Development of a web resource for elucidating glycan function

• Project/Area Number: 20680017
• Research Category: Grant-in-Aid for Young Scientists (A)
• Allocation Type: Single-year Grants
• Research Field: Bioinformatics/Life informatics
• Research Institution: Soka University
• Principal Investigator: KINOSHITA Kiyoko 創価大学, 工学部生命情報工学科, 準教授 (50440235)
• Project Period (FY): 2008 – 2010
• Project Status: Completed (Fiscal Year 2010)
• Budget Amount: ¥25,610,000 (Direct Cost: ¥19,700,000、Indirect Cost: ¥5,910,000); Fiscal Year 2010: ¥7,540,000 (Direct Cost: ¥5,800,000、Indirect Cost: ¥1,740,000); Fiscal Year 2009: ¥7,540,000 (Direct Cost: ¥5,800,000、Indirect Cost: ¥1,740,000); Fiscal Year 2008: ¥10,530,000 (Direct Cost: ¥8,100,000、Indirect Cost: ¥2,430,000)
• Keywords: バイオインフォマティクス / 糖鎖インフォマティクス / ウェブリソース / 機械学習 / 糖鎖 / 糖鎖関連データベース / 解析システム

Research Abstract

This project focused on the development of a web resource to analyze glycans using algorithmic and machine learning tools which glycobiologists could access and utilize easily. During the time of this project, we developed (a) DrawRINGS, a glycan structure drawing and search tool, (b) Glycan Miner, a tool to extract glycan features using machine learning, (c) Glycan Pathway Predictor, a tool to predict N-glycan biosynthesis pathways, (d) Kernel Tool, a tool for classifying different data sets of glycan structures, and (e) Profile PSTMM, a tool of a probabilistic model to extract glycan profiles.

