Yamasaki Chisato, Murakami Katsuhiko, Fujii Yasuyuki, Sato Yoshiharu, Harada Erimi, Takeda Jun-ichi, Taniya Takayuki, Sakate Ryuichi, Kikugawa Shingo, Shimada Makoto, Tanino Motohiko, Koyanagi Kanako O, Barrero Roberto A, Gough Craig, Chun Hong-Woo, Habara Takuya, Hanaoka Hideki, Hayakawa Yosuke, Hilton Phillip B, Kaneko Yayoi, Kanno Masako, Kawahara Yoshihiro, Kawamura Toshiyuki, Matsuya Akihiro, Nagata Naoki, Nishikata Kensaku, Noda Akiko Ogura, Nurimoto Shin, Saichi Naomi, Sakai Hiroaki, Sanbonmatsu Ryoko, Shiba Rie, Suzuki Mami, Takabayashi Kazuhiko, Takahashi Aiko, Tamura Takuro, Tanaka Masayuki, Tanaka Susumu, Todokoro Fusano, Yamaguchi Kaori, Yamamoto Naoyuki, Okido Toshihisa, Mashima Jun, Hashizume Aki, Jin Lihua, Lee Kyung-Bum, Lin Yi-Chueh, Nozaki Asami, Sakai Katsunaga, Tada Masahito, Miyazaki Satoru, Makino Takashi, Ohyanagi Hajime, Osato Naoki, Tanaka Nobuhiko, Suzuki Yoshiyuki, Ikeo Kazuho, Saitou Naruya, Sugawara Hideaki, O'Donovan Claire, Kulikova Tamara, Whitfield Eleanor, Halligan Brian, Shimoyama Mary, Twigger Simon, Yura Kei, Kimura Kouichi, Yasuda Tomohiro, Nishikawa Tetsuo, Akiyama Yutaka, Motono Chie, Mukai Yuri, Nagasaki Hideki, Suwa Makiko, Horton Paul, Kikuno Reiko, Ohara Osamu, Lancet Doron, Eveno Eric, Graudens Esther, Imbeaud Sandrine, Debily Marie Anne, Hayashizaki Yoshihide, Amid Clara, Han Michael, Osanger Andreas, Endo Toshinori, Thomas Michael A, Hirakawa Mika, Makalowski Wojciech, Nakao Mitsuteru, Kim Nam-Soon, Yoo Hyang-Sook, De Souza Sandro J, Bonaldo Maria de Fatima, Niimura Yoshihito, Kuryshev Vladimir, Schupp Ingo, Wiemann Stefan, Bellgard Matthew, Shionyu Masafumi, Jia Libin, Thierry-Mieg Danielle, Thierry-Mieg Jean, Wagner Lukas, Zhang Qinghua, Go Mitiko, Minoshima Shinsei, Ohtsubo Masafumi, Hanada Kousuke, Tonellato Peter, Isogai Takao, Zhang Ji, Lenhard Boris, Kim Sangsoo, Chen Zhu, Hinz Ursula, Estreicher Anne, Nakai Kenta, Makalowska Izabela, Hide Winston, Tiffin Nicola, Wilming Laurens, Chakraborty Ranajit, Soares Marcelo Bento, Chiusano Maria Luisa, Suzuki Yutaka, Auffray Charles, Yamaguchi-Kabata Yumi, Itoh Takeshi, Hishiki Teruyoshi, Fukuchi Satoshi, Nishikawa Ken, Sugano Sumio, Nomura Nobuo, Tateno Yoshio, Imanishi Tadashi, Gojobori Takashi
Japan Biological Information Research Center, Japan Biological Informatics Consortium, Japan.
Nucleic Acids Res. 2008 Jan;36(Database issue):D793-9. doi: 10.1093/nar/gkm999. Epub 2007 Dec 18.
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.
