Protein 3000

2002

2006

-

Total Amount: 53.5 billion yen (RIKEN: 33.4 billion yen, Major research institutions: 13.6 billion yen, Other institutions: 6.6 billion yen)

FY:
9.5 billion yen (FY2003)
9.0 billion yen (FY2004)
9.8 billion yen (FY2005)
8.6 billion yen (FY2006)

Chief Researcher: Shigeyuki Yokoyama (RIKEN Structural Genomics/Proteomics Initiative)
Other chief researchers of central organizations:
・Masaru Tanokura (University of Tokyo Graduate School of Agricultural and Life Sciences)
・Isao Tanaka (Hokkaido University Graduate School of Life Science, Faculty of Advanced Life Science)
・Yoshifumi Nishimura (Yokohama City University, International Graduate School of Arts and Sciences)
・Soichi Wakatsuki (Institute of Materials Structure Science)
・Kunio Miki (Kyoto University Graduate School of Science)
・Fuyuhiko Inagaki (Hokkaido University Graduate School of Pharmaceutical Sciences)
・Atsushi Nakagawa (Institute for Protein Research, Osaka University)
・Seiki Kuramitsu (Osaka University Graduate School of Science)

Elucidation of basic structure and function for approximately 3,000 major proteins

From Post-Project Evaluation Report( http://www.tanpaku.org/old_project/protein02a.php , Japanese)
- Structures were determined for approximately 3,000 different proteins by protein crystallization and crystallography and NMR-based structural analysis.
- The Project is composed of the "Comprehensive Analysis Program" in which the basic structure of protein is comprehensively analyzed and the "Individual Analysis Program" in which the proteins related to the designated biological research themes are analyzed.
- The Individual Analysis Program, focusing on seven biological research themes including "metabolic system," "brain and nervous system," "intracellular signalling," "formation of higher-order structure and expression of function for protein," "post-translational modification and transport," "transcription and translation (I and II)" and "development/differentiation and DNA replication and repair," was implemented by 8 central organizations spread over universities nation-wide and their affiliated organizations.
- In both programs, the number of proteins with their three-dimensional structures analyzed and registered exceeded their respective initial goals (2,500 or more proteins for basic structure in the former and 500 or more proteins for analysis in the latter).
- Most of the protein structures were made available to the public on the wwPDB (while PDBJ is used for input), structural analysis was performed on 4,517 proteins (4,187 proteins for basic structure), the number of registered proteins in the Protein Data Bank (PDB) was 3,923, the number of applied patents was 403, and 4,195 papers were published.

From "Protein Structural Information to Protein Functional Information." Preliminary Proceedings of Protein 3000 Comprehensive Symposium, p.18. ( http://www.kuba.co.jp/sympo/pdf/protein070227.pdf , Japanese only ).
- As of 2006-end, 918 out of 2,732 peptide chains publicly available from public database have new structure (30 % or less homology with known structure), 122 domains of which have new folds (shapes). PSI, which is a PJ in the US, has 1,043 peptide chains, 597 new sequences and 48 new domain folds. Protein 3000 achieved about twice as much in terms of both new sequence and new domain.

Construction of an integrated database of the experimental data not included in public database is currently carried out as a subsidiary program of the Integrated Database Project. ( http://lifesciencedb.mext.go.jp/project/hokan.html , Japanese ).

Excerpts from "Introduction" of the Protein 3000 Project Evaluation Report ( http://www.tanpaku.org/old_project/protein02a.php , Japanese)

　"Japan's Strategies in Structural Genomics Research" (November 17, 2000) published by Genomics Committee of Science and Technology Council estimated that determination of structures for proteins representing 10,000 to 12,000 families or more would determine the structures for approximately 70 % of the remaining proteins, and stated that it would be appropriate to aim at determining three-dimensional structures for all (representative) protein families through international cooperation, and at determining the draft structure for about 10,000 proteins in 5 to 10 years. As for Japan, the document suggested that it would be appropriate to aim at determining the basic structure (Note 1) for about one-third or more of all protein families (consisting of about 10,000 to 12,000 different proteins) in the next five years by building up a cooperative framework for the entire country.
　Against such a background, it was decided to promote protein structural and functional analyses based on the policies set forth in the "Promotion of Post-Genomic Strategies (December 2000, Policy Committee of Science and Technology Council)" and the "Field-Specific Promotion Strategies of Council for Science and Technology Policy (September 2001)" and the most recent developments in structural biology. In response to this, it was decided to start a project (Protein 3000 Project) designed to analyze the structure and function of approximately 3,000 or more proteins, estimated to account for one-third of the entire basic structure of protein, in a five-year period starting in the fiscal year 2002 as part of the "New Century Priority Research Creation Plan (Research Revolution 2002 or RR2002) (Note 2), which was conceived to advocate Japan as a nation built on the platform of scientific and technological creativity, in accordance with the "Concepts Concerning Short-Term Promotion of Research and Development (August 2001)" and the "Specific Implementation Policies for New Priority Project (February 2002)" put together by the Life Science Committee of the Subdivision on Planning and Evaluation, Council for Science and Technology.

