2004 Fiscal Year Final Research Report Summary
Discovery of regularities in genome sequence information
| Project/Area Number |
15013209
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| Research Category |
Grant-in-Aid for Scientific Research on Priority Areas
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| Allocation Type | Single-year Grants |
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| Review Section |
Biological Sciences
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| Research Institution | The University of Tokyo |
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Principal Investigator |
NAKAI Kenta U.Tokyo, Institute of Medical Science, Professor, 医科学研究所, 教授 (60217643)
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| Co-Investigator(Kenkyū-buntansha) |
BANNAI Hideo The University of Tokyo, Institute of Medical Science, Research Associate, 医科学研究所, 助手 (20323644)
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| Project Period (FY) |
2003 – 2004
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| Keywords | genome sequence analysis / database / transcription factor / prediction of regulons / transcriptional start site / CpG island / subcellular localization signal / lone intron |
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| Research Abstract |
For five years, we have attempted to clarify various kinds of regularities hidden in either DNA, RNA, or amino acid sequence. In the first three years, this project belonged to the "genome information science" area while it belonged to "genome biology" in the last two years. At that second term, we also explored possibilities to collaborate with wet biologists. Two main outcomes of the project are as follows:
1. Comprehensive analyses of the transcriptional regulatory system in Bacillus subtilis
We have constructed, maintained, and updated DBTBS: database on transcription factors and promoters of B. subtilis, which is one of the most well characterized bacteria. Moreover, we have conducted a number of predictive studies based on the data in DBTBS, including prediction of regulons based on the genome comparison of related bacteria, prediction of sigma factor-dependency for each gene using microarray data, comparative analysis of the results of terminator prediction, and prediction of transcription factor-binding sites using Bayesean statistics.
2. Studies of transcriptional start sites (TSSs) and their upstream regions of human and mouse genes
Collaborating with Prof Sumio Sugano's group, we have updated the DBTSS database, which is a collection of TSSs determined by the sequences of cDNAs having the intact cap structure. Using DBTSS, a series of studies were carried out For example, we discovered that the peak of the distribution of CpG islands corresponds to the TSS of each gene statistically and that the existence of a CpG island near the TSS of a gene highly correlates with the tissue specificity of its expression. In addition, we performed a systematic prediction of so-called TOP (terminal oligo-pyrimidine-rich) genes in the human as well as mouse genomes.
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Research Products
(63 results)
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[Journal Article] Cancer gene expression database (CGED) : a database for gene expression profiling with accompanying clinical information of human cancer tissues2005
Author(s)
Kato, K., Yamashita, R., Matoba, R., Monden, M., Noguchi, S., Takagi, T., Nakai, K.
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Journal Title
Nucl. Acids Res. 33
Pages: D533-D536
Description
「研究成果報告書概要(和文)」より
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[Journal Article] Parameter landscape analysis for common motif discovery programs, in Eskin,E. ＆ Workman, C. (eds.) Regulatory Genomics, RECOMB 2004 International Workshop, RRG 2004, San Diego, CA, USA, March 26-27, 2004, Revised Selected Papers.2005
Author(s)
Poluliakh, N., Konno, M., Horton, P., Nakai, K.
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Journal Title
Lecture Notes in Computer Science 3318 Springer
Pages: 79-87
Description
「研究成果報告書概要(和文)」より
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[Journal Article] Bayesian joint prediction of associated transcription factors in Bacillus subtilis, Pacific Symposium on Biocomputing 2005 (Altman et al ed.)2005
Author(s)
Makita, Y., De Hoon, M.J.L., Ogasawara, N., Miyano, S., Nakai, K.
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Journal Title
World Scientific
Pages: 507-518
Description
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[Journal Article] Predicting gene regulation by sigma factors in Bacilllus subtilis from genome-wide data2004
Author(s)
De Hoon, M.J.L., Makita, Y., Imoto, S., Kobayashi, K., Ogasawara, N., Nakai, K., Miyano, S.
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Journal Title
Bioinformatics 20 (Supp. 1)
Pages: I101-I108
Description
「研究成果報告書概要(和文)」より
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[Journal Article] Large-scale collection and characterization of promoters of human and mouse genes2004
Author(s)
Suzuki, Y., Yamashita.R., Shirota, M., Sakakibara, Y., Chiba, J., Mizushima-Sugano, J., Kel, A.E., Arakawa, T., Caminci, P., Kawai, J., Hayashizaki, Y., Takagi, T., Nakai, K., Sugano, S.
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Journal Title
In silico Biol. 4
Pages: 0036
Description
「研究成果報告書概要(和文)」より
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[Journal Article] Finding optimal pairs of patterns2004
Author(s)
Bannai, H., Hyyro, H., Shinohara, A., Takeda, M., Nakai, K., Miyano, S.
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Journal Title
Lecture Notes in Comp. Sci. (WABI 2004) 3240
Pages: 450-462
Description
「研究成果報告書概要(和文)」より
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[Journal Article] Finding optimal pairs of cooperative and competing patterns with bounded distance2004
Author(s)
Inenaga, S., Bannai, H., Hyyro, H., Shinohara, A., Takeda, M., Nakai, K., Miyano, S.
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Journal Title
Lecture Notes in Comp. Sci. (DS 2004) 3245
Pages: 32-46
Description
「研究成果報告書概要(和文)」より
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[Journal Article] An O(N^2) algorithm for discovering optimal boolean pattern pairs2004
Author(s)
Bannai, H., Hyyro, H., Shinohara, A., Takeda.M., Nakai, K., Miyano, S.
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Journal Title
IEEE/ACM Transactions on Computational Biology and Bioinformatics(special section on the Workshop on Algorithms in Bioinformatics) 1(4)
Pages: 159-170
Description
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[Journal Article] PSORT-B : Improving protein subcelular localization prediction for Gram-negative bacteria2003
Author(s)
Gardy, J.L., Spencer, C., Wang, K., Ester, M., Tusnady, G.E., Simon, I., Hua, S., deFays, K., Lambert, C., Nakai, K., Brinkman, F.S.L.
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Journal Title
Nucl. Acids Res. 31(13)
Pages: 3613-3617
Description
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[Journal Article] Learning Conformation Rules. In Proceedings of the 4nd International Conference of Discovery Science (Lecture Notes in Artificial Intelligence, 2226)2001
Author(s)
Maruyama, O., Shoudai, T., Furuichi, E., Kuhara, S., Miyano, S.
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Journal Title
Springer-Verlag
Pages: 243-257
Description
「研究成果報告書概要(和文)」より
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