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H-Invitational Database, an integrated database of human genes and transcripts


NAR Molecular Biology Database Collection entry number 685
Takeda, J.1, Yamasaki, C. 1, Murakami, K. 1, Sera, M.1, Hara, Y. 1, Nagai, Y. 1, Mamiya, K. 1, Endo, T. 1, Habara, T. 1, Obi, N. 1, Imanishi, T. 1 and Gojobori, T. 1,2
1Integrated Database and Systems Biology Team, Biomedicinal Information Research Center National Institute of Advanced Industrial Science and Technology, AIST Bio-IT Research Bldg Aomi 2-4-7, Koto-ku, Tokyo 135-0064, Japan.
2Center for Information Biology and DNA Data Bank of Japan, National Institute of Genetics, Research Organization of Information and Systems, Yata, Mishima 411-8540, Japan.

Database Description

H-InvDB (http://h-invitational.jp/) is 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, 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-). H-InvDB consists of three main views, Transcript view, Locus view and Protein view, and six sub-databases with web-based viewers; G-integra, H-ANGEL, DiseaseInfo Viewer, Evola, PPI view and Gene Family/Group view, and provided as flat files, XML files and sequence fasta files.

Recent Developments

To use H-InvDB more effectively, Navigation Search and H-InvDB Enrichment Analysis Tool (HEAT) were developed. HEAT (http://h-invitational.jp/HEAT/) is a data mining tool for automatically identifying features specific to a given human gene set. To obtain H-InvDB data more easily, web service APIs (SOAP and REST) were also provided.

Acknowledgements

The authors acknowledge all the members of the H-Invitational consortium and the Genome Information Integration Project (GIIP) for participating in the annotation work of human full-length cDNAs and all the staffs of H-InvDB. H-InvDB is financially supported by National Institute of Advanced Industrial Science and Technology (AIST) and Ministry of Economy, Trade and Industry of Japan (METI).

References

1. Imanishi, T., Itoh, T., Suzuki, Y., O'D;onovan, C., Fukuchi, S., Koyanagi, K.O., Barrero, R.A., Tamura, T., Yamaguchi-Kabata, Y., Tanino, M., et al. (2004) Integrative annotation of 21,037 human genes validated by full-length cDNA clones, PLoS Biol, 2, 856-875
2. Tanino, M., Debily, M.A., Tamura, T., Hishiki, T., Ogasawara, O., Murakawa, K., Kawamoto, S., Itoh, K., Watanabe, S., de Souza, S.J., et al. (2005) The human anatomic gene expression library (H-ANGEL), the H-Inv integrative display of human gene expression across disparate technologies and platforms, Nucleic Acids Res, 33, D567-D572
3. Yamasaki, C., Kawashima, H., Todokoro, F., Imamizu, Y., Ogawa, M., Tanino, M., Itoh, T., Gojobori, T., Imanishi and T. (2006) TACT: transcriptome auto-annotation conducting tool of H-InvDB, Nucleic Acids Res, 34, W345-W349
4. Yamasaki, C., Murakami, K., Fujii, Y., Sato, Y., Harada, E., Takeda, J., Taniya, T., Sakate, R., Kikugawa, S., Shimada, M., et al. (2008) The H-Invitational Database (H-InvDB), a comprehensive annotation resource for human genes and transcripts, Nucleic Acids Res, 36, D793-D799
5. Matsuya, A., Sakate, R., Kawahara, Y., Koyanagi, K.O., Sato, Y., Fujii, Y., Yamasaki, C., Habara, T., Nakaoka, H., Todokoro, F., et al. (2008) Evola: Ortholog database of all human genes in H-InvDB with manual curation of phylogenetic trees, Nucleic Acids Res, 36, D787-D792
6. Kawahara, Y., Sakate, R., Matsuya, A., Murakami, K., Sato, Y., Zhang, H., Gojobori, T., Itoh, T., and Imanishi, T. (2009) G-compass: a web-based comparative genome browser between human and other vertebrate genomes, Bioinformatics, 15, 25(24), 3321-2
7. Shimada, M.K., Matsumoto, R., Hayakawa, Y., Sanbonmatsu, R., Gough, C., Yamaguchi-Kabata, Y., Yamasaki, C., Imanishi, T. and Gojobori, T. (2009) VarySysDB: a human genetic polymorphism database based on all H-InvDB transcripts, Nucleic Acids Res, 37, D810-5
8. Imanishi, T. and Nakaoka, H. (2009) Hyperlink Management System and ID Converter System: enabling maintenance-free hyperlinks among major biological databases, Nucleic Acids Res, 37, W17-22
9. Takeda, J., Suzuki, Y., Sakate, R., Sato, Y., Gojobori, T., Imanishi, T. and Sugano, S. (2010) H-DBAS: human-transcriptome database for alternative splicing: update 2010, Nucleic Acids Res, 38, D86-90
10. Taniya, T., Tanaka, S., Yamaguchi-Kabata, Y., Hanaoka, H., Yamasaki, C., Maekawa, H., Barrero, R.A., Lenhard, B., Datta, M.W., Shimoyama, M., et al. (2012) A prioritization analysis of disease association by data-mining of functional annotation of human genes, Genomics, 99(1), 1-9

Subcategory: Human ORFs

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