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1.发明授权公开(公告)号：US07277798B2
公开(公告)日：2007-10-02
申请号：US09739525
申请日：2000-12-14
Applicant: Tsunehiko Watanabe , Yasuyuki Nozaki , Ryo Nakashige , Takuro Tamura
Inventor： Tsunehiko Watanabe , Yasuyuki Nozaki , Ryo Nakashige , Takuro Tamura
Abstract: The present invention provides methods for extracting similar expression patterns and related biopolymers considering natures that are characteristic of expression data of, for example, genes. A segment of experiment cases which includes an expression of interest is selected as a search range among an expression pattern of a reference gene or the like. By comparing the selected segment of the expression pattern with expression patterns of a group of candidate genes or the like, genes having an expression pattern with at least a partial similarity are searched from the group of candidate genes. A partially taken out curve (a part of an, expression pattern) is transferred to overlap an expression pattern curve of a candidate gene to search expression patterns with a similar pattern shape.
Abstract translation: 本发明提供了考虑到例如基因表达数据的特征的性质来提取类似表达模式和相关生物聚合物的方法。 选择包括感兴趣的表达的实验病例段作为参考基因等的表达模式之间的搜索范围。 通过将所选择的表达模式片段与一组候选基因等的表达模式进行比较，从候选基因组中搜索具有至少部分相似性的表达模式的基因。 转移部分取出的曲线（表达模式的一部分）与候选基因的表达模式曲线重叠以搜索具有相似图案形状的表达模式。
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公开(公告)号：US07031847B1
公开(公告)日：2006-04-18
申请号：US09677042
申请日：2000-09-29
Applicant: Yasuyuki Nozaki , Ryo Nakashige , Tsunehiko Watanabe , Takuro Tamura
Inventor： Yasuyuki Nozaki , Ryo Nakashige , Tsunehiko Watanabe , Takuro Tamura
CPC classification number: G06K9/6218 , G06F19/20 , G06F19/24 , G06F19/26 , G06K2209/07
Abstract: The present invention discloses a method for displaying gene expression patterns of multiple genes that change according to the experiment cases, where a first axis represents the genes and a second axis represents the experiment cases. The method comprises two steps. The first step consists of designating a segment along the second axis in the expression pattern data of the multiple genes. The second step comprises clustering the expression pattern data within the designated segment along the second axis based on a predetermined reference value, repeating clustering within the same cluster in a forward or reverse direction along the second axis while changing the reference value, and displaying the results according to a predetermined display format.
Abstract translation: 本发明公开了一种用于显示根据实验情况而变化的多个基因的基因表达模式的方法，其中第一轴代表基因，第二轴代表实验情况。 该方法包括两个步骤。 第一步包括在多个基因的表达模式数据中沿着第二个轴指定一个片段。 第二步包括基于预定参考值沿着第二轴聚集指定段内的表达模式数据，在改变参考值的同时沿着第二轴沿正向或相反方向重复在同一簇内的聚类，并显示结果 根据预定的显示格式。
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公开(公告)号：US07035738B2
公开(公告)日：2006-04-25
申请号：US10141099
申请日：2002-05-07
Applicant: Toshiko Matsumoto , Ryo Nakashige , Yasuyuki Nozaki , Shingo Ueno , Takuro Tamura
Inventor： Toshiko Matsumoto , Ryo Nakashige , Yasuyuki Nozaki , Shingo Ueno , Takuro Tamura
CPC classification number: G06F19/20 , C12Q1/6811 , G06F19/22
Abstract: Where a DNA chip corresponding to a bacterium that is a subsequently added identification object is produced, temporal and pecuniary cost is reduced, and even where a probe unique to the DNA sequence of an identification object cannot be designed, precision in identifying DNA comprised in a sample is maximized. First, on designing a probe, a plurality of different probes are prepared to one kind of bacterium. Where some probes come to be not available by addition of bacteria that are new identification objects, identification is carried out using the remaining probes. Where a probe unique to an identification target bacterium cannot be designed, a probability of correct identification is increased by using multiple probes. Moreover, in consideration with a possibility that multiple kinds of bacteria simultaneously exist, a combination of probes that maximizes a probability of correct identification is selected.
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公开(公告)号：US07127354B1
公开(公告)日：2006-10-24
申请号：US10129251
申请日：2000-09-19
Applicant: Yasuyuki Nozaki , Ryo Nakashige , Takuro Tamura
Inventor： Yasuyuki Nozaki , Ryo Nakashige , Takuro Tamura
IPC: G01N33/48
Abstract: A method of displaying gene data assists in discovering expression patterns specific to gene functions and inferring the function of a gene of which the function is unknown. A threshold value representing the degree of similarity of expression patterns is established in advance, and genes having the same function and genes with similar expression patterns to them are extracted and displayed. Cluster analysis is performed on the extracted genes by re-selecting the experiment patterns for clustering. Calculations are performed to see how many functions the genes belonging to a subtree have, and the proportion of each function in the subtree is determined. If a proportion exceeds a predetermined threshold value, they are regarded as a cluster (collection of genes with similar functions) and extracted.
