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

Genome Information Integration Project and H-Invitational 2 Consortium

Research output: Contribution to journalArticlepeer-review

42 Scopus citations


Here we report the new features and improvements in our latest release of the H-Invitational Database (H-InvDB;, 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.

Original languageEnglish (US)
Pages (from-to)D793-D799
JournalNucleic acids research
Issue numberSUPPL. 1
StatePublished - Jan 2008
Externally publishedYes

Bibliographical note

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.

ASJC Scopus subject areas

  • Genetics


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