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 Takeda Takayuki Taniya Ryuichi Sakate Shin Kikugawa Makoto Shimada Motohiko Tanino Kanako Koyanagi Roberto Barrero Craig Gough Hong-Woo Chun Takuya Habara Yosuke Hayakawa Phillip Hilton Yayoi Kaneko Masako Kanno Yoshihiro Kawahara Toshiyuki Kawamura Aki Matsuya Naoki Nagata Ken Nishikata Aki 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 Ji 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 Hide 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 H Nagasaki Makiko Suwa Paul Horton Reiko Kikuno Osamu Ohara Doron Lancet Eric Eveno 1 Esther Graudens Sandrine Imbeaud Anne Debily Yoshihide Hayashizaki Clara Amid Michael Han Andreas Osanger Toshinori Endo Michael Thomas Mika Hirakawa Wojciech Makalowski Mitsuteru Nakao Nam-Soon Kim Hyang-Sook Yoo Sandro de Souza Maria de Fatima Bonaldo Yoshihito Niimura Vladimir Kuryshev Ingo Schupp Stefan Wiemann Matthew Bellgard Masafumi Shionyu Ji 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 Ken 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
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.
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https://hal.archives-ouvertes.fr/hal-02115283
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Submitted on : Tuesday, April 30, 2019 - 10:50:24 AM
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Chisato Yamasaki, Katsuhiko Murakami, Yasuyuki Fujii, Yoshiharu Sato, Erimi Harada, et al.. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Nucleic Acids Research, Oxford University Press, 2007, 36 (Database), pp.D793-D799. ⟨10.1093/nar/gkm999⟩. ⟨hal-02115283⟩

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