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H-InvDB

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H-Invitational Database (H-InvDB),
an integrated database of human genes and transcripts.


By extensive analyses of all human transcripts, we provide curated annotations of human genes and transcripts that include gene structures, alternative splicing variants, non-coding functional RNAs, protein functions, functional domains, sub-cellular localizations, metabolic pathways, protein 3D structure, genetic polymorphisms (SNPs, indels and microsatellite repeats) , relation with diseases, gene expression profiling, and molecular evolutionary features , protein-protein interactions (PPIs) and gene families/groups.
H-InvDB is produced by the "Genome Information Integration Project" (2005-2008) based upon the annotation technology established in the H-Invitational Project for annotation of human full-length cDNAs, and presented as a key integrated database of human genes in METI integrated database project (2008-).
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H-Invitational Database 8.3

What's new

  • [26-MAR-13] H-InvDB Rel. 8.3 released.
    The features of this minor release include:
    - Update in ID correspondence in orthologue information
    - Update in human protein-protein interaction (PPI) and HIP information (PPI view)
    - Updates of HIT and HIX information in expression subdatabase (H-ANGEL)

  • [19-AUG-12] We published "Human Gene Book"
    For the memorial of the 7th Anniversary of H-InvDB, we published a large book, "Human Gene Book" for the exhibition.
    Details: About "Human Gene Book"

  • [20-APR-12] H-InvDB Rel. 8.0 released.
    The features of this minor release include:
    - 249,012 human transcripts in 45,847 human gene clusters (loci).
    - Updates of human genome sequences to NCBI b37.1 (UCSC hg19).
    - new relase of positional information in GFF3 format at Download/Results of computational analysis.
    - updates of subdatabases; DiseaseInfo Viewer, H-ANGEL, G-integra

  • [08-DEC-11] Presentation at MBSJ2011
    Oral and poster resentation about H-InvDB and MEDALS
    Date & place: Dec. 13 - 16, in Yokohama
    URL: http://h-invitational.jp/mbsj2011_en.html

  • [22-JUN-11] Presentation and exhibition at 10th INT'L BIO FORUM & BIO EXPO JAPAN
    Presentation at academic forum: "Data-mining techniques using H-InvDB, an integrated database of human genes and transcripts" (14:50-15:20 on 30th June [ACA3])
    Exhibition (booth No.L-11): presenting H-InvDB and MEDALS
    Date & place: June 29 - July 1, at Tokyo Big Sight
    URL: BIO ACADEMIC FORUM, 10th INT'L BIO FORUM & BIO EXPO JAPAN

  • [10-SEP-10] H-InvDB Rel. 7.5 released.
    The features of this minor release include:
    - Re-difinition of human gene clusters on NCBI b37.1 (UCSC hg19) by re-filtering the predicted gene models
    - 242,813 human transcripts in 44,806 human gene clusters (loci).
    - Improvement on alternative splicing annotation pipeline and update of H-DBAS
    - Update in human protein-protein interaction (PPI) and update of PPI view
    - Updates of subdatabases; G-integra, DiseaseInfo Viewer, H-ANGEL

  • [14-JAN-10] Renewal of HEAT
    H-InvDB Enrichment Analysis Tool (HEAT), was renewed. We newly included analysis of common sequence motifs in promoter regions based on the JASPAR database in addition to 8 kinds of annotation such as GO and KEGG pathway. Moreover, HEAT became more useful as it accepts more kinds of IDs and the download function was added. Please try the HEAT.
    URL: http://hinv.jp/HEAT/

  • [28-DEC-09] DDBJ server is closing
    The H-InvDB at the DDBJ site will be closed on December 31, 2009.
    Please use the BIRC site (http://h-invitational.jp/hinv/ahg-db/index.jsp).

  • [06-FEB-09] Major update of the portal site about databases/tools for life science (medals.jp)
    Major update of the portal site that provides various information on databases and analysis tools for life science which were developed by the projects directly sponsored by METI, or developed by the Institutes sponsored by METI. The name of the site, "MEDALS", stands for METI Database portal for Life Science.
    URL: http://medals.jp/etop
    This project "life science database integration project", commissioned by METI, aims to facilitate the research and development in both industry and academia.

The main papers:

  1. H-InvDB in 2009: extended database and data mining resources for human genes and transcripts. Yamasaki C, et al. (2010) Nucleic Acids Research Jan;38(Database issue):D626-32.
  2. The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts. Yamasaki C, et al. (2008) Nucleic Acids Research 36, Database issue D793-D799.
  3. Integrative Annotation of 21,037 Human Genes Validated by Full-Length cDNA Clones. T. Imanishi et al. (2004) PLoS Biology 2 (6), 856-875.

Related papers:

  1. VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts. Shimada MK, et al. (2008) Nucleic Acids Research 37(Database issue):D810-5
  2. Distribution and effects of nonsense polymorphisms in human genes. Yamaguchi-Kabata Y, et al. (2008) PLOS One2008;3(10):e3393
  3. Low conservation and species-specific evolution of alternative splicing in humans and mice: comparative genomics analysis using well-annotated full-length cDNAs Takeda J, et al. (2008) Nucleic Acids Research2008 Nov;36(20):6386-95.
  4. Diversity of preferred nucleotide sequences around the translation initiation codon in eukaryote genomes. Nakagawa S, et al. (2008) Nucleic Acids Research
  5. Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees. Matsuya A, et al. (2008) Nucleic Acids Research 36, Database issue D787-D792.
  6. Mapping of chimpanzee full-length cDNAs onto the human genome unveils large potential divergence of the transcriptome. Sakate R, et al. (2007) Gene 399(1): 1-10.
  7. Frequent emergence and functional resurrection of processed pseudogenes in the human and mouse genomes. Sakai H, et al. (2007) Gene 389(2) 196-203.
  8. H-DBAS: Alternative splicing database of completely sequenced and manually annotated full-length cDNAs based on H-Invitational. Takeda, J. et al. (2007) Nucleic Acids Research 35, Database issue D104-D109.
  9. Large-scale identification and characterization of alternative splicing variants of human gene transcripts using 56 419 completely sequenced and manually annotated full-length cDNAs. Takeda, J. et al. (2006) Nucleic Acids Research 34 (14), 3917-3928.
  10. Alternative splicing in human transcriptome: Functional and structural influence on proteins. Yura, K. et al. (2006) Gene 380 (2), 63-71.
  11. TACT: Transcriptome Auto-annotation Conducting Tool of H-InvDB, Yamasaki C. et al. (2006) Nucleic Acids Research 34 Web Server issue W345-W349.
  12. Investigation of protein functions through data-mining on integrated human transcriptome database, H-Invitational Database (H-InvDB). Yamasaki C. et al. (2005) Gene 364, 99-107.
  13. A web tool for comparative genomics: G-compass. Fujii Y. et al.(2005) Gene 364, 45-52.
  14. Comparative genomics of bidirectional gene pairs and its implications for the evolution of a transcriptional regulation system. Koyanagi K.O. et al. (2005) Gene 353 (2), 169-176.
  15. Large-scale analysis of human alternative protein isoforms: pattern classification and correlation with subcellular localization signals M. Nakao et al. (2005) Nucleic Acids Research 33 (8), 2355-2363.
  16. The Human Anatomic Gene Expression Library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms. M. Tanino et al. (2005) Nucleic Acids Research 33 Database issue, D567-D572.