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  1. Herb Ingredient Targets
    Resource Category : Databases -> Other Molecular Biology Databases -> Drugs and drug design

    Brief Description : Herbal active Ingredients and their Targets

    Institute/s :
    School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
    Address of Institute/s :
    School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
    Country : China

    Associated Institutes :

    • State Key Laboratory of Bioreactor Engineering, East China University of Science and Technology, Shanghai 200237
    • Shanghai Center for Bioinformation Technology, 100 Qinzhou Road, Shanghai 200235
    • School of Life Sciences and Technology, Tongji University, Shanghai 200092, China
    • NUS Graduate School for Integrative Sciences and Engineering, Singapore, 117456
    • Bioinformatics and Drug Design Group, Center for Computational Science and Engineering, Department of Pharmacy
    • National University of Singapore, Singapore, 117543
    • Bioinformatics Center, Key Lab of Systems Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200031, China

    Associated Country : China; Singapore


    Authors/Contributors : Hao Ye; Li Ye; Hong Kang; Duanfeng Zhang; Lin Tao; Kailin Tang; Xueping Liu; Ruixin Zhu; Qi Liu; Y. Z. Chen; Yixue Li; Zhiwei Cao
    Contact Email : zwcao@tongji.edu.cn
    Year : 2010
    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


  3. HGVbaseG2P
    Resource Category : Databases -> Human Genes and Diseases -> General polymorphism databases

    Brief Description : HGVbaseG2P (http://www.hgvbase.org) was set up in 1998 in an effort to improve analysis of common human genetic polymorphism by maintaining a high-quality database of all publicly available genomic variation data (primarily SNPs). Currently maintained by an academic European consortium it contains close to 2 million non-redundant entries. Data is harvested from three main areas, (i) collaboration with other variation databases, (ii) extraction from scientific literature and (iii) submissions from various research groups. Bi-directional data exchange with dbSNP (SNP repository at the NCBI) was established in 2000. Collaboration with the Human Genome Variation Society (HGVS) has led to HGVbaseG2P becoming a central repository for clinical mutations and associated disease phenotypes of interest. Automated and manual data checking ensures internal consistency, and addresses errors often present in the original source information. All markers have a given position in a reference EMBL or GenBank sequence and have been mapped to the human draft genome. These positions are verified and updated in every new build of HGVbaseG2P. Each variant is presented in the context of detailed genome annotation (coding regions and splice sites), as well as repeat regions and genome duplication information. Genotypes, haplotypes and allele frequencies are included as they become available. Work performed to increase the utility of SNP information includes the provision of genotyping assays for every SNP, and functional predictions for non-synonymous SNPs. A prototype system for handling phenotypes, based on a flexible framework relying on user provided information rather than a phenotype ontology, has recently been created. Online search tools facilitate data interrogation by keywords, sequence and chromosomal location. Core HGVbase data is also represented within the Ensembl project (www.ensembl.org) as sequence features with links to the HGVbase database for full information. Downloads of HGVbase are available in a variety of formats (XML, Fasta, SRS, MySQL dumps and tagged-text files). Current developments include graphical tools for data interrogation and further genome annotation by the representation of promoter and synteny regions. A full database description is provided online and accompanying web pages summarize SNP-related meetings, genotyping methods, SNP-databases, and analysis software.

    Institute/s :
    Center for Genomics and Bioinformatics,
    Address of Institute/s :
    Karolinska Institute,
    Country : Sweden

    Associated Institutes :

    • European Bioinformatics Institute, United Kingdom
    • European Molecular Biology Laboratory, Germany

    Associated Country : United Kingdom; Germany


    Authors/Contributors : D. Fredman; G. Munns; D. Rios; F. Sjoholm; M. Siegfried; B. Lenhard; H. Lehvaslaiho; A. J. Brookes
    Contact Email : anthony.brookes@cgb.ki.se
    Year : 2003
    Language : English