Abstract translation: 显示基因数据的方法有助于发现基因功能特异性的表达模式，并推断功能未知的基因的功能。 预先建立表示模式相似程度的阈值，提取并显示具有相同功能的基因和具有相似表达模式的基因。 通过重新选择聚类的实验模式对提取的基因进行聚类分析。 执行计算以查看属于子树的基因有多少功能，并确定子树中每个功能的比例。 如果比例超过预定阈值，则将其视为簇（具有相似功能的基因的集合）并提取。
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公开(公告)号：US06453243B1
公开(公告)日：2002-09-17
申请号：US09884833
申请日：2001-06-18
Applicant: Tsunehiko Watanabe , Yasuyuki Nozaki , Ryo Nakashige , Takuro Tamura
Inventor： Tsunehiko Watanabe , Yasuyuki Nozaki , Ryo Nakashige , Takuro Tamura
IPC: C12Q168
Abstract: A method for displaying results of hybridization experiments using a biochip is provided. In the method, a plurality of control spots spotted in each of a plurality of sections defined on a biochip is measured. The measured data are plotted on a graph for each section, and all of the graphs are simultaneously displayed on a single screen in the same arrangement as that of the sections on the biochip. By simultaneously displaying all of the graphs on a single screen, it is possible to skim the whole biochip to find experimental errors. Also, experimental errors can be quantified with respect to the dispersion of control data on the basis of the linearity of the data points and slope angles defined for each data points on a graph.
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Patent Agency Ranking
公开(公告)号：US07315785B1
公开(公告)日：2008-01-01
申请号：US09890929
申请日：2000-11-17
Applicant: Yasuyuki Nozaki , Tsunehiko Watanabe , Ryo Nakashige , Takuro Tamura
Inventor： Yasuyuki Nozaki , Tsunehiko Watanabe , Ryo Nakashige , Takuro Tamura
IPC: G06F19/00
CPC classification number: G06F19/26 , G06F19/24 , G06K9/6219 , G06K9/6254
Abstract: The present invention represents a global state of branches in a whole dendrogram as well as detail of states of individual subtrees, to aid focusing of groupings and selection of a clustering method. The present invention selects a branch/subtree in a dendrogram displays the subtree on a separate window, replaces the subtree with an icon then restores the icon into the original subtree, and/or searches keywords contained in information of biopolymers in the subtree then highlight the locations of biopolymers containing the keywords in its information.
Abstract translation: 本发明表示整个树状图中的分支的全局状态以及各个子树的状态的细节，以帮助分组的聚焦和聚类方法的选择。 本发明选择树形图中的分支/子树在单独的窗口上显示子树，用图标替换子树，然后将图标恢复到原始子树中，和/或搜索包含在子树中的生物聚合物的信息中的关键字，然后突出显示 在其信息中含有关键词的生物聚合物的位置。
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公开(公告)号：US07010430B2
公开(公告)日：2006-03-07
申请号：US09819179
申请日：2001-03-27
Applicant: Ryo Nakashige , Yasuyuki Nozaki , Takuro Tamura , Tsunehiko Watanabe
Inventor： Ryo Nakashige , Yasuyuki Nozaki , Takuro Tamura , Tsunehiko Watanabe
Abstract: The present invention aims at providing a visual display which is useful in roughly understanding the state of groupings and changes, by comparing expression data of genes from two experiments based on expression data of one sample common to both experiments.In order to compare data of expression levels obtained from different experiments each using two types of samples, three types of expression levels are displayed in three-dimension as mediated by the data of the common sample used in both experiments. Specifically, expression level data for Samples A and B and expression level data for Samples A and C are combined and converted into single three-dimensional data and displayed as points inside a sphere. Alternatively, expression states of each gene to Samples A, B and C are mapped on a sphere with respect to a ratio between Sample A and Sample B and a ratio between Samples A and C, and displayed as distribution on the surface of the sphere. A clustering analysis is performed based on the distributed points inside or on the sphere, to visually understand the expression state of genes for the three types of samples. In addition, the expression level data displayed as points inside or on the sphere are linked as a line or a curve for each gene or for each gene group resulting from the clustering analysis, to visually understand the changes of expression states with time.
