; A.O. Noda; S. Nurimoto; N. Saichi; H. Sakai; R. Sanbonmatsu; R. Shiba; M. Suzuki; K. Takabayashi; A. Takahashi; T. Tamura; M. Tanaka; S. Tanaka; F. Todokoro; K. Yamaguchi; N. Yamamoto; T. Okido; J. Mashima; A. Hashizume; L. Jin; K-B Lee; Y-C Lin; A. Nozaki; K. Sakai; M. Tada; S. Miyazaki; T. Makino; H. Ohyanagi; N. Osato; N. Tanaka; Y. Suzuki; K. Ikeo; N. Saitou; H. Sugawara; C. O’Donovan; T. Kulikova; E. Whitfield; B. Halligan; M. Shimoyama; S. Twigger; K. Yura; K. Kimura; T. Yasuda; T. Nishikawa; Y. Akiyama; C. Motono; Y. Mukai; H. Nagasaki; M. Suwa; P. Horton; R. Kikuno; O. Ohara; D. Lancet; E. Eveno; E. Graudens; S. Imbeaud; M. Debily; Y. Hayashizaki; C. Amid; M. Han; A. Osanger; T. Endo; M.A. Thomas; M. Hirakawa; W. Makalowski; M. Nakao; N-S Kim; H-S Yoo; S.J. De Souza; M. Bonaldo; Y. Niimura; V. Kuryshev; I. Schupp; S. Wiemann; M. Bellgard; M. Shionyu; L. Jia; D. Thierry-Mieg; J. Thierry-Mieg; L. Wagner; Q. Zhang; M. Go; S. Minoshima; M. Ohtsubo; K. Hanada; P. Tonellato; T. Isogai; J. Zhang; B. Lenhard; S. Kim; Z. Chen; U. Hinz; A. Estreicher; K. Nakai; I. Makalowska; W. Hide; N. Tiffin; L. Wilming; R. Chakraborty; M.B. Soares; M.L. Chiusano; C. Auffray; Y. Yamaguchi-Kabata; T. Itoh; T. Hishiki; S. Fukuchi; K. Nishikawa; S. Sugano; N. Nomura; Y. Tateno; T. Imanishi; T. Gojobori

doi:10.1093/nar/gkm999

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

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

C. Yamasaki, K. Murakami, Y. Fujii, Y. Sato, E. Harada, J-I Takeda, T. Taniya, R. Sakate, S. Kikugawa, M. Shimada, …

Nucleic Acids Research, Vol.36(Supp 1), pp.D793-D799

2008

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

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Abstract

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, protein–protein 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.

