TY - JOUR
T1 - The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts
AU - Genome Information Integration Project and H-Invitational 2 Consortium
AU - Yamasaki, Chisato
AU - Murakami, Katsuhiko
AU - Fujii, Yasuyuki
AU - Sato, Yoshiharu
AU - Harada, Erimi
AU - Takeda, Jun Ichi
AU - Taniya, Takayuki
AU - Sakate, Ryuichi
AU - Kikugawa, Shingo
AU - Shimada, Makoto
AU - Tanino, Motohiko
AU - Koyanagi, Kanako O.
AU - Barrero, Roberto A.
AU - Gough, Craig
AU - Chun, Hong Woo
AU - Habara, Takuya
AU - Hanaoka, Hideki
AU - Hayakawa, Yosuke
AU - Hilton, Phillip B.
AU - Kaneko, Yayoi
AU - Kanno, Masako
AU - Kawahara, Yoshihiro
AU - Kawamura, Toshiyuki
AU - Matsuya, Akihiro
AU - Nagata, Naoki
AU - Nishikata, Kensaku
AU - Noda, Akiko Ogura
AU - Nurimoto, Shin
AU - Saichi, Naomi
AU - Sakai, Hiroaki
AU - Sanbonmatsu, Ryoko
AU - Shiba, Rie
AU - Suzuki, Mami
AU - Takabayashi, Kazuhiko
AU - Takahashi, Aiko
AU - Tamura, Takuro
AU - Tanaka, Masayuki
AU - Tanaka, Susumu
AU - Todokoro, Fusano
AU - Yamaguchi, Kaori
AU - Yamamoto, Naoyuki
AU - Okido, Toshihisa
AU - Mashima, Jun
AU - Hashizume, Aki
AU - Jin, Lihua
AU - Lee, Kyung Bum
AU - Lin, Yi Chueh
AU - Nozaki, Asami
AU - Sakai, Katsunaga
AU - Tada, Masahito
N1 - Funding Information:
We acknowledge all the members of the H-Invitational 2 consortium and Genome Information Integration Project (GIIP), especially the staffs of JBIRC for construction of H-InvDB, Ryo Aono, Tomohiro Endo, Yukie Makita, Hiromi Kubooka, Yuji Shinso, Harutoshi Maekawa, Yasuhiro Fukunaga, Hajime Nakaoka, Yoshito Ueki, Yoshihide Mimiura, Ryuzou Matsumoto, Seigo Hosoda, Yo Takahashi, Taichirou Sugisaki, Hiroki Hokari, Hiroaki Kawashima, Yasuhiro Imamizu, Makoto Ogawa for their technical assistance. This research is financially supported by the Ministry of Economy, Trade and Industry of Japan (METI), the Ministry of Education, Culture, Sports, Science and Technology of Japan (MEXT) and the Japan Biological Informatics Consortium (JBIC). Also, this work is partly supported by the Research Grant for the RIKEN Genome Exploration Research Project from MEXT to Y.H. and the Grant for the RIKEN Frontier Research System, Functional RNA research program. Funding to pay the Open Access publication charges for this article was provided by JBIC.
PY - 2008/1
Y1 - 2008/1
N2 - 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.
AB - 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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U2 - 10.1093/nar/gkm999
DO - 10.1093/nar/gkm999
M3 - Article
C2 - 18089548
AN - SCOPUS:38549163285
SN - 0305-1048
VL - 36
SP - D793-D799
JO - Nucleic acids research
JF - Nucleic acids research
IS - SUPPL. 1
ER -