Bioinformatics strategy for unveiling hidden genome signatures and biodiversity

• Project/Area Number: 16570190
• Research Category: Grant-in-Aid for Scientific Research (C)
• Allocation Type: Single-year Grants
• Section: 一般
• Research Field: Evolutionary biology
• Research Institution: The Graduate University for Advanced Studies (Sokendai), Hayama Center for Advanced Research
• Principal Investigator: IKEMURA Toshimichi The Graduate University for Advanced Studies, Hayama Center for Advanced Research, Proffesor, 葉山高等研究センター, 教授 (50025475)
• Co-Investigator(Kenkyū-buntansha): HORATA Shinichi The Graduate University for Advanced Studies, Hayama Center for Advanced Research, Research Associate, 上級研究員 (70377125) ; ABE Takashi National Institute of Genetics, DDBJ, Assistant Proffesor, 生命情報DDBJセンター, 助手 (30390628) ; FUKAGAWA Tasuo National Institute of Genetics, Molecular Genetics, Associate Proffesor, 分子遺伝研究所, 助教授 (60321600)
• Project Period (FY): 2004 – 2005
• Project Status: Completed (Fiscal Year 2005)
• Budget Amount: ¥3,600,000 (Direct Cost: ¥3,600,000); Fiscal Year 2005: ¥1,000,000 (Direct Cost: ¥1,000,000); Fiscal Year 2004: ¥2,600,000 (Direct Cost: ¥2,600,000)
• Keywords: Self-Organizing Map / SOM / genome signature / phylogenetic prediction / oligonucleotide frequency / the Earth Simulator / transcription factor / uncultured microorganisms / phylogenetic classification / oligonucleotide frequencies / オリゴヌクレオチド頻度 / 自己組織化マップ / 環境微生物 / 系統推定 / 連続塩基頻度 / ゲノム配列

Research Abstract

Novel tools are needed for comprehensive comparisons of interspecies characteristics of massive amounts of genomic sequences currently available. An unsupervised neural network algorithm, Self-Organizing Map (SOM), is an effective tool for clustering and visualizing high-dimensional complex data on a single map. We modified the conventional SOM, on the basis of batch-learning SOM, for genome informatics making the learning process and resulting map independent of the order of data input. We generated the SOMs for tri-and tetranucleotide frequencies in 10-and 100-kb sequence fragments from 38 eukaryotes for which almost complete genome sequences are available. SOM recognized species-specific characteristics (key combinations of oligonucleotide frequencies) in the genomic sequences, permitting species-specific classification of the sequences without any information regarding the species. We also generated the SOM for tetranucleotide frequencies in 1-kb sequence fragments from the human g enome and found sequences for four functional categories (5' and 3' UTRs, CDSs and introns) were classified primarily according to the categories. Because the classification and visualization power is very high, SOM is an efficient and powerful tool for extracting a wide range of genome information.
SOM that was constructed with oligonucleotide frequencies in 10-kb sequences from human genome sequences identified oligonucleotides with frequencies characteristically biased from random occurrence level, and 10-kb sequences rich in these biased oligonucleotides were self-organized on the map. Because these oligonucleotides often corresponded to functional signal sequences (e.g. binding sites for transcription factors) or their constituent elements, we categorized occurrence patterns and frequencies of such pentanucleotides in the human genome that are thought to regulate transcription. SOM analysis is dependent only on oligonucleotide frequencies and thus applicable even for the sequenced genomes with little additional experimental data. In order to know TSS, experimental data were required, but to know start sites of protein-coding sequences, such data were not required in most cases. When known signal sequences of various species with enough experimental data are characterized systematically, we can develop an in silico method of signal sequence prediction for a wide range of species. Recently, we have developed a novel bioinformatics tool for phylogenetic classification of genomic sequence fragments derived from uncultured microorganism mixtures in environmental and clinical samples