NA

Publicly released

Database for Protein-3000 Project ( http://p3krs.protein.osaka-u.ac.jp/p3kdb/v_menu.php?lang=1 )

None

Abstract of "Protein 3000" (in Targeted Proteins Research Program's website) ( http://www.tanpaku.org/old_project/01.php )(Japanese)

Ministry of Education, Culture, Sports, Science and Technology (MEXT)

NA

Post-Project Evaluation Report ( http://www.tanpaku.org/old_project/protein02a.php ）(Japanese)

NA

- Project overview ( http://www.tanpaku.org/eng/pdf/project_overview.pdf )
- Preliminary Proceedings of Protein 3000 Comprehensive Symposium (February 27, 2007) ( http://www.kuba.co.jp/sympo/pdf/protein070227.pdf , Japanese)
- Preliminary Proceedings of Protein 3000-Genome Network Joint Forum (July 18, 2006) ( http://www.kuba.co.jp/sympo/pdf/p3kg2006.pdf , Japanese)
- "What Protein 3000 Project Has Produced." Protein, Nucleic Acid and Enzyme Vol.53 No.5. (Japanese)
- "What Protein 3000 Has Left." Chemistry Today No.434 (in Japanese)"Focus: Developments in Structural Genomic Project." Protein, Nucleic Acid and Enzyme Vol.50 No.7 (Japanese)
- "Protein 3000 Project." Idenshi Igaku MOOK Vol.2 (Japanese)
- Nature 443, p382 (28 September 2006) 'Big science' protein project under fire. (News story about Protein 3000) （ http://www.nature.com/nature/journal/v443/n7110/full/443382a.html ）
- Nature 445, p21 (4 January 2007)　RIKEN aids international structural genomics efforts. (Comment on the above news story) ( http://www.ncbi.nlm.nih.gov/pubmed/17203040?ordinalpos=2&itool=EntrezSystem2.PEntrez.Pubmed.Pubmed_ResultsPanel.Pubmed_RVDocSum )

Research for the Future Program (Genome Research)

1996

2004

1996-1999 (completed) , Human Genome 2000-2004 (completed) Genome Research

11.08 billion yen (2000-2004)

Research Promotion Committee Chairpersons: Kenichi Matsubara (DNA Chip Research Inc.) and Hiroshi Yoshikawa (Adviser, JT Biohistory Research Hall)
Project Leaders:
・Itsuro Inoue (University of Tokyo, Institute of Medical Science)
・Yusuke Nakamura (University of Tokyo, The Institute of Medical Science)
・Satoru Miyano (University of Tokyo, Institute of Medical Science)
・Shoji Tsuji (University of Tokyo Graduate School of Medicine)
・Mitsuo Itakura (University of Tokushima, Institute for Genome Research)
・Nobuyoshi Shimizu (Keio University School of Medicine)
・Hidetoshi Inoko (Tokai University School of medicine)
・Mitsuru Emi (Institute of Gerontology, Nippon Medical School)
・Minoru Kanehisa (Kyoto University, Institute for Chemical Research)
・Naoyuki Kamatani (Institute of Rheumatology, Tokyo Women’s Medical University)
・Hideo Hayashi (University of Tsukuba, Institute of Basic Medical Sciences)
・Satoru Kuhara (Kyushu University, Faculty of Agriculture)
・Masatoshi Takeda　(Osaka University Graduate School of Medicine)

