Macroscopic Genome Structure Comparison Based on Gene Locations
| Project/Area Number |
15310134
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| Research Category |
Grant-in-Aid for Scientific Research (B)
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| Allocation Type | Single-year Grants |
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| Section | 一般 |
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| Research Field |
基礎ゲノム科学
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| Research Institution | The University of Tokyo |
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Principal Investigator |
HORIMOTO Katsuhisa The University of Tokyo, Institute of Medical Science, Project Professor, 医科学研究所, 科学技術振興特任教員 (40238803)
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| Co-Investigator(Kenkyū-buntansha) |
FUKUCHI Satoshi Center for Information Biology and DNA Databank, National Institute of Genetics, Assistant, 生命情報DDBJ研究センター, 助手 (70360336)
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| Project Period (FY) |
2003 – 2004
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| Project Status |
Completed (Fiscal Year 2004)
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| Budget Amount *help |
¥15,700,000 (Direct Cost: ¥15,700,000)
Fiscal Year 2004: ¥8,500,000 (Direct Cost: ¥8,500,000)
Fiscal Year 2003: ¥7,200,000 (Direct Cost: ¥7,200,000)
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| Keywords | genome structure comparison / genome duplication / chromosome comparison / gene configuration / orthologous genes / paralogous genes / Directional Statistics / Spatial Statistics / paraloous遺伝子 / ゲノム比較 / 空間統計 / 統計解析 / クロモゾーム構造 |
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| Research Abstract |
In this study, we have established a macroscopic method for comparing the genome structure based on the locations of related genes, and have applied it to pursuit the clarity of the mechanism of dynamical genome structure. Concomitantly, the relationship between the genome structure, the genomic sequences and the gene expressions was also investigated The details of this study are as follows :
1)The method recently developed for comparing the genome structure based on the gene location has been improved in terms of statistical test. Furthermore, a new measure for the genome structure comparison has been designed based on the Directional Statistics.
2)The orthologs in bacterial genomes was classified in terms of gene function, and the sgene configuration for each function was investigated by our method. As a result, the locations of genes related with the metabolism and the information processing were quite different from each other, apart from their evolutionary relationships.
3)The possibility of whole genome duplication in Cyanobacterium Anabena sp. PCC7020 was investigated by comparing the locations of paralogs, and the results strongly suggest the occurrence of whole genome duplication during the bacterial genome evolution.
4)The method for comparing the linear chromosomes has been improved based on the quantification of the related-gene configuration. The analyses revealed the ancestral chromosome pairs in yeast genome, in which the whole genome duplication occurred.
5)The programs for the macroscopic genome comparison have been constructed to be open through the web site.
6)To investigate the genome structure change from the genomic sequences, a method for detecting the repeat sequences has been devised.
7)To investigate the relationship between the genome structure change and the gene expressions, a method for inferring the regulatory network have been improved, and the web site for utilizing the method has been opened.
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Report
(3 results)
Research Products
(43 results)
