statistical model for protein expression data analysis and its application to individualized medicine for cancer patients

• Project/Area Number: 19500250
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Statistical science
• Research Institution: Japanese Foundation For Cancer Research
• Principal Investigator: MIYATA Satoshi Japanese Foundation For Cancer Research, ゲノムセンター, 研究員 (60360343)
• Project Period (FY): 2007 – 2008
• Project Status: Completed (Fiscal Year 2008)
• Budget Amount: ¥4,420,000 (Direct Cost: ¥3,400,000、Indirect Cost: ¥1,020,000); Fiscal Year 2008: ¥1,950,000 (Direct Cost: ¥1,500,000、Indirect Cost: ¥450,000); Fiscal Year 2007: ¥2,470,000 (Direct Cost: ¥1,900,000、Indirect Cost: ¥570,000)
• Keywords: プロテオーム情報処理 / 蛋白発現データ / adaptive density estimation / adaptive model selection / adaptive regression spline / adaptive model selection criterion

Research Abstract

質量分析計からの二次元蛋白データは、相関構造を持ったTOF/MSデータの集合であり、蛋白発現プロファイルの関数データの抽出にはinhomogeneously smoothな関数の平滑化が必要である。このため、不連続点あるいは微分不能な点を含む目的関数を、ノイズを含んだデータから推定するのに適したadaptive free-knot splineの理論的研究およびプログラム開発を行った。また、蛋白発現データを微分不能な点を持つ確率分布から得られたものと解釈し、きわめて特異な確率密度関数の推定問題として研究した。さらにこれらを用いた判別問題への応用も検討した
これら不均一な滑らかさを持つ関数データの抽出、確率密度関数の推定、判別問題の解決は、多重節点を持つスプライン関数を用いてモデル化された。スプライン関数のtuning parameterである節点の最適化は、適応型モデル選択基準 (adaptive model selection criterion) を最適化することで行われた。この最適化問題は複雑な非線形問題となるが、遺伝的アルゴリズムを適用することで、大域的な最適解を探索することで解決した
研究の成果は、日本癌学会学術総会、統計関連学会連合大会などの国内学会、および、台北大学で行われた中国統計学会、日本統計学会、韓国統計学会合同のjoint statistical conference of CSA-JSS-KSSでの招待講演で報告した。また主要研究成果は論文発表のため投稿準備中である

Research Products

• [Journal Article] Increased Fat Content and Body Shape Have Little Effect on the Accuracy of Lymph Node Retrieval and Blood Loss in Laparoscopic Distal Gastrectomy for Gastric Cancer (2009)
  • Author(s): Hiki, N., Fukunaga, T., Yamaguchi, T., Ogura, T., Miyata, S., Tokunaga, M., Sano, T.
  • Journal Title: Journal of Gastrointestinal Surgery No.13, Vol.4 Pages: 626-33
  • Peer Reviewed
• [Journal Article] Association of Cytologic Micropapillary Clusters with Lymphatic Spread in Clinical Stage I Lung Adenocarcinomas (2009)
  • Author(s): Satoh, Y., Hoshi, R., Horai, T., Okumura, Nakagawa, K., Ishikawa, Y., Miyata, S
  • Journal Title: Lung Cancer Vol.64, No.3 Pages: 277-281
  • Peer Reviewed
• [Journal Article] Inference on biological mechanisms using an integrated phenotype prediction model (2008)
  • Author(s): Enomoto, Y., Ushijima, M., Miyata, S., Matsuura, M., Ohtaki, M.
  • Journal Title: Hiroshima J Med Sci Vol.57, No.1 Pages: 7-15
  • NAID: 120005323916
  • Peer Reviewed
• [Journal Article] Correlation between morphology and EGFR mutations in lung adenocarcinomas Significance of the micropapillary pattern and the hobnail cell type (2008)
  • Author(s): Ninomiya, H., Hiramatsu, M., Inamura, K., Nomura, K., Okui, M., Miyoshi, T., Okumura, S., Satoh, Y., Nakagawa, K., Nishio, M., Horai, T., Miyata, S., Tsuchiya, E., Fukayama, M., Ishikawa, Y.