Human genome sequencing and its applied studies

From the List of Research Themes for Research for the Future Program (Genome Research), ( http://www.jsps.go.jp/j-rftf/project/l014.htm , Japanese)
●Itsuro Inoue (University of Tokyo, Institute of Medical Science)　 Systematic Genetic Study of Asthma and Atopic Dermatitis Based on the Genome-Wide SNP Informatics
●Yusuke Nakamura (University of Tokyo, The Institute of Medical Science) Systematic Expression Profile Analysis and its Application to Personalized Medicine
●Satoru Miyano (University of Tokyo, Institute of Medical Science) Genome-Wide Analysis of Genes Related to Disease Susceptibility and Drug Responsiveness
●Shoji Tsuji (University of Tokyo) Identification of Genes Involved in Brain Diseases
●Mitsuo Itakura (University of Tokushima) Whole Body Functional Genomics Directing toward the Understanding of Disease-Related Genes
●Nobuyoshi Shimizu (Keio University) Human Molecular Biology and Medicine Based on Genome Analysis
●Hidetoshi Inoko (Tokai University) Identification of Disease-Related Genes Using Microsatellite Polymorphisms
●Mitsuru Emi (Nippon Medical School) Genetic Analysis of Osteoporosis by Systematic SNP Typing
●Minoru Kanehisa (Kyoto University) Biological Systems Database and Genome Information Science
●Naoyuki Kamatani (Tokyo Women’s Medical University) Development and Application of Computer Programs for Mapping Disease-Related Genes Using Polymorphic Markers
●Tetsuya Hayashi (University of Miyazaki) Virulent/Valuable Genome System in Microorganism
●Satoru Kuhara (Kyushu University) Computational Biology on Genome Function Based on Expression and Phenotype Data
●Masatoshi Takeda (Osaka University) Analysis of Alzheimer Disease-Related Genes

Excerpts from Overview of Research for the Future Program (Genome Research)(
http://www.jsps.go.jp/j-rftf/outl/l014.htm, Japanese)
　In this Project, new genomic analysis techniques will be developed, and will be utilized to help using genomic data and genomic polymorphism data for successful identification of disease genes. Moreover, new findings to be gained from the results of studies of model organisms and disease models will be applied to these data to develop new therapeutic approaches against malignant diseases, hypertension, diabetes, asthma and atopic disease and to delay the onset of these diseases,
　Also, bioinformatics research will be carried out to understand the systems of life from the genomic information.
　Furthermore, experimental and bioinformatic analyses of the genome of microorganisms and model organisms will be performed to discover pathogenic and useful genes related to human disease and health, and to elucidate gene functions, and finally technological and theoretical models that are necessary for human genome functional analyses will be established through the evolutionary studies of the systems of life.

NA

Partially shared,Partially publicly released,Partially unknown

Leader Names (Public database)
・Inoue
・Nakamura (JSNP( http://snp.ims.u-tokyo.ac.jp/index.html ))
・Tsuji
・Miyano
・Itakura (Asian SNPs( http://www.genome.tokushima-u.ac.jp/dgi/ENGDGI/ASNPs_E/index_English.html ))
・Shimizu (KMDB/MutationView( http://mutview.dmb.med.keio.ac.jp/ ))
・Inoko
・Emi
・Kanehisa (KEGG( http://www.kegg.jp/ ))
・Kamatani ( http://www.jpma.or.jp/psc/11data/index.html , found in the Summary of Report of Research Project Results)
・Hayashi
・Kuhara
・Takeda

-

Research for the Future Program( http://www.jsps.go.jp/j-rftf/project/l014.htm )

Ministry of Education, Culture, Sports, Science and Technology (MEXT)

NA

List of Reports of Research Project Results for FY2004 Research for the Future Program( http://www.jsps.go.jp/j-rftf/saishu/h16/index.html , Japanese)

- Final evaluation ( http://www.jsps.go.jp/j-rftf/life_i.htm , Japanese )(Click the frame on left "Final Evaluation/Researches that started in FY2000.”)
- Summary of "Final Evaluation" Report( http://www.jsps.go.jp/j-rftf/saishu_hyouka_12/data/houkoku_h12.pdf , Japanese )
- Summary of Research Project Results( http://www.jsps.go.jp/j-rftf/life_i.htm , Japanese)(Click "Summary of Research Project Results" on the page for final evaluation.)

-

SNP Research

2000

2003

2000-2003 completed

Total Amount: 9.35 billion yen (2000-2003)
FY2000: 1.85 billion yen
FY2001: 2.5 billion yen
FY2002: 2.5 billion yen
FY2003: 2.5 billion yen (requested amount)

Chief Researcher: Yusuke Nakamura (University of Tokyo, The Institute of Medical Science)
Other leading researchers:
- Michiaki Kubo (University of Tokyo, The Institute of Medical Science, RIKEN SNP Research Center)
- Naoyuki Kamatani (Institute of Rheumatology, Tokyo Women’s Medical University)
- Toshihiro Tanaka (University of Tokyo, The Institute of Medical Science, RIKEN SNP Research Center)

Acquisition and analysis of information related to SNP in genes of human genome

From the Goals of Millennium Project ( http://snp.ims.u-tokyo.ac.jp/mission_ja.html , Japanese)
- 24 Japanese (3 persons in each pool) were screened for SNPs (rSNP, iSNP, cSNP, sSNP) in gene regions (exons and promoters).
From "Millennium Genome Project Final Evaluation Report" ( http://www.kantei.go.jp/jp/mille/genomu/report/17report.pdf , Japanese)
- Approximately 40 % of all gene regions, and especially all exon regions were screened by sequencing of approximately 140 million-base regions. As of March 2005, the data of 195,134 SNPs in total are made available to the public on the JSNP database.

