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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
摘要： 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.
摘要翻译： 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
CPC分类号： G06K9/6218 , G06F19/20 , G06F19/24 , G06F19/26 , G06K2209/07
摘要： 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.
摘要翻译： 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：US06453243B1
公开(公告)日：2002-09-17
申请号：US09884833
申请日：2001-06-18
IPC分类号： C12Q168
摘要： 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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公开(公告)号：US07315785B1
公开(公告)日：2008-01-01
申请号：US09890929
申请日：2000-11-17
IPC分类号： G06F19/00
CPC分类号： G06F19/26 , G06F19/24 , G06K9/6219 , G06K9/6254
摘要： 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.
摘要翻译： 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
摘要： 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：US07127354B1
公开(公告)日：2006-10-24
申请号：US10129251
申请日：2000-09-19
申请人： Yasuyuki Nozaki , Ryo Nakashige , Takuro Tamura
发明人： Yasuyuki Nozaki , Ryo Nakashige , Takuro Tamura
IPC分类号： G01N33/48
摘要： 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.
摘要翻译： 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：US07035738B2
公开(公告)日：2006-04-25
申请号：US10141099
申请日：2002-05-07
CPC分类号： G06F19/20 , C12Q1/6811 , G06F19/22
摘要： 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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8.发明申请System and computer software program for visibly processing an observed information's relationship with knowledge accumulations 有权系统和计算机软件程序，可视化处理观察信息与知识积累的关系公开(公告)号：US20050203889A1
公开(公告)日：2005-09-15
申请号：US11039176
申请日：2005-01-20
申请人： Kousaku Okubo , Takuro Tamura
发明人： Kousaku Okubo , Takuro Tamura
IPC分类号： G06F17/30
CPC分类号： G06F17/30716 , G06F17/2735
摘要： A system for visibly processing observed information may include a configuration for systematizing information; a knowledge accumulation housing unit for storing knowledge accumulations from knowledge information belonging to each such configuration; an observed information receiving unit for receiving, from a user, information observed by the user; a fixed quantity processing unit for assigning a fixed quantity to a relationship between the observed information and the knowledge information belonging to each configuration for the knowledge accumulations; and a fixed quantity value display processing unit for displaying a numerical value of the fixed quantity, in accordance with the fixed quantity processing unit, together with its relationship with each configuration of the knowledge accumulations.
摘要翻译： 用于可视地处理观察信息的系统可以包括用于使信息系统化的配置; 知识积累住房单元，用于从属于每个这样的配置的知识信息中存储知识积累; 观察信息接收单元，用于从用户接收用户观察到的信息; 固定数量处理单元，用于将固定数量分配给观察信息与属于知识积累的每个配置的知识信息之间的关系; 以及固定量值显示处理单元，用于根据固定量处理单元与其与知识积累的每个配置的关系显示固定量的数值。
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9.发明授权Microarray, method for producing the same, and method for correcting inter-pin spotting amount error of the same 失效微阵列及其制造方法，以及用于校正针脚间点位量误差的方法公开(公告)号：US06733968B2
公开(公告)日：2004-05-11
申请号：US09797918
申请日：2001-03-01
申请人： Tomoyuki Yamamoto , Takuro Tamura
发明人： Tomoyuki Yamamoto , Takuro Tamura
IPC分类号： C12Q168
CPC分类号： B01L3/0244 , B01J19/0046 , B01J2219/00387 , B01J2219/00527 , B01J2219/00585 , B01J2219/0059 , B01J2219/00596 , B01J2219/00605 , B01J2219/00621 , B01J2219/00659 , B01J2219/00695 , B01J2219/00698 , B01J2219/00722 , B01J2219/00725 , C40B40/06 , C40B40/10 , C40B60/14 , G01N35/1067 , G01N2035/1037 , G01N2035/1069
摘要： The present invention has an objective of obtaining more accurate data of microarray experiments by correcting an inter-pin spotting amount error caused upon microarray production using a plurality of pins. Upon microarray production, samples are immobilized on a microarray support using all pins as controls for correcting the inter-pin spotting amount errors. After the microarray experiments, luminescent intensities of the samples used as control spots for correcting the inter-pin spotting amount errors are measured and used to obtain correction parameters for the inter-pin spotting amount errors of respective pins. These parameters are used to correct luminescent intensities of other samples.
摘要翻译： 本发明的目的是通过使用多个引脚校正由微阵列产生引起的引脚间点位量误差来获得更准确的微阵列实验数据。 在制备微阵列时，将样品固定在微阵列支架上，使用所有引脚作为校正针间点位量误差的对照。 在微阵列实验之后，测量用作校正针间点位量误差的控制点的样品的发光强度，并用于获得各针的针间点位量误差的校正参数。 这些参数用于校正其他样品的发光强度。
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10.发明申请公开(公告)号：US20090240560A1
公开(公告)日：2009-09-24
申请号：US12066978
申请日：2006-07-12
申请人： Takuro Tamura
发明人： Takuro Tamura
CPC分类号： G06F16/9535 , G06F16/93
摘要： The present invention is intended for all documents and specifically provides matters-of-interest to users and characteristic information of those matters-of-interest in correspondence to identifiers within the documents and allows related services to be utilized through these documents. An information display system 1 having an input device 11, a display device 10, a memory device 7, an information display software 15 that reads document data, and a CPU 5, wherein the memory device 7 comprises a usable information storage unit 17 that describes multiple matters-of-interest, identifiers which identify one or more matters-of-interest from among the multiple matters-of-interest, characteristic information of each matter-of-interest, and related information of each matter-of-interest, with the association with the identification information of the matters-of-interest; and a program storage unit 14 that stores computer software executed by a CPU 5; the system comprises functions for receiving from the input unit the selection of an identifier type to be extracted from document data by a system software 16, specifying an identifier pertaining to the selection in the document data read by the information display software 15, requesting the usable information storage unit 17 or the information delivery server system 3 for the characteristic information of a matter-of-interest based on the specified identifier, acquiring the characteristic information of the matter-of-interest based on the specified identifier from the usable information storage unit 17 or the information delivery server system 3, displaying the acquired characteristic information in a display device by embedding the information in the vicinity of the location of the identifier, and utilizing related information of the matter-of-interest via the identifier and characteristic information.
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