  • Journal Title: Lung Cancer ol.63. No.2 Pages: 235-240
  • Peer Reviewed
• [Journal Article] Identification of the molecular mechanisms for dedifferentiation at the invasion front of colorectal cancer by a gene expression analysis (2008)
  • Author(s): Oku, Y., Shimoji, T., Takifuji, K., Hotta, T., Yokoyama, S., Matsuda, K., Higashiguchi, T., Tominaga, T., Nasu, T., Tamura, K., Matsuura, M., Miyata, S., Kato, Y., Yamaue, H., Miki, Y.
  • Journal Title: Clinical Cancer Research No.14, Vol.22 Pages: 7215-7222
  • Peer Reviewed
• [Journal Article] Identification of Sentinel Lymph Node Location Based on Body Surface Landmarks in Early Breast Cancer Patients (2008)
  • Author(s): Ueda, N., Tada, K., Miyata, S., Koizumi, M., Kuroda, Y., and Iwase, T.
  • Journal Title: Epub ahead of print in Breast Cancer
  • NAID: 10025373329
  • Peer Reviewed
• [Journal Article] Incidence of gastric cancer in the remnant stomach after proximal gastrectomy (2008)
  • Author(s): Nunobe, S., Ohyama, S., Miyata, S., Matsuura, M., Hiki, N., Fukunaga, T., Seto, Y., Ushijima, M., and Yamaguchi, T.
  • Journal Title: Hepatogastroenterology No.55, Vol.86-87 Pages: 1855-1858
  • Peer Reviewed
• [Journal Article] Inference on biological mechanisms using an integrated phenotype prediction model (2008)
  • Author(s): Enomoto, Y., Miyata, S., et al.
  • Journal Title: Hiroshima J Med Sci. Vol. 57, No. 1 Pages: 7-15
  • NAID: 120005323916
• [Journal Article] Correlation between morphology and EGFR mutations in lung aden ocarcinomas Significance of the micropapillary pattern and the hobnail cell type (2008)
  • Author(s): Ninomiya, H., Miyata, S., et al.
  • Journal Title: Lung Cancer Vol. 63, No. 2 Pages: 235-240
  • Peer Reviewed
• [Journal Article] Identification of the molecular mechanisms for dedifferentiati on at the invasion front of colorectal cancer by a gene expression analysis (2008)
  • Author(s): Oku, Y., Miyata, S., et al.
  • Journal Title: Clinical Cancer Research No. 14, Vol. 22 Pages: 7215-7222
  • Peer Reviewed
• [Journal Article] Identification of Sentinel Lymph Node Location Based on Body Surface Landmarks in Early Breast Cancer Patients (2008)
  • Author(s): Ueda, N., Miyata, S., et al.
  • Journal Title: Epub ahead of print in Breast Cancer
  • NAID: 10025373329
  • Peer Reviewed
• [Journal Article] Incidence of gastric cancer in the remnant stomach after proximal gastrectomy (2008)
  • Author(s): Nunobe, S., Miyata, S., et al.
  • Journal Title: Hepatogastroenterology No. 55, Vol. 86-87 Pages: 1855-1858
  • Peer Reviewed
• [Journal Article] Increased Fat Content and Body Shape Have Little Effect on the Accuracy of Lymph Node Retrieval and Blood Loss in Laparoscopic Distal Gastrectomy for Gastric Cancer (2008)
  • Author(s): Hiki, N. , Miyata, S., et al.
  • Journal Title: Epub ahead of print in Journal of Gastrointe stinal Surgery Vol. 4, No. 13 Pages: 626-633
  • Peer Reviewed
• [Journal Article] Association of Cytologic Micropapillary Clusters with Lymphatic Spread in Clinical Stage I Lung Adenocarcinomas (2008)
  • Author(s): Satoh, Y., Miyata, S., et al.