From "Millennium Genome Project Final Evaluation Report" ( http://www.kantei.go.jp/jp/mille/genomu/report/17report.pdf , Japanese)
- Gene regions were searched and analyzed for finding 15 thousands of standard SNPs and a standard SNP database was developed.

NA

Unpublished

JSNP Database( http://snp.ims.u-tokyo.ac.jp/index.html )

- SNP frequency data, etc. ( ftp://ftp.hgc.jp/pub/hgc/db/snp/ )
- XML (mapping data, etc.) ( http://snp.ims.u-tokyo.ac.jp/XML_ja.html )
- Search tool ( http://snp.ims.u-tokyo.ac.jp/map/Dump/ )

-

Ministry of Education, Culture, Sports, Science and Technology (MEXT)

NA

-

- Millennium Genome Project Final Evaluation Report (July 2005) ( http://www.kantei.go.jp/jp/mille/genomu/report/17report.pdf )

- Journal of Human Genetics, 2002; 47(11): 605-610
References ( http://www.ncbi.nlm.nih.gov/pubmed/12436197?dopt=Abstract ）
- Publications ( http://snp.ims.u-tokyo.ac.jp/publications.html )

RIKEN SNP

-

-

Implementation of this project is not based on a limited period because budgetary steps are taken on the basis of RIKEN's medium-term operational plan.

2.2 billion yen (FY2003)
2.1 billion yen (FY2004)
1.7 billion yen (FY2005)
1.6 billion yen (FY2006)
1.6 billion yen (FY2007)
1.6 billion yen (FY2008)
1.6 billion yen (FY2009)
1.6 billion yen (FY2010 budget request)

FY2010
Director: Naoyuki Kamatani
Deputy Director: Toshihiro Tanaka
Group Leaders:
- Michiaki Kubo

Operation by RIKEN SNP Research Center (until FY2007) and by RIKEN Center for Genomic Medicine (from FY2008)

The research institute in RIKEN involved in this project is named "SNP Research Center" between fiscal years 2000 and 2007, and "Center for Genomic Medicine" from the fiscal year 2008 on.
In this Project, proteomic analysis and studies of disease genes in general will also be carried out in addition to SNP studies.

Excerpts from the “Basice Research Principles”( http://www.src.riken.go.jp/english/outline/plan/index.html ))

Our mission is to understand individual gene variation and to apply this knowledge to healthcare in order to promote full and healthy lives

Quality of life.

Everyone hopes for a full and healthy life.
Unfortunately, lifestyle-related diseases and other conditions are currently on the increase.
Healthcare and long-term care are also becoming national issues, as our society faces high longevity rates never seen before.

Present healthcare techniques can be likened to off-the-rack clothing.
Such clothing does not necessarily provide a perfect fit for everyone, as it is sometimes too long in the sleeve or too tight in the waist.
The same principles apply to pharmaceuticals.
Individuals respond differently to drugs, with some people responding well or others being susceptible to side effects.
Ideally, patients should be able to choose medical procedures and drugs that are suited to their individual profile, providing the best efficacy and the fewest side effects.
This concept is termed "personalized medicine".
If individuals know in advance whether they are susceptible to a specific disease, they could adjust their lifestyle and prevent the onset of disease.
We now know that the differences in individual make-up are associated with genetic differences.

We are investigating individual gene variation in the genome and identifying the relationship to disease onset and drug response, in order to develop preventive and therapeutic techniques to suit each individual.
----- This is the mission of the Center for Genomic Medicine.

It seems that the data obtained jointly with other projects are made public at other sites (such as JSNP).
For those data not available at JSNP, the public release status is unknown.

