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HGPD


NAR Molecular Biology Database Collection entry number 1286
Maruyama, Yukio; Kawamura, Yoshifumi; Nishikawa, Tetsuo; Isogai, Takao; Nomura, Nobuo; Goshima, Naoki

Database Description

The Human Gene and Protein Database (HGPD) is a unique database that stores information from a set of human Gateway entry clones and in vitro expression data relating to human proteins, in compilation with public cDNA sequence data (Human ESTs, RefSeq, Ensembl, MGC, etc.). HGPD was released at the end of 2008. HGPD is accessed though http://www.HGPD.jp/ or http://www.HGPD.lifesciencedb.jp/ (mirror site).
In a project of the New Energy and Industrial Technology Development Organization (NEDO) in Japan, full-length human cDNA sequencing of approximately 30,000 human cDNA clones has been carried out (FLJ project; 1,2). For comprehensive and high-throughput expression of human proteins, both full-length cDNA clones and a versatile system for using these clones are essential. For functional analysis of proteins, one often needs to fuse various tags at either the N- or C-termini, to adjust the reading frames of the open reading frame (ORF) and tags or to locate adequate regulatory sequences [promoters, enhancers, internal ribosomal entry sites (IRESes), etc.] close to the ORF. These manipulations can be extremely difficult when a large number of clones are being handled. The Gateway cloning system (Invitrogen, Carlsbad, CA USA) is based on versatile expression vectors and has the potential to overcome these barriers (3). We have therefore adopted Gateway technology and constructed 33,275 human Gateway entry clones (4).
In HGPD, biological data such as in vitro expression data of human proteins are presented on the context of cDNA clusters. To build the basic framework, sequences of FLJ cDNAs and others deposited in public databases (Human ESTs, RefSeq, Ensembl, MGC, etc.) are assembled onto genome sequences. Information relating to human Gateway entry clones is presented with the source cDNAs.
Gateway entry clones are available from NITE Biological Resource Center (NBRC), Department of Biotechnology, National Institute of Technology and Evaluation. Distribution of clones by NBRC requires the signing of an MTA for both private companies and academic institutions (http://www.nbrc.nite.go.jp/e/hgentry-e.html).

Recent Developments

In the web interface, "Protein Info" of "Information Overview" has been improved. In HGPD, when a user "ID search" from the top page results in a hit, "Information Overview" is presented. This view shows all information available relating to members of the cluster that contains the queried sequence. In this improvement, open reading frame (ORF) is clearly indicated in "Protein Info" by a red line. With this annotation, the ORF regions for each cDNA mapping to a given locus are easily seen. Thus, any user can easily browse clone information and request a clone of interest.

References

1. Ota, T., Suzuki, Y., Nishikawa, T., Otsuki, T., Sugiyama, T., Irie, R., Wakamatsu, A., Hayashi, K., Sato, H., Nagai, K., et al. (2004) Complete sequencing and characterization of 21,243 full-length human cDNAs. Nat. Genet. 36, 40-45
2. Kimura, K., Wakamatsu, A., Suzuki, Y., Ota, T., Nishikawa, T., Yamashita, R., Yamamoto, J., Sekine, M., Tsuritani, K., and Wakaguri, H., et al. (2006) Diversification of transcriptional modulation: large-scale identification and characterization of putative alternative promoters of human genes. Genome Res. 16, 55-65
3. Hartley, J., Temple, G., and Brasch, M. (2000) DNA cloning using in vitro site-specific recombination. Genome Res. 10, 1788-1795
4. Goshima, N., Kawamura, Y., Fukumoto, A., Miura, A., Honma, R., Satoh, R., Wakamatsu, A., Yamamoto, J.-I, Kimura, K., and Nishikawa, T., et al. (2008) Human protein factory for converting the transcriptome into an in vitro-expressed proteome. Nat. Methods 5, 1011-1017

Subcategory: Human ORFs

Go to the abstract in the NAR 2009 Database Issue.
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