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公开(公告)号：US20110106846A1
公开(公告)日：2011-05-05
申请号：US13000393
申请日：2009-06-25
Applicant: Toshiko Matsumoto , Ryo Nakashige , Yasuyuki Nozaki
Inventor： Toshiko Matsumoto , Ryo Nakashige , Yasuyuki Nozaki
IPC: G06F17/30
CPC classification number: G06F17/30115
Abstract: Provided is a file (document) management process for efficiently understanding a summary of files in a folder without checking the contents of the individual subfolders or files. A summary of a plurality of files included in a folder is generated dynamically (each time the folder is accessed by placing a cursor on the folder, for example) and is displayed. For example, a summary of a feature of files included in a folder, which is recognized as being different from the feature of a plurality of files included in a sibling folder through comparison, determined on the basis of a feature or tendency of a file attribute, is described, and a location distribution of query-hit documents in the tiered folder is displayed.
Abstract translation: 提供了一种用于在不检查各个子文件夹或文件的内容的情况下有效地理解文件夹中的文件的摘要的文件（文档）管理过程。 动态地生成包含在文件夹中的多个文件的摘要（每次通过将光标放置在文件夹上进行访问时），并显示。 例如，基于文件属性的特征或倾向来确定包含在文件夹中的文件的特征的摘要，其被识别为不同于通过比较的兄弟文件夹中包括的多个文件的特征 ，并且显示分层文件夹中的查询命中文档的位置分布。
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公开(公告)号：US08661064B2
公开(公告)日：2014-02-25
申请号：US13000393
申请日：2009-06-25
Applicant: Toshiko Matsumoto , Ryo Nakashige , Yasuyuki Nozaki
Inventor： Toshiko Matsumoto , Ryo Nakashige , Yasuyuki Nozaki
CPC classification number: G06F17/30115
Abstract: Provided is a file (document) management process for efficiently understanding a summary of files in a folder without checking the contents of the individual subfolders or files. A summary of a plurality of files included in a folder is generated dynamically (each time the folder is accessed by placing a cursor on the folder, for example) and is displayed. For example, a summary of a feature of files included in a folder, which is recognized as being different from the feature of a plurality of files included in a sibling folder through comparison, determined on the basis of a feature or tendency of a file attribute, is described, and a location distribution of query-hit documents in the tiered folder is displayed.
Abstract translation: 提供了一种用于在不检查各个子文件夹或文件的内容的情况下有效地理解文件夹中的文件的摘要的文件（文档）管理过程。 动态地生成包含在文件夹中的多个文件的摘要（每次通过将光标放置在文件夹上进行访问时），并显示。 例如，基于文件属性的特征或倾向来确定包含在文件夹中的文件的特征的摘要，其被识别为不同于通过比较的兄弟文件夹中包括的多个文件的特征 ，并且显示分层文件夹中的查询命中文档的位置分布。
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公开(公告)号：US07783430B2
公开(公告)日：2010-08-24
申请号：US11705055
申请日：2007-02-12
Applicant: Yu Nakami , Ryo Nakashige , Yasuyuki Nozaki , Toshiko Matsumoto
Inventor： Yu Nakami , Ryo Nakashige , Yasuyuki Nozaki , Toshiko Matsumoto
IPC: G06F7/00
CPC classification number: G06F19/18 , C12Q2600/156
Abstract: A method and a system for evaluating results of differentiating genotype signals and noise signals when a DNA fragment containing a gene to be analyzed is amplified by PCR and detected by electrophoresis are provided.An outlier of genotyping results is detected based on the fact that, when using the same marker, the height ratio of a stutter peak to a true peak and the height ratio of a +A peak to a true peak are reproducible, and that a constant size value is obtained with the use of the same allele of the same marker. In addition, a waveform obtained in past processes with the use of the same marker or the same allele is obtained utilizing a database by focusing on reproducibility. Also, a database is extended so as to obtain improved evaluation ability in a manner such that appropriate waveform data from which an outlier is not obtained is additionally registered in a database.
Abstract translation: 提供了当通过PCR扩增含有待分析基因的DNA片段并通过电泳检测时，鉴别鉴别基因型信号和噪声信号的结果的方法和系统。 基于以下事实来检测基因分型结果的异常值：当使用相同的标记时，口吃峰与真实峰的高度比和+ A峰与真实峰的高度比是可重现的，并且恒定 使用相同标记的相同等位基因获得大小值。 此外，通过关注再现性，利用数据库获得使用相同标记或相同等位基因的过去方法获得的波形。 此外，扩展数据库以便以使得没有获得异常值的适当波形数据另外登记在数据库中的方式获得改进的评估能力。
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