  4. hiPathDB
    Resource Category : Databases -> Metabolic and Signaling Pathways -> Metabolic pathways

    Brief Description : Human Integrated Pathway Database

    Institute/s :
    KRIBB, Daejeon 305-806, Korea
    Address of Institute/s :
    KRIBB, Daejeon 305-806, Korea
    Country : Korea

    Associated Institutes :

    • Korean Bioinformation Center (KOBIC), KRIBB, Daejeon 305-806
    • Ewha Research Center for Systems Biology (ERCSB), Ewha Womans University, Seoul 120-750, Korea

    Associated Country : Korea


    Authors/Contributors : Namhee Yu; Jihae Seo; Kyoohyoung Rho; Yeongjun Jang; Jinah Park; Wan Kyu Kim; Sanghyuk Lee
    Contact Email : sanghyuk@kribb.re.kr
    Year : 2011
    Language : English


  5. HitPredict
    Resource Category : Databases -> Metabolic and Signaling Pathways -> Protein-protein interactions

    Brief Description : Quality assessed protein-protein interactions in 9 species

    Institute/s :
    Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan
    Address of Institute/s :
    Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639, Japan
    State : Tokyo
    Country : Japan

    Associated Institutes :

    • Human Genome Center, The Institute of Medical Science, The University of Tokyo, 4-6-1 Shirokane-dai, Minato-ku, Tokyo 108-8639
    • Institute for Protein Research, Osaka University, 3-2 Yamadaoka, Suita, Osaka 565-0871, Japan

    Associated Country : Japan


    Authors/Contributors : Ashwini Patil; Kenta Nakai; Haruki Nakamura
    Contact Email : ashwini@hgc.jp
    Year : 2010
    Language : English


  6. HLungDB
    Resource Category : Databases -> Human Genes and Diseases -> Cancer gene databases

    Brief Description : Database of Human Lung Cancer Research

    Institute/s :
    Shanghai Institutes for Biological Sciences, China
    Address of Institute/s :
    Shanghai Institutes for Biological Sciences, China
    Country : China

    Associated Institutes :

    • Center for Bioinformatics and Computational Biology, The Institute of Biomedical Sciences, College of Life Science, East China Normal University, Shanghai 200241
    • Laboratory of Molecular Cell Biology, Institute of Biochemistry and Cell Biology, Shanghai Information Center for Life Sciences, Shanghai Institutes for Biological Sciences, Chinese Academy of Science, Shanghai 200031, China

    Associated Country : China


    Authors/Contributors : Lishan Wang; Yuanyuan Xiong; Yihua Sun; Zhaoyuan Fang; Li Li; Hongbin Ji; Tieliu Shi
    Contact Email : tlshi@sibs.ac.cn
    Year : 2009
    Language : English


  7. HORDE - Human Olfactory Receptor Data Exploratorium
    Resource Category : Databases -> Human Genes and Diseases -> Gene, system or disease specific databases

    Brief Description : Olfactory receptors (ORs) constitute the largest multi-gene family in multi-cellular organisms. Their evolutionary proliferation has been driven by the need to provide recognition capacity for millions of potential odorants with arbitrary chemical configuration. The Human Olfactory Receptor Data Exploratorium (http://bioportal.weizmann.ac.il/HORDE, HORDE), is a database which aim to provide a comprehensive view of the human OR universe. Currently, HORDE contains 853 OR entries, of which 386 have an intact open reading frame and the rest are probable pseudogenes. This collection constitutes the most update repertoire of human ORs, deciphered by computational data-mining procedure out of the public and Celera genomic complete human genome assemblies. To allow orthologues-paralogues comparisons, HORDE includes information on ORs from other mammalian species - mouse, dog and chimpanzee. Based on phylogenetic analysis, HORDE classifies the OR repertoire into seventeen families. A HUGO-approved systematic nomenclature is provided, which affords an instant guide to the position of a gene in a phylogenetic tree: OR1A2 signifies family 1, subfamily A, member 2.