Research Products

• [Journal Article] Extracting Glycan Motifs using a Biochemically-Weighted Kernel (2011)
  • Author(s): Jiang, H., Aoki-Kinoshita, K.F. and Ching, W.
  • Journal Title: Bioinformation Volume: Vol. 7 No. 8 Pages: 405-412
  • URL: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3280441/
  • Peer Reviewed
• [Journal Article] A weighted q-gram method for glycan structure classification (2010)
  • Author(s): Li, L., Ching, W.K., Yamaguchi, T., Aoki-Kinoshita, K.F.
  • Journal Title: BMC Bioinformatics Volume: Vol. 11, Suppl 1, No. S33 Issue: S1
  • DOI: 10.1186/1471-2105-11-s1-s33
  • Peer Reviewed
• [Journal Article] The RINGS resource for glycome informatics analysis and data mining on the Web (2010)
  • Author(s): Akune, Y., Hosoda, M., Kaiya, S., Shinmachi, D., Aoki-Kinoshita, K.F.
  • Journal Title: OMICS Volume: Vol. 14, No. 4 Pages: 2010-2010
  • URL: http://www.ncbi.nlm.nih.gov/pubmed/20726803
  • Peer Reviewed
• [Journal Article] The RINGS resource for glycome informatics analysis and data mining on the web (2010)
  • Author(s): Yukie Akune
  • Journal Title: OMICS Volume: 14 Pages: 475-486
  • Peer Reviewed
• [Presentation] RINGS : a web resource of data mining and analytical tools for glycomics research (2012)
  • Author(s): 木下聖子
  • Organizer: The 15^<th> Annual San Diego Glycobiology Symposium
  • Place of Presentation: サンジエゴ(米国)
  • Year and Date: 2012-03-16
• [Presentation] RINGS: a web resource of data mining and analytical tools for glycomics research (2012)
  • Author(s): Aoki-Kinoshita KF
  • Organizer: The 15th Annual San Diego Glycobiology Symposium
  • Place of Presentation: San Diego, CA, USA
• [Presentation] Methods and applications of glycome informatics (2011)
  • Author(s): 木下聖子
  • Organizer: The 71^<st> Okazaki Conference
  • Place of Presentation: 岡崎市(日本)
  • Year and Date: 2011-10-14
• [Presentation] "Development of a tool for profile analysis of glycan recognition patterns" 4P-0456 (2011)
  • Author(s): Hosoda, M, Aoki-Kinoshita KF
  • Organizer: The Japanese Biochemical Society Annual Meeting
  • Place of Presentation: Kyoto, Japan
  • Year and Date: 2011-09-24
• [Presentation] "RINGS:A web resource for glycome infomatics" 4P-0458 (2011)
  • Author(s): Fujita, A, Mori, T, Aoki-Kinoshita KF
  • Organizer: The Japanese Biochemical Society Annual Meeting
  • Place of Presentation: Kyoto, Japan
  • Year and Date: 2011-09-24
• [Presentation] "Glycan biomarker prediction using Glycan Kernel Tool" 4P-0454 (2011)
  • Author(s): Akune, Y, Aoki-Kinoshita KF
  • Organizer: The Japanese Biochemical Society Annual Meeting
  • Place of Presentation: Kyoto, Japan
  • Year and Date: 2011-09-24
• [Presentation] Mining meaningful glycan structures from CFG resources (2011)
  • Author(s): 木下聖子
  • Organizer: CFG Participating Investigators Meeting
  • Place of Presentation: ワシントンDC(米国)
  • Year and Date: 2011-07-29
• [Presentation] Development of a Multiple Glycan Alignment Tool (2011)
  • Author(s): Hosoda, M, Aoki-Kinoshita KF
  • Organizer: Annual Meeting for the Japanese Society for Bioinformatics
  • Place of Presentation: Kobe, Japan
• [Presentation] Methods and applications of glycome informatics (2011)
  • Author(s): Aoki-Kinoshita KF
  • Organizer: The 71st Okazaki Conference on New Perspectives on Molecular Science of Glycoconjugates
  • Place of Presentation: Okazaki, Japan
• [Presentation] RINGS: a web resource for glycome informatics analysis (2011)
  • Author(s): Fujita A, Mori T, Aoki-Kinoshita KF
  • Organizer: The 71st Okazaki Conference on "New perspectives on molecular science of glycoconjugates"
  • Place of Presentation: Okazaki, Japan
• [Presentation] Mining meaningful glycan structures from CFG resources (2011)
  • Author(s): Aoki-Kinoshita KF
  • Organizer: CFG Participating Investigators Meeting, NIH campus
  • Place of Presentation: Bethesda, MD, USA
• [Presentation] Identifying key glycan components in influenza virus infection using glycan structure mining techniques (2011)
  • Author(s): Aoki-Kinoshita KF, Ichimiya T, Takase-Yoden S, Nishihara S
  • Organizer: 2nd Beilstein Symposium on Glyco-Bioinformatics
  • Place of Presentation: Potsdam, Germany
• [Presentation] "Development of a web resource for glycan structure analysis" P-085 (2011)
  • Author(s): Mori T, Fujita A, Aoki-Kinoshita KF
  • Organizer: 30th Japanese Carbohydrate Symposium
  • Place of Presentation: Nagaoka, Japan
• [Presentation] "Development of a tool for prediction of glycan recognition patterns" P-087 (2011)
  • Author(s): Hosoda M, Aoki-Kinoshita KF
  • Organizer: 30th Japanese Carbohydrate Symposium
  • Place of Presentation: Nagaoka, Japan
• [Presentation] "A tool for glycan biomarker prediction using kernel" P-088 (2011)
  • Author(s): Akune Y, Aoki-Kinoshita KF
  • Organizer: 30th Japanese Carbohydrate Symposium
  • Place of Presentation: Nagaoka, Japan
• [Presentation] "Improved usability of RINGS for glycome informatics research" S01 (2010)
  • Author(s): Mori T, Uchida T, Yasuoka H, Fujita A, Aoki-Kinoshita KF
  • Organizer: 2010 Annual Conference of the Japanese Society for Bioinformatics
  • Place of Presentation: Fukuoka, Japan
• [Presentation] "Development of a new kernel tool for glycan biomarker prediction" P039 (2010)
  • Author(s): Akune Y, Jiang H, Aoki-Kinoshita KF
  • Organizer: 2010 Annual Conference of the Japanese Society for Bioinformatics
  • Place of Presentation: Fukuoka, Japan
• [Presentation] "Multiple Tree Alignment for Glycan Profile Analysis of Glycan Binding Proteins" P023 (2010)
  • Author(s): Hosoda M, Aoki-Kinoshita KF
  • Organizer: 2010 Annual Conference of the Japanese Society for Bioinformatics
  • Place of Presentation: Fukuoka, Japan
• [Presentation] "Development of a New Glycan Score Matrix" P031 (2009)
  • Author(s): Akune Y, Aoki-Kinoshita KF
  • Organizer: 20th International Conference on Genome Informatics
  • Place of Presentation: Yokohama, Japan
• [Presentation] "Improvements to Profile PSTMM for Glycan Recognition Profile Prediction" P101 (2009)
  • Author(s): Kaiya S, Hosoda M, Aoki-Kinoshita KF
  • Organizer: 20th International Conference on Genome Informatics
  • Place of Presentation: Yokohama, Japan
• [Presentation] "A Web Resource for Glycan Function Analysis: RINGS", P-075 (2009)
  • Author(s): Hosoda M, Katoda T, Shinmachi D, Kaiya S, Akune Y, Aoki-Kinoshita KF
  • Organizer: 29th Japanese Carbohydrate Symposium
  • Place of Presentation: Takayama, Japan
• [Presentation] 糖鎖構造解析のためのリソース:RINGS (2009)
  • Author(s): 阿久根幸恵、木下聖子
  • Organizer: 文科省統合データベースプロジェクト「データベースが拓くこれからのライフサイエンス」、第58回FCCAセミナー、日本糖質学会
  • Place of Presentation: 東京、愛知、岐阜
• [Presentation] The RINGS resource for glycome analysis (2008)
  • Author(s): Kiyoko F. Aoki-Kinoshita
  • Organizer: Society for Glycobiology
  • Place of Presentation: 米国テキサス州フォートワース市
  • Year and Date: 2008-11-13
• [Remarks]
  • URL: http://www.rings.t.soka.ac.jp
• [Remarks]
  • URL: http://www.rings.t.soka.ac.jp/
• [Remarks]
  • URL: http://rings.t.soka.ac.jp/