-

- JSNP DATABASE( http://snp.ims.u-tokyo.ac.jp/index_ja.html )
- International HapMap Project ( http://hapmap.ncbi.nlm.nih.gov/index.html.en )

-

RIKEN Center for Genomic Medicine website( http://www.src.riken.go.jp/english/index.html )

Ministry of Education, Culture, Sports, Science and Technology (MEXT)

-

Annual Reports of Research Activities 2003( http://www.riken.jp/r-world/info/release/pamphlet/annual/2003/conts03/j_yokohama.html , Japanese)

Advisory Council Report( http://www.src.riken.go.jp/english/outline/advisory/index.html )

-

RIKEN plant

-

-

Implementation of this project is not based on a limited period because budgetary steps are taken on the basis of RIKEN’s medium-term operational plan.

1.7 billion yen (FY2003)
1.6 billion yen (FY2004)
1.5 billion yen (FY2005)
1.7 billion yen (FY2006)
1.6 billion yen (FY2007)
1.5 billion yen (FY2008)
1.5 billion yen (FY2009)
1.4 billion yen (FY2010 budget request)

FY2010
Chief Researcher: Kazuo Shinozaki
Deputy Director: Kazuki Saito
Group Directors:
- Yuji Kamiya
- Hitoshi Sakakibara
- Ken Shirasu
- Minami Matsui

Operation by RIKEN Plant Science Center

The project, consisting of six groups in charge of studying plant genome, immunity and metabolism, and other aspects of plant, is designed to perform researches to increase productivity of crops and trees.
- Metabolomics Research Division
- Gene Discovery Research Group
- Growth Regulation Research Group
- Plant Productivity Systems Research Group
- Plant Immunity Research Group
- Plant Functional Genomics Research Team

Excerpts from "Director's message, RIKEN Plant Science Center"( http://www.psc.riken.jp/english/outline/message/index.html )
Plants with their distinct biological features, such as photosynthesis, adaptation to many different environments, seed production, and organ formation, are essential to many important industries including those involved in the production of food, biomaterials, and energy; they also play a vital role in preserving the global environment. At the end of the 20th century and the beginning of the 21st century, genomics has led to extensive developments in plant science. On the basis of genetics and genomics, important functions of plant genes involved in growth, morphology, photosynthesis, metabolism, and environmental responses have been found. Elucidating the unique physiologies of plants is expected to help us gain a basic understanding of plant systems which will lead to technological developments useful for the production of food, biomaterials, and energy, and also for environmental sustainability.

The rapid increase in population accompanied by rapid industrialization that is occurring in Asia and other areas as we enter the 21st century has caused imbalances in the supply of food and energy, leading many to predict that a global crisis of food and energy will occur around 2020. Research and development based on plant science is thought to be extremely important for solving this problem.

In the first phase of research at the RIKENPlantScienceCenter, we achieved a high level of basic research (especially in genetics, molecular biology, biochemistry, and organic chemistry) in the areas of plant hormone metabolism and signaling, morphology, development, and metabolism using model plants. In the second phase of research at the Center, we are conducting projects aimed at improving plant production, both quantitatively and qualitatively, based on the plant science research activities at RIKEN. This new research program is founded on functional genomics in model plants with known genomic sequences, such as Arabidopsis and rice, and particularly on metabolome research for the understanding of metabolic systems. On the basis of these genomic studies, we are exploring important genes and analyzing the molecular functions involved in plant productivity, and are promoting research that emphasizes the understanding of genomic systems unique to plants. We also collaborate with universities, institutes, industry, and international organizations with the aim of linking research findings on model plants to the improved production of crops and trees. This research program contributes to uncovering new plant functions that can ensure a reliable supply of food, materials, and energy from plants, and to supporting human health. We believe that our new program will contribute to the sustainability of human life.

Downloadable databases are available, but limited in number.

Partially shared,Publicly released

RIKEN Plant Science Center public database( http://www.psc.riken.go.jp/english/database/index.html )

- RARGE( http://rarge.psc.riken.jp/archives/ )
- TriMEDB( http://trimedb.psc.riken.jp/download.pl )
- AtGenExpress Data Downloader( http://igrt1.psc.riken.jp/ , Japanese)
- TriFLDB( http://trifldb.psc.riken.jp/download.pl )

RIKEN Plant Science Center website( http://www.psc.riken.go.jp/english/index.html )

Ministry of Education, Culture, Sports, Science and Technology (MEXT)

-

Annual Report( http://www.psc.riken.go.jp/english/outline/annual/index.html )

Advisory Council Report ( http://www.riken.jp/engn/r-world/info/report/yokohama/plant/no3/RIKEN_PSC2_2006_Gruissem13.pdf )

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Integrated Database Project (LSDB)

