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

2007; Oxford University Press; Volume: 36; Issue: Database Linguagem: Inglês

10.1093/nar/gkm999

1362-4962

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, Roberto A. Barrero, Hong-Woo Chun, Takuya Habara, Hideki Hanaoka, Yosuke Hayakawa, Phillip B. Hilton, Yayoi Kaneko, Masako Kanno, Yoshihiro Kawahara, T. Kawamura, Akihiro Matsuya, Naoki Nagata, Kensaku Nishikata, Akiko Noda, Shin Nurimoto, Naomi Saichi, Hiroaki Sakai, Ryoko Sanbonmatsu, Rie Shiba, Mami Suzuki, K 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 J Whitfield, Brian Halligan, Mary Shimoyama, Simon Twigger, Kei Yura, Kouichi Kimura, Tomohiro Yasuda, Tetsuo Nishikawa, Yutaka Akiyama, C. Motono, Yuri Mukai, Hideki Nagasaki, Makiko Suwa, Paul Horton, Reiko Kikuno, Osamu Ohara, Doron Lancet, Éric Eveno, Esther Graudens, Sandrine Imbeaud, Marie Anne Debily, Yoshihide Hayashizaki, Clara Amid, Michael Han, Andreas Osanger, Toshinori Endo, Michael A. Thomas, Mika Hirakawa, Wojciech Makałowski, Mitsuteru Nakao, Nam-Soon Kim, Hyang‐Sook Yoo, Sandro J. de Souza, Maria de Fátima Bonaldo, Yoshihito Niimura, Vladimir Kuryshev, Ingo Schupp, Stefan Wiemann, M. Bellgard, Masafumi Shionyu, Libin Jia, Danielle Thierry‐Mieg, Jean Thierry‐Mieg, Lukas Wagner, Qinghua Zhang, Mitiko Gō, Satoshi Minoshima, Masafumi Ohtsubo, Kousuke Hanada, Peter J. Tonellato, Takao Isogai, Ji Zhang, Boris Lenhard, Sangsoo Kim, Zhu Chen, Ursula Hinz, Anne Estreicher, Kenta Nakai, Izabela Makałowska, Yoshihide Hayashizaki, Nicki Tiffin, Laurens Wilming, Ranajit Chakraborty, Marcelo B. 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,

RNA and protein synthesis mechanisms

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.