Details

Title: The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
Authors/Creators: C. Yamasaki (Author/Creator)
K. Murakami (Author/Creator)
Y. Fujii (Author/Creator)
Y. Sato (Author/Creator)
E. Harada (Author/Creator)
J-I Takeda (Author/Creator)
T. Taniya (Author/Creator)
R. Sakate (Author/Creator)
S. Kikugawa (Author/Creator)
M. Shimada (Author/Creator)
M. Tanino (Author/Creator)
K.O. Koyanagi (Author/Creator)
R.A. Barrero (Author/Creator)
C. Gough (Author/Creator)
H-W Chun (Author/Creator)
T. Habara (Author/Creator)
H. Hanaoka (Author/Creator)
Y. Hayakawa (Author/Creator)
P.B. Hilton (Author/Creator)
Y. Kaneko (Author/Creator)
M. Kanno (Author/Creator)
Y. Kawahara (Author/Creator)
T. Kawamura (Author/Creator)
A. Matsuya (Author/Creator)
N. Nagata (Author/Creator)
K. Nishikata (Author/Creator)
A.O. Noda (Author/Creator)
S. Nurimoto (Author/Creator)
N. Saichi (Author/Creator)
H. Sakai (Author/Creator)
R. Sanbonmatsu (Author/Creator)
R. Shiba (Author/Creator)
M. Suzuki (Author/Creator)
K. Takabayashi (Author/Creator)
A. Takahashi (Author/Creator)
T. Tamura (Author/Creator)
M. Tanaka (Author/Creator)
S. Tanaka (Author/Creator)
F. Todokoro (Author/Creator)
K. Yamaguchi (Author/Creator)
N. Yamamoto (Author/Creator)
T. Okido (Author/Creator)
J. Mashima (Author/Creator)
A. Hashizume (Author/Creator)
L. Jin (Author/Creator)
K-B Lee (Author/Creator)
Y-C Lin (Author/Creator)
A. Nozaki (Author/Creator)
K. Sakai (Author/Creator)
M. Tada (Author/Creator)
S. Miyazaki (Author/Creator)
T. Makino (Author/Creator)
H. Ohyanagi (Author/Creator)
N. Osato (Author/Creator)
N. Tanaka (Author/Creator)
Y. Suzuki (Author/Creator)
K. Ikeo (Author/Creator)
N. Saitou (Author/Creator)
H. Sugawara (Author/Creator)
C. O’Donovan (Author/Creator)
T. Kulikova (Author/Creator)
E. Whitfield (Author/Creator)
B. Halligan (Author/Creator)
M. Shimoyama (Author/Creator)
S. Twigger (Author/Creator)
K. Yura (Author/Creator)
K. Kimura (Author/Creator)
T. Yasuda (Author/Creator)
T. Nishikawa (Author/Creator)
Y. Akiyama (Author/Creator)
C. Motono (Author/Creator)
Y. Mukai (Author/Creator)
H. Nagasaki (Author/Creator)
M. Suwa (Author/Creator)
P. Horton (Author/Creator)
R. Kikuno (Author/Creator)
O. Ohara (Author/Creator)
D. Lancet (Author/Creator)
E. Eveno (Author/Creator)
E. Graudens (Author/Creator)
S. Imbeaud (Author/Creator)
M. Debily (Author/Creator)
Y. Hayashizaki (Author/Creator)
C. Amid (Author/Creator)
M. Han (Author/Creator)
A. Osanger (Author/Creator)
T. Endo (Author/Creator)
M.A. Thomas (Author/Creator)
M. Hirakawa (Author/Creator)
W. Makalowski (Author/Creator)
M. Nakao (Author/Creator)
N-S Kim (Author/Creator)
H-S Yoo (Author/Creator)
S.J. De Souza (Author/Creator)
M. Bonaldo (Author/Creator)
Y. Niimura (Author/Creator)
V. Kuryshev (Author/Creator)
I. Schupp (Author/Creator)
S. Wiemann (Author/Creator)
M. Bellgard (Author/Creator)
M. Shionyu (Author/Creator)
L. Jia (Author/Creator)
D. Thierry-Mieg (Author/Creator)
J. Thierry-Mieg (Author/Creator)
L. Wagner (Author/Creator)
Q. Zhang (Author/Creator)
M. Go (Author/Creator)
S. Minoshima (Author/Creator)
M. Ohtsubo (Author/Creator)
K. Hanada (Author/Creator)
P. Tonellato (Author/Creator)
T. Isogai (Author/Creator)
J. Zhang (Author/Creator)
B. Lenhard (Author/Creator)
S. Kim (Author/Creator)
Z. Chen (Author/Creator)
U. Hinz (Author/Creator)
A. Estreicher (Author/Creator)
K. Nakai (Author/Creator)
I. Makalowska (Author/Creator)
W. Hide (Author/Creator)
N. Tiffin (Author/Creator)
L. Wilming (Author/Creator)
R. Chakraborty (Author/Creator)
M.B. Soares (Author/Creator)
M.L. Chiusano (Author/Creator)
Y. Suzuki (Author/Creator)
C. Auffray (Author/Creator)
Y. Yamaguchi-Kabata (Author/Creator)
T. Itoh (Author/Creator)
T. Hishiki (Author/Creator)
S. Fukuchi (Author/Creator)
K. Nishikawa (Author/Creator)
S. Sugano (Author/Creator)
N. Nomura (Author/Creator)
Y. Tateno (Author/Creator)
T. Imanishi (Author/Creator)
T. Gojobori (Author/Creator)
Publication Details: Nucleic Acids Research, Vol.36(Supp 1), pp.D793-D799
Publisher: Oxford University Press
Identifiers: 991005542117407891
Copyright: © 2007 The Author(s)
Murdoch Affiliation: Centre for Comparative Genomics
Language: English
Resource Type: Journal article
Note: This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/ by-nc/2.0/uk/) which permits unrestricted non-commercial use, distribution, and reproduction in any medium, provided the original work is properly cited.

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