  • Journal Title: Lung Cancer Vol. 64, No. 3 Pages: 277-281
  • Peer Reviewed
• [Journal Article] プロテオームデータ解析の現状および統計的諸問題 (2008)
  • Author(s): 牛嶋大, 宮田敏, 松浦正明
  • Journal Title: 統計関連学会連合大会講演報告集 Pages: 155-155
• [Journal Article] Adaptive Model Selection for Nonparametric Density Estimation (2008)
  • Author(s): Satoshi Miyata
  • Journal Title: Proceedings of Statistical Conference, joint session of CSA-JSS-KSS Pages: 63-63
• [Journal Article] Trib1 and Evi1 cooperate with Hoxa and Meis1 in myeloid leukemogenesis (2007)
  • Author(s): Jin, G., Yamazaki, Y., Takuwa, M., Takahara, T., Kaneko, K., Kuwata, T., Miyata, S. and Nakamura, T
  • Journal Title: Blood Vol.109, No.9 Pages: 3998-4005
  • Peer Reviewed
• [Journal Article] Gene expression analysis of primary lesion of supraclavicular lymph node metastasis-positive breast cancer (2007)
  • Author(s): Oishi, Y., Nagasaki, K., Miyata, S., Matsuura, M., Nishimura, S., Iwase, T., Kasumi, F., Futoshi Akiyama, F., Sakamoto, G., Iwai, T., and Miki, Y
  • Journal Title: ournal of Human Genetics Vol.52, No.3 Pages: 271-279
  • Peer Reviewed
• [Journal Article] Identifying haplotype block structure by using ancestor-derived model and MDL principle (2007)
  • Author(s): Fujisawa, H., Isomura, M., Eguchi, S., Ushijima, M., Miyata, S., Miki, Y., and Matsuura, M
  • Journal Title: Journal of Human Genetics Vol.52, No.9 Pages: 738-746
  • Peer Reviewed
• [Journal Article] Common peak approach by semi-supervised learning using mass spectrometry datasets for predicting effects on anticancer drugs on breast cancer (2007)
  • Author(s): Ushijima, M., Miyata, S., Eguchi, S., Kawakita, M., Yoshimoto, M., Iwase, T., Akiyama, F., Sakamoto, G., Nagasaki, K., Miki, Y., Noda, T., Hoshikawa, Y. and Matsuura, M.
  • Journal Title: Cancer Informatics Vol.3 Pages: 285-293
  • Peer Reviewed
• [Journal Article] 適応型モデル選択基準に基づく確率密度推定 (2007)
  • Author(s): 宮田 敏
  • Journal Title: 2007年度統計関連学会連合大会講演報告集 Pages: 246-246
• [Journal Article] 質量分析計データを用いた判別解析とバイオマーカー探索 (2007)
  • Author(s): 牛嶋 大、宮田 敏、松浦 正明
  • Journal Title: 2007年度統計関連学会連合大会講演報告集 Pages: 72-72
• [Journal Article] 適応型モデル選択基準に基づく回帰分析、判別分析および密度推定 (2007)
  • Author(s): 宮田 敏
  • Journal Title: 科学研究費研究集会「統計的モデリングの方法と理論」講演報告集 Pages: 91-98
• [Presentation] Adaptive Model Selection for Nonparametric Density Estimation (2008)
  • Author(s): Miyata, S.
  • Organizer: Joint Session of CSA-JSS-KSS
  • Place of Presentation: Taipei University
  • Year and Date: 2008-12-19
• [Presentation] コネクティヴィティマップを用いた潜在的に有効な抗がん剤の遺伝子発現印章に基づく識別 (2008)
  • Author(s): 宮田敏、牛嶋大、松浦正明
  • Organizer: 第67回日本癌学会総会
  • Place of Presentation: 名古屋国際会議場
  • Year and Date: 2008-10-29
• [Presentation] プロテオームデータ解析の現状および統計的諸問題 (2008)
  • Author(s): 牛嶋大、宮田敏、松浦正明
  • Organizer: 統計関連学会連合大会
  • Place of Presentation: 慶應義塾大学
  • Year and Date: 2008-09-09
• [Presentation] Genome-wide survey of genetic polymorphisms associated with cytotoxicity of paclitaxel using HapMap cell lines derived from Japanese population (2008)
  • Author(s): Isomura, M., Miyata, S., et al.