    Institute/s :
    Department of Molecular Genetics, The Weizmann Institute of Science, 76100 Rehovot, Israel
    Address of Institute/s :
    Department of Molecular Genetics, The Weizmann Institute of Science, 76100 Rehovot, Israel
    Country : Israel

    Associated Institutes :

    • Department of Biological Services (Bioinformatics Unit), The Weizmann Institute of Science, 76100 Rehovot, Israel
    • Department of Molecular Genetics, The Weizmann Institute of Science, 76100 Rehovot, Israel

    Associated Country : Israel


    Authors/Contributors : Marilyn Safran; Vered Chalifa-Caspi; Orit Shmueli; Tsviya Olender; Michal Lapidot; Naomi Rosen; Michael Shmoish; Yakov Peter; Gustavo Glusman; Ester Feldmesser; Avital Adato; Inga Peter; Miriam Khen; Tal Atarot; Yoram Groner; Doron Lancet
    Contact Email : marilyn.safran@weizmann.ac.il
    Year : 2002
    Language : English


  8. HotRegion
    Resource Category : Databases -> Metabolic and Signaling Pathways -> Protein-protein interactions

    Brief Description : Database of interaction Hotspots

    Institute/s :
    Koc University, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
    Address of Institute/s :
    Koc University, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey
    Country : Turkey

    Associated Institutes :

    • Center for Computational Biology and Bioinformatics and College of Engineering, Koc University, Rumelifeneri Yolu, 34450 Sariyer Istanbul, Turkey

    Associated Country : Turkey


    Authors/Contributors : Engin Cukuroglu; Attila Gursoy; Ozlem Keskin
    Contact Email : okeskin@ku.edu.tr
    Year : 2011
    Language : English


  9. HRTBLDb
    Resource Category : Databases -> Human Genes and Diseases -> Gene, system or disease specific databases

    Brief Description : Hormone Receptors Target Binding Loci

    Institute/s :
    Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210,
    Address of Institute/s :
    Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210,
    State : Columbus
    Country : USA

    Associated Institutes :

    • Department of Biomedical Informatics, The Ohio State University, Columbus, OH 43210
    • Department of Pharmaceutical Sciences, SUNY at Buffalo, Buffalo, NY 14260, USA
    • Human Cancer Genetics Program, The Ohio State University, Columbus, OH 43210

    Associated Country : USA


    Authors/Contributors : Brian A. Kennedy; Wenqing Gao; Tim H.-M. Huang; Victor X. Jin
    Contact Email : victor.jin@osumc.edu
    Year : 2009
    Language : English


  10. Human BAC Ends Database
    Resource Category : Databases -> Human and other Vertebrate Genomes -> Human genome databases, maps and viewers

    Brief Description : The human BAC ends database includes all non-redundant human BAC end sequences (BESs) generated by The Institute for Genomic Research (TIGR), the University of Washington (UW) and California Institute of Technology (CalTech). It incorporates the available BAC mapping data from different genome centers and the annotation results of each end sequence for the contents of repeats, ESTs and STS makers. For each BAC end the database integrates the sequence, the phred quality scores, the map and the annotation, and provides links to sites of the library information, the reports of GenBank, dbGSS and GDB, and other relevant data. The database is freely accessible via the web and supports sequence or clone searches and anonymous FTP. The relevant sites and resources are described at http://www.jcvi.org/cms/research/projects/tdb/overview.

    Institute/s :
    The Institute for Genomic Research,
    Address of Institute/s :
    9712 Medical Center Drive, Rockville, MD 20850,
    Country : USA

    Associated Institutes :

    • The Institute for Genomic Research, 9712 Medical Center Drive, Rockville, MD 20850, USA

    Associated Country : USA


    Authors/Contributors : Shaying Zhao
    Contact Email : szhao@tigr.org
    Year : 1999
    Language : English


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