2006

-

2006

290 million yen (FY2006)
1.6 billion yen (FY2007)
1.1 billion yen (FY2008)
0.9 billion yen (FY2009)
0.4 billion yen (FY2010 budget request)

Chief Researcher: Toshihisa Takagi (Database Center for Life Science)
- Central Organization: Research Organization of Information and Systems, Database Center for Life Science
(Participating Organizations)
　・Japan Science and Technology Agency
　・National Institute of Advanced Industrial Science and Technology, Computational Biology Research Center
　・Kazusa DNA Research Institute
　・Kyushu University
　・Nara Institute of Science and Technology
　・Nagahama Institute of Bio-Science and Technology
　・University of Tokyo
　・Ochanomizu University
- Representatives of Allocation Organizations (Integration of medical care database)
　・Minoru Kanehisa (Kyoto University, Institute for Chemical Research, Bioinformatics Center)
　・Hiroshi Tanaka (Tokyo Medical and Dental University, Information Center for Medical Sciences)
　・Katsushi Tokunaga (University of Tokyo Graduate School of Medicine)
- Representatives of Organizations Involved in Subsidiary Program
　・Tetsuro Toyoda (RIKEN)
　・Hisashi Narimatsu (National Institute of Advanced Industrial Science and Technology)
　・Takashi Gojobori (National Institute of Genetics)
　・Akinori Sarai (Kyushu Institute of Technology)

Aiding formulation of strategy for database in life science field, and establishing and improving portal site

- Comprehensive promotion by improvement of a central organization (Research Organization of Information and Systems)
- Development and operation of integrated database
- Links with literature information and addition of annotation to data
- Integration of medical care database concerning compounds and drugs and clinical and disease data by allocation organizations (University of Tokyo, Tokyo Medical and Dental University and Kyoto University)
- Acceleration of database integration by the organizations involved in subsidiary program (RIKEN, National Institute of Advanced Industrial Science and Technology, National Institute of Genetics and Kyushu Institute of Technology)
- Acceptance of valuable database that has become difficult to maintain
- Development of human resources for database development

Excerpts from MEXT Integrated Database Project ( http://lifesciencedb.mext.go.jp/en/index.html )
　 The Integrated Database Project aims to add functions in order to support the drafting of a national strategy determined by the government, and to direct its execution with regard to the establishment of databases for fields in the life sciences. As well as reappraising existing efforts, the project supports a portal site on the Internet, and works to improve the ease of use and integration of Japan's life sciences databases. In this way, it promotes the wider utilization of these resources by the general public and others.

The project aims to make all of the outcomes publicly available.

Shared

LifeScienceDB( http://lifesciencedb.jp/?lng=en )

- http://lifesciencedb.jp/?pg=4 (Japanese)
- Life Science Database Archive( http://dbarchive.lifesciencedb.jp/ )(Japanese)

- Database Center for Life Science (http://dbcls.rois.ac.jp/en/ )
- Integrated Database Project(MEXT) (http://lifesciencedb.mext.go.jp/en/ )

Ministry of Education, Culture, Sports, Science and Technology (MEXT)

-

- 2006 Achievement Report Web Site ( http://lifesciencedb.jp/MEXT_H18/ ) (Japanese)
- Integrated Database Project(MEXT) Achievement page (http://lifesciencedb.mext.go.jp/en/result/index.html )

- Interim appraisal reports (http://lifesciencedb.mext.go.jp/hyouka/index.html ) (Japanese)
- Evaluation from outside( http://lifesciencedb.jp/lsdb.cgi?gg=hyouka ) (Japanese)

-

Human full-length cDNA project

2000

2001

2000-2001, Completed

Total Amount: 4.88 billion yen

Chief Researcher: Sumio Sugao (University of Tokyo, The Institute of Medical Science)
Other Leading Researchers:
・Takao Isogai (Helix Research Institute)
・Nobuo Nomura (Advanced Industrial Science and Technology - Biological Information Research Center)
・Participating Companies (Kyowa Hakko Kogyo Co., Ltd., Otsuka Pharmaceutical Co., Ltd., Fujiya Co., Ltd., Hitachi, Ltd., Takara Shuzo Co., Ltd., Hitachi Science Systems, Nisshinbo Industries, Inc., Unitech, Daiichi Pharmaceutical Co., Ltd., Mitsui Knowledge Industry Co., Ltd., Hitachi Software Engineering Co., Ltd. and Aisin Cosmos R&D Co., Ltd.)