Research Products

• [Journal Article] A large-scale Self-Organizing Map (SOM) unveils sequence characteristics of a wide range of eukaryote genomes. (2006)
  • Author(s): Abe, T., Sugawara, H., Kinouchi, M., Kanaya, S., Ikemura, T.
  • Journal Title: Gene 365 Pages: 27-34
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Bisulfite sequencing and dinucleotide content analysis of 15 imprinted mouse differentially methylated regions (DMRs) : paternally methylated DMRs contain less CpGs than maternally methylated DMRs (2006)
  • Author(s): Kobayashi, H., Suda, C., Abe, T., Kohara, Y., Ikemura, T., Sasaki, H.
  • Journal Title: Cytogenet Genome Res. 113 Pages: 130-137
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] A large-scale Self-Organizing Map(SOM) unveils sequence characteristics of a wide range of eukaryote genomes. (2006)
  • Author(s): Abe, T., Sugawara, H., Kinouchi, M., kanaya, S., Ikemura, T.
  • Journal Title: Gene 365 Pages: 27-34
• [Journal Article] Novel phylogenetic studies of genomic sequence fragments derived from unchltured micobe mixtures in environmental and clinical samples. (2005)
  • Author(s): Abe, T., Sugawara, H., Kinouchi, M., Kanaya, S., Ikemura, T.
  • Journal Title: DNA Research 12 Pages: 281-290
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. (2005)
  • Author(s): Uchiyama, T., Abe, T., Ikemura, T, Watanabe, K.
  • Journal Title: Nature Biotechnology 23 Pages: 88-93
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] A novel bioinformatics strategy for phylogenetic study of genomic sequence fragments : Self-Organizing Map (SOM) of oligonucleotide frequencies, (2005)
  • Author(s): Abe, T., Ikemura, T., Kanaya, S., Kinouchi, M., Sugawara, H.
  • Journal Title: Proceedings of Workshop 2005 Self-Organizing Maps 2005 Pages: 669-676
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Torus Self-Organizing Map for Bioinformatics (2005)
  • Author(s): Horata, S., Ikemura, T., Yukawa
  • Journal Title: Proceedings of Workshop 2005 on Self-Organizing Maps 2005 Pages: 235-242
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Direct cloning of genes encoding novel xylanases from humangut (2005)
  • Author(s): Hayashi, H., Abe, T., Sakamoto, M., Ohara, H., Ikemura, T., Sakka, K., Benno, Y.
  • Journal Title: Canadian Journal of Microbiology 51 Pages: 251-259
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] GeneLook : a novel ab initio gene identification system suitable for automated annotation of prokaryotic sequences (2005)
  • Author(s): Nishi, T., Ikemura, T., Kanaya, S.
  • Journal Title: Gene 346 Pages: 115-125
  • Description: 「研究成果報告書概要(和文)」より
• [Journal Article] Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples (2005)
  • Author(s): Abe, T., Sugawara, H., Kinouchi, M., Kanaya, S., Ikemura, T.
  • Journal Title: DNA Research 12 Pages: 281-290
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A large-scale Self-Organizing Map (SOM) constructed with the Earth Simulator unveils sequence characteristics of a wide range of eukaryotic genomes (2005)
  • Author(s): Abe, T., Sugawara, H., Kinouchi, M., Kanaya, S., Matsuura, Y., Tokutaka, H., Ikemura, T.
  • Journal Title: Proceedings of Workshop 2005 on Self-Organizing Maps Pages: 187-194
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes (2005)
  • Author(s): Uchiyama, T., Abe, T., Ikemura, T., Watanabe, K.
  • Journal Title: Nature Biotechnology 23 Pages: 88-93
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Direct cloning of genes encoding novel xylanases from human gut (2005)
  • Author(s): Hayashi, H., Abe, T., Sakamoto, M., Ohara, H., Ikemura, T., Sakka, K., Benno, Y.
  • Journal Title: Canadian Journal of Microbiology 51 Pages: 251-259
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] A novel bioinformatics strategy for phylogenetic study of genomic sequence fragments : Self-Organizing Map (SOM) of oligonucleotide frequencies (2005)
  • Author(s): Abe, T., Ikemura, T., Kanaya, S., Kinouchi, M., Sugawara, H.
  • Journal Title: Proceedings of Workshop 2005 on Self-Organizing Maps Pages: 669-676
  • Description: 「研究成果報告書概要(欧文)」より
• [Journal Article] Novel phylogenetic studies of genomic sequence fragments derived from uncultured microbe mixtures in environmental and clinical samples. (2005)
  • Author(s): Abe, T., Sugawara, H., Kinouchi, M., Kanaya, S., Ikemura, T.
  • Journal Title: DNA Research 12 Pages: 281-290
• [Journal Article] Substrate-induced gene-expression screening of environmental metagenome libraries for isolation of catabolic genes. (2005)
  • Author(s): Uchiyama, T., Abe, T., Ikemura, T., Watanabe, K.
  • Journal Title: Nature Biotechnology 23 Pages: 88-93
• [Journal Article] A novel bioinformatics strategy for phylogenetic study of genomic sequence fragments : Self-Organizing Map (SOM) of oligonucleotide frequencies, (2005)
  • Author(s): Abe, T.Ikemura, T., Kanaya, S., Kinouchi, M., Sugawara, H.
  • Journal Title: Proceedings of Workshop 2005 on Self-Organizing Maps, 2005 Pages: 669-676
• [Journal Article] Torus Self-Organizing Map for Bioinformatics, (2005)
  • Author(s): Horata, S., Ikemura, T., Yukawa
  • Journal Title: Proceedings of Workshop 2005 on Self-Organizing maps 2005 Pages: 235-242
• [Journal Article] Direct cloning of genes encoding novel xylanases from human gut (2005)
  • Author(s): Hayashi, H., Abe, T., Sakamoto M., Ohara, H., Ikemura, T., Sakka, K., Benno, Y.
  • Journal Title: Canadian Journal of Microbiology 57 Pages: 251-259
• [Journal Article] Direct cloning of genes encoding novel xylanases from human gut (2005)
  • Author(s): Hayashi, H., Abe, T., Sakamoto, M., Ohara, H., Ikemura, T., Sakka, K., Benno, Y.
  • Journal Title: Canadian Journal of Microbiology (In press)
• [Journal Article] Genome informatics for unveiling hidden genome signatures (2004)
  • Author(s): Abe, T., Kanaya, S., Kinouchi, M., Ikemura, T.
  • Journal Title: Proceedings of the Institute of Statistical Mathematics 52 Pages: 207-215
• [Journal Article] Novel genome informatics for unveiling hidden signatures in genome sequences : self-organizing map (SOM) of oligonucleotide frequencies (2004)
  • Author(s): Abe, T., Ikemura, T., Kanaya, S., Kinouchi, M., Sugawara, H.
  • Journal Title: Proceedings of Information-Based Induction Sciences Pages: 94-99