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  1. HGPD
    Resource Category : Databases -> Human and other Vertebrate Genomes -> Human ORFs

    Brief 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).

    Institute/s :
    National Institute of Advanced Industrial Science and Technology (AIST), Japan
    Address of Institute/s :
    National Institute of Advanced Industrial Science and Technology (AIST), Japan
    Country : Japan

    Associated Institutes :

    • Japan Biological Informatics Consortium (JBIC), Aomi, Koto-ku, Tokyo 135-8073
    • National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Koto-ku, Tokyo 135-0064
    • Reverse Proteomics Research Institute, Kisarazu, Chiba 292-0818, Japan
    • Graduate School of Pharmaceutical Sciences
    • The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033
    • Life Science Research Laboratory
    • Central Research Laboratory, Hitachi, Ltd., Kokubunji, Tokyo 185-8601
    • Database Center for Life Science Research Organization of Information and Systems, Yayoi, Bunkyo-ku, Tokyo 113-0032
    • Department of Medical Genome Sciences
    • Graduate School of Frontier Sciences
    • The University of Tokyo, Shiroganedai, Minato-ku, Tokyo 108-8639, Japan

    Associated Country : Japan


    Authors/Contributors : Yukio Maruyama; Ai Wakamatsu; Yoshifumi Kawamura; Kouichi Kimura; Jun-ichi Yamamoto; Tetsuo Nishikawa; Yasutomo Kisu; Sumio Sugano; Naoki Goshima; Takao Isogai; Nobuo Nomura
    Contact Email : n-goshima@aist.go.jp
    Year : 2008
    Language : English


  2. HGPD
    Resource Category : Databases -> Human and other Vertebrate Genomes -> Human ORFs

    Brief 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).

    Institute/s :
    National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Koto-ku, Tokyo 135-0064, Japan
    Address of Institute/s :
    National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Koto-ku, Tokyo 135-0064, Japan
    State : Tokyo
    Country : Japan

    Associated Institutes :

    • Japan Biological Informatics Consortium (JBIC), Aomi, Koto-ku, Tokyo 135-8073
    • National Institute of Advanced Industrial Science and Technology (AIST), Aomi, Koto-ku, Tokyo 135-0064
    • Reverse Proteomics Research Institute, Kisarazu, Chiba 292-0818, Japan
    • Graduate School of Pharmaceutical Sciences, The University of Tokyo, Hongo, Bunkyo-ku, Tokyo 113-0033
    • Life Science Research Laboratory, Central Research Laboratory, Hitachi, Ltd., Kokubunji, Tokyo 185-8601
    • Database Center for Life Science Research Organization of Information and Systems, Yayoi, Bunkyo-ku, Tokyo 113-0032
    • Department of Medical Genome Sciences, Graduate School of Frontier Sciences, The University of Tokyo, Shiroganedai, Minato-ku, Tokyo 108-8639, Japan

    Associated Country : Japan


    Authors/Contributors : Yukio Maruyama; Ai Wakamatsu; Yoshifumi Kawamura; Kouichi Kimura; Jun-ichi Yamamoto; Tetsuo Nishikawa; Yasutomo Kisu; Sumio Sugano; Naoki Goshima; Takao Isogai; Nobuo Nomura
    Contact Email : nomura.88@aist.go.jp
    Year : 2008
    Language : English