Acquisition and analysis of about 30,000 full-length cDNA sequence data

From "Millennium Genome Project Final Evaluation Report"　( http://www.kantei.go.jp/jp/mille/genomu/report/17report.pdf ) (Japanese)
・Part of ” Millennium Genome Project” “Genome Diversity Project”.
・Full-length human cDNA clones based on the oligo-capping method (produced by the Institute of Medical Science of the University of Tokyo and Helix Research Institute) were sequenced by about a dozen companies with their respective assignments. (30,000 full-length cDNA sequences and 1.5 million full-length cDNA 5’-end sequences)
Both full-length human cDNA sequence (30,000) and 5’ one-pass sequence (1.38 million) were determined and deposited in DDBJ.

Excerpts from "Full-length cDNA sequencing project and draft sequence of human genome"( http://www.nedo.go.jp/bioiryo/bio-e/index_syokai.html , Japanese, currently not available)
　 The Full-length Human cDNA Sequencing Project is designed to obtain and sequence the full-length cDNA of as many genes as possible. However, gene expression is regulated both spatially and temporally, and the expression level varies from gene to gene. Thus, it is considered challenging to obtain the full-length cDNA for all human genes. The full-length cDNA project in Japan sponsored by NEDO has the goal of 30,000 genes.
　The Japanese full-length cDNA project is carried out by the organization shown in the Figure. In this project, a large number of clones are isolated from various cDNA libraries. After sequencing of segments, new putative full-length genes are selected, and the clones are sequenced. Initially, the Institute of Medical Science of the University of Tokyo and Helix Research Institute supplied the selected clones, and the sequencing team consisted of 8 companies (See Note) performed the full-length sequencing. Currently, the clone selection team consisted of three companies led by Hitachi, Ltd. is using the cDNA library supplied by Helix Research Institute to perform a range of works from clone isolation to clone selection, and supplying the clones to the full-length sequencing team. The Institute of Medical Science is also independently creating the library and performing segment sequencing, and the Institute is planning to supply the clones for full-length sequencing from time to time.
　To obtain full-length cDNA in large quantities, you need to put a twist on the way to create cDNA libraries because reverse transcriptase, which is used to make cDNA from mRNA, is not always highly efficient to produce full-length cDNA, and the library contains many cDNAs that are not full-length. Any such library is low in efficiency for the work aimed at obtaining many full-length cDNAs while sequencing segments. Therefore, the library with the high proportion of full-length cDNAs in the entire set of clones is required in the full-length cDNA project. Creating this type of full-length cDNA library is the specialty of Japanese scientists, and we have the oligo-capping method developed by ourselves and the cap-trapper method developed by Dr. Hayashizaki and others. In the NEDO project, more than 20 types of cDNA library were used, and all of them were created by the oligo-capping method.

After releasing both full-length sequences (30,000) and 5’ one-pass sequences (1.38 million) to consortium members, they were deposited in one of the International Nucleotide Sequence Databases, DDBJ.
All-file download is partially unavailable.

Partially shared,Partially publicly released

FLJ-DB ( http://flj.lifesciencedb.jp/top/ )

Download Full Length cDNAs( http://cdna.ims.u-tokyo.ac.jp/download.html )

Website of Full-length Human cDNA Sequencing Project: http://www.nedo.go.jp/bioiryo/bio/

Ministry of Economy, Trade and Industry (METI)

Description of the JBIC Results Consortium in the JBIC column "About NEDO Protein Functional Analysis and Utilization Project"( http://www.jbic.or.jp/bio/c/column.html , Japanese )

1. " Human Full-length cDNA Sequencing Project"Outcome Utilization Consortium (1999-2002)
　　Participating Organizations: 65 (Founding members: 15 organizations; Public members: 50 organizations)
2. Human cDNA Terminal Sequence Information Utilization Consortium (2002-2003)
　　Participating Organizations: 34 (Founding members: 19 organizations; Public members: 15 organizations)
3. “Human Full-length cDNA Sequencing Project” Application Project (2002-2006)

1. FY2000 Report Outcome Report (for FY1999 budget)
2. FY2000 Report Outcome Report (for FY2000 budget)
3. FY2001 Report Outcome Report
The report may be obtained at the NEDO Outcome Report website( http://app3.infoc.nedo.go.jp/informations/koubo/databaselist ) by running a search by using the project name “Full-length human cDNA sequencing project” as the keyword.

Millennium Genome Project Final Evaluation Report (July 2005)

- "Bioinformatics - Basics and Clinical Applications - Basics - Full-length Human cDNA and Bioinformatics." Gendai Iryo. 36, 5.
- "Genomic Medicine and Bioinformatics from the Basics: From Human Genome Database, Homology Search, SNP, Proteomic Analysis to Disease Analysis and Application to Drug Discovery. Chapter 3. Informatics for Experiment Support. 2. cDNA Analysis Data and Annotation." Jikken Igaku. 19, 11.

