Hitachi Software Engineering Company, Ltd.

Bits Kabushikigaisha

Takuro Tamura

Yasuyuki Nozaki

Ryo Nakashige

Tsunehiko Watanabe

Toshimasa Watanabe

Kenji Yamamoto

Noriyuki Yamamoto

Tomoyuki Yamamoto

Katsuya Mizuno

Shigeru Yatsuzuka

Jyunji Yoshii

Isamu Muto

Iwao Yamashita

Toshiaki Ito

Junji Yoshii

Toshiko Matsumoto

Nobuaki Suzuki

Kousaku Okubo

Shingo Ueno

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.

System and computer software program for visibly processing an observed information's relationship with knowledge accumulations

Provided is a means capable of high-speed analysis of a large-scale correlation among sequences of biopolymers and reutilization of any analyzed profile. A large-scale profile databaseis provided with which the correlation among sequences of biopolymers can be analyzed at a high speed, and any profile can be extracted from the profile database.

Profile database and method for preparing profile

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.

Method and system for displaying dendrogram

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.

Methods for extracting similar expression patterns and related biopolymers

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.

Method for correcting inter-pin spotting amount error for a microarray

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.

Method of displaying gene data, and recording medium

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.

Probe designing apparatus and probe designing method

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.

Method and apparatus for displaying gene expression patterns

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.

Method for displaying gene experiment data

In a method for verifying the accuracy of hybridization experiments in which a plurality of probe biopolymers are hybridized to sample biopolymers, information concerning the hybridization level for each of the probe biopolymers obtained from the hybridization experiment is displayed together with similarity scores representing the similarities between base sequences of the respective probe biopolymers.

Method for displaying results of hybridization experiment

The present invention aims at easy and efficient selection of bands present on a lane. A regionis set on a display of a lanehaving a plurality of bandstobased on an input cursorof a pointing unit. The bandstowithin the regionare displayed to be in a selection candidate state. The size of the regionmay be altered by an input of a predetermined key of a keyboard. Along with the size alteration of the regionbands to be displayed in the selection candidate state also change. By selecting with the mouse button, a band of interest is accurately selected from the bands in the selection candidate state.

Device and method for selecting electrophoresis band

A method for indexing and coding element information of at least one biological element provided on a microarray chip thereby identifying the microarray chip. Some of the element spots arranged on the microarray chip are used as index spots to be selectively provided with at a detective colorant. By doing so, the microarray chip is specified, and the element information as well as experimental information of the chip is automatically managed.

Microarray chip and method for indexing the same

A method of comparing dendrograms created by different references or algorithms displays individual dendrograms () on a screen in an overlapped yet distinguishable manner. The overlapped portions of the dendrograms are displaced vertically or horizontally from one another and indicated by different colors for individual dendrograms. A specified branch and elements hanging therefrom can be highlighted when displayed, such that differences in the manner in which individual elements of the overlapped dendrograms are clustered can be easily recognized.

Dendrogram displaying method

Microarray, method for producing the same, and method for correcting inter-pin spotting amount error of the same

A method for displaying microarray information by which unknown but useful information is extracted from a mass amount of sample information obtained with microarrays. Luminescent intensity information of sample spots obtained with the microarrays is standardized for each microarray and displayed as a graph as a difference from the standardized luminescent intensity of a sample spot of interest. Accordingly, information can be compared without being influenced by a difference of experiment status between the microarrays or a difference of physical properties between the samples. A three-dimensional graph is displayed by sorting the set of samples and the set of microarrays to which the sample spots belong, under predetermined conditions, and assigning the set of sorted samples and the set of sorted microarrays to X-axis and Y-axis, and the accumulated luminescence intensity to Z-axis.

Growing community of inventors

Kanagawa, Japan

Takuro Tamura