  • Organizer: Second JCA-AACR Special Joint Conference. The Latest Advances in Breast Cancer Research
  • Place of Presentation: Awaji Yumebutai International Conference Center
  • Year and Date: 2008-06-14
• [Presentation] Genome-wide survey of genetic polymorphisms associated with cytotoxicity of paclitaxel using HapMap cell lines derived from Japanese population (2008)
  • Author(s): Isomura, M., Matsuura, M., Nagasaki, K., Ushijima, M., Miyata, S., Noda, T., Miki, Y.
  • Organizer: Second JCA-AACR Special Joint Conference. The Latest Advances in Breast Cancer Research
• [Presentation] Adaptive Model Selection for Nonparametric Density Estimation (2008)
  • Author(s): Satoshi Miyata
  • Organizer: Joint Session of Chinese Statistical Association (CSA), Japanese Statistical Society (JSS) and Korean Statistical Society (KSS)
• [Presentation] プロテオームデータ解析の現状および統計的諸問題 (2008)
  • Author(s): 牛嶋 大、宮田 敏、松浦 正明
  • Organizer: 2008年度統計関連学会連合大会
• [Presentation] コネクティヴィティマップを用いた潜在的に有効な抗がん剤の遺伝子発現印章に基づく識別 (2008)
  • Author(s): 宮田 敏、牛嶋 大、松浦正明
  • Organizer: 第67回日本癌学会総会
• [Presentation] Adaptive Model Selection for Regression,Classification and Density Estimation (2007)
  • Author(s): 宮田 敏
  • Organizer: 一橋大学科学研究費シンポジウム「統計的モデリングの方法と理論」
  • Place of Presentation: 一橋大学
  • Year and Date: 2007-11-27
• [Presentation] 適応型モデル選択基準に基づく確率密度推定 (2007)
  • Author(s): 宮田 敏
  • Organizer: 2007年度統計関連学会連合大会
  • Place of Presentation: 神戸大学
  • Year and Date: 2007-09-08
• [Presentation] 質量分析計データを用いた判別解析とバイオマーカー探索 (2007)
  • Author(s): 宮田 敏
  • Organizer: 2007年度統計関連学会連合大会
  • Place of Presentation: 神戸大学
  • Year and Date: 2007-09-07
• [Presentation] Adaptive model selection for regression,classification and density estimation (2007)
  • Author(s): 宮田 敏
  • Organizer: 京都大学経済研究所計量経済学セミナー
  • Place of Presentation: 京都大学
  • Year and Date: 2007-06-20
• [Presentation] Adaptive model selection for regression, classification and density estimation (2007)
  • Author(s): 宮田 敏
  • Organizer: 京都大学経済研究所計量経済学セミナー
• [Presentation] 質量分析計データを用いた判別解析とバイオマーカー探索 (2007)
  • Author(s): 牛嶋大*、宮田敏、松浦正明
  • Organizer: 2007年度統計関連学会連合大会
• [Presentation] 適応型モデル選択基準に基づく確率密度推定 (2007)
  • Author(s): 宮田敏*
  • Organizer: 2007年度統計関連学会連合大会
• [Presentation] Gene expression profiles related with dedifferentiation at the invasion front of colorectal cancer (2007)
  • Author(s): Yoshimasa Oku, Yakashi Shimoji, Masaaki Matsuura, Satoshi Miyata, Katsunari Takifuji, Tsukasa Hotta, Yo Katou, Tetsuo Noda, Yoshio Miki
  • Organizer: 第66回日本癌学会総会
• [Presentation] The System for prediction of phenotype and inference of their regulations mechanism using multivariate analysis (2007)
  • Author(s): Yumi Enomoto, Masaru Ushijima, Satoshi Miyata, Masaaki Matsuura
  • Organizer: 第66回日本癌学会総会
• [Presentation] Adaptive Model Selection for Regression, Classification and Density Estimation (2007)
  • Author(s): Satoshi Miyata
  • Organizer: 一橋大学科学研究費シンポジウム「統計的モデリングの方法と理論」
• [Presentation] 適応型モデル選択基準に基づく回帰分析、判別分析および密度推定 (2007)
  • Author(s): 宮田 敏
  • Organizer: 名古屋統計セミナー