Genome Informatics Technology Development Project

1998

2002

1998-2002, Completed

Total Amount: 6.639 billion yen

Project leader was not appointed, and the project was driven by the Strategic Technology Committee.
Chairman: Michio Oishi (Kazusa DNA Research Institute) and seven other committee members (Murakami, Sekiya, Jigami, Yoshikawa, Isono, Takagi and Sakaki)

Development of technology for effective use of genome-sequence information

Development of computer software, establishment of analytical method related to gene transcriptional regulation, and development of genomic DNA-related instrumentations were carried out for the purpose of effective use of genomic DNA sequence information. The following works were divided and assigned to Advanced Industrial Science and Technology (Computational Biology Research Center, Age Dimension Research Center, and Research Center for Medical Glycoscience), National Institute of Technology and Evaluation and 12 companies.
- Comparative genomic analysis technology (Hitachi and others)
- Gene sequence information modeling technology (Yamanouchi and others)
- Gene expression frequency information analysis technology (Hitachi Software Engineering and others)
- Transcriptional regulation information analysis technology (Sumitomo Electric Industries and others)

Excerpts from "Genome Informatics Technical Brochure” (http://www.nedo.go.jp/informations/panel/pdf/bio/bio_003.pdf [currently not available] (Japanese))
　As a result of advances in biotechnology in recent years, development of automated and high-throughput medical and biological experiments has accelerated. This is accompanied by generation of a wide variety of experimental results in large quantities related to genes and proteins. Now, how to find useful information from a myriad of information is one of the crucial challenges for biologists.
　To address this challenge, this research and development project will aim at the development of a system to support the gene network research by organizing and integrating a large volume of information taking diverse forms. The workbench system is designed to support the establishment of the gene network involving a group of genes of interest through repetition of the research cycle shown on the diagram on right by biologists. First, the researcher inputs a group of genes of interest in the system. Then, the system will reconstruct a gene network related to these genes by referring to the rearrangement database and the expression profile provided separately to the system as well as other information, and present the data to the user. In response to the network produced by the system, the user can operate the system interactively to position the network to facilitate understanding, and refer to other experimental results, the sequence information analysis results and a variety of other information related to the genes of interest.
　Moreover, the researcher can use the functions provided by the system to analyze the network from a variety of perspectives, and also use the system like a simulator to see any change in the network whenever the researcher’s hypothesis, such as a regulatory relationship is added, for example. If any new finding or suggestion, such as the existence of gene function or regulatory factor, is gained in relation to a group of genes of interest as a result of this interaction, a new experimental system as an extension of the current results can also be constructed. By inputting the results obtained from this experiment in this system again to ensure that the system reflect the results, and by repeating the research cycle centering on this system, the user will be able to gradually zero in on the real image of the gene regulation network that involves a group of genes of interest.

Outcomes are patents related to technology developed by the project, and product commercialization. No database was created.
The reports listed in the Report(s) section are the only publicly released materials concerning the project.

Partially publicly released

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-

-

Ministry of Economy, Trade and Industry (METI)

NA

1. Basic Plan　( http://www.nedo.go.jp/iinkai/hyouka/bunkakai/15h/37/1/4-1.pdf , Japanese )
2. Original Project Description ( http://www.nedo.go.jp/iinkai/hyouka/bunkakai/15h/37/1/4-2.pdf , Japanese )
3. Project Overview ( http://www.nedo.go.jp/iinkai/hyouka/bunkakai/15h/37/1/4-3.pdf , Japanese )

Webpage of 1st “Genome Informatics Technology Development” (Post-Project Evaluation) Subcommittee ( http://www.nedo.go.jp/iinkai/hyouka/bunkakai/15h/37/1/index.html , Japanese )

Other Literatures Number of Related Papers Published: 129
・“Medical Technology Built by Precision Engineering: Genetic Analysis System” J. Japan Society for Precision Engineering. 69, 5.
・”Genome Informatics Technology Development Interim Monitoring Evaluation Report”
・“About Biotechnology Research and Development - About Genome Informatics Technology Development Project.” Kogyo Gijutsu. 39, 5.
・“About Biotechnology Research and Development - Future Development in Biotechnology Research and Development Measures in the Industrial Science Technology Research and Development System - Based on Fiscal Year 1998 Biotechnology-related Budget.” Kogyo Gijutsu. 39, 5.