JP2002183153A - Device and method for providing physiological- phenomenon-related gene information and recording medium stored with program for providing the same - Google Patents

Abstract

PROBLEM TO BE SOLVED: To provide related gene information by computing the development frequency of a gene provided by a user according to genome databases wherein specific gene groups are classified. SOLUTION: This physiological-phenomenon-related gene providing device 20 which provides a physiological-phenomenon-related gene including the development frequency of the gene for gene information from the user includes a user data management unit 30 which receives the gene information from the user, a physiological-phenomenon-related genome database having genome databases 51, 52, and 53 which consist of physiological-phenomenon-related gene groups and have the respective physiological-phenomenon-related gene groups in advance, and an arithmetic unit 40 which compares the gene information provided by the user and counts genes included in gene information matching genes belonging to the classified genome databases to compute the development frequency of the genes. Further, the device has an output means which outputs the physiological-phenomenon-related genes including the manifestation frequency of the genes.

Description

DETAILED DESCRIPTION OF THE INVENTION

[0001]

The present invention relates to an apparatus for providing physiological phenomenon-related gene information, and more particularly, to the provision of gene information from a user and the expression frequency of a gene based on a physiological phenomenon-related genome database. TECHNICAL FIELD The present invention relates to an apparatus for providing physiological phenomenon-related gene information, including a method for providing the same, and a recording medium storing a program for providing the apparatus.

[0002]

2. Description of the Related Art Northern blotting and differential hybridization have been conventionally known as techniques for analyzing the base sequence of DNA, which is the main body of a gene. However, since samples are analyzed one by one,
An enormous amount of time and effort was required. In recent years, as a rapid analysis method, a DNA chip, a microarray, or the like, which is a diagnostic tool for examining the presence or absence of a disease-related gene or the like, has attracted attention. A DNA chip is a DNA chip that reacts unknown bases with various base sequences fixed on a substrate.
And thousands or more different genes (DNA fragments) are arranged at high density.
When a sample obtained by treating blood or cells is flowed on a chip, a specific gene and a DNA fragment on the chip are combined, and a gene having the same gene sequence can be determined.

[0003] A sample obtained from a patient's cell or tissue is dropped on a chip for a gene whose function is known, specifically, a gene related to cancer, and the patient is combined with the gene on the gene chip in the sample. It is found to have genes associated with cancer. If the function of a gene is known, the link between a particular gene and the disease will be clear, but otherwise it will not be effective.

[0004] There are a number of genes associated with a disease depending on the type of the disease. In living organisms, genes do not work alone, but exert their functions by interacting. For example, one gene activates another gene, and the activated gene represses another gene.

[0005] Recently, it has been reported that the relationship between a gene and a disease is to be obtained based on the classification of the gene. Specifically, Tavazoi et al. Performed a systematic determination of the gene network architecture, in which they found distinct expression patterns of yeast mRNA, and then identified DNA sequence patterns specific to each expression pattern. (Nature Gen
etics, Vol. 22 281-285, July 1999). Furthermore, the expression probability of the gene within the functional classification is determined, and the grouping of the gene within the same functional classification is reported based on the expression probability.

Further, Scherf et al. Evaluated the gene expression profile of 60 human cancer cell lines using a cDNA microarray and reported a correlation between gene expression and drug activity pattern (Nature Gene, Vol. 24, 236-24
4, March 2000).

[0007] Genetic information not only knows the predisposition to the disease, but will also provide clues for the development of therapeutic drugs in the future. Under such a background, for example, when a certain drug is administered to a mouse or the like, genes that are simultaneously expressed in the mouse body are commonly controlled in the living body, for example, by the same transcription factor. Because it may be expressed, if it is known how a specific gene group is commonly controlled and how it changes, it is possible to predict the function from the movement of that gene group. Become. Such information is becoming increasingly important for new drug development.

[0008]

DISCLOSURE OF THE INVENTION The present invention has been made in view of the above-mentioned problems, and has been made based on the results of experiments on genes obtained by a user using a DNA chip or the like based on the results of experiments on genes related to physiological phenomena. An object of the present invention is to calculate a frequency of expression of a gene provided by a user related to a physiological phenomenon based on a genome database in which groups are classified in advance, and to provide physiological phenomenon-related gene information.

[0009]

According to the first aspect of the present invention,
A physiological phenomenon-related gene information providing device that provides physiological phenomenon-related gene information including a gene expression frequency with respect to gene information from a user, comprising: a user data management unit configured to receive the gene information from a user; A physiological phenomenon-related genomic database comprising a genomic database in which each physiological phenomenon-related gene group is classified in advance, and the gene information provided by a user based on the classified genomic database. And an operation unit having calculation means for counting the number of genes included in the gene information corresponding to the genes belonging to the classified genomic database and calculating the expression frequency of the genes, wherein the user data management unit The data calculated by the arithmetic unit is stored for each user. Means, in which was characterized by providing apparatus for physiological phenomena related genetic information and an output means for outputting a physiological phenomena related gene information including the expression frequency of the gene.

According to a second aspect of the present invention, in the first aspect, the physiological phenomenon-related gene group includes a gene group associated with ischemia in mouse brain and a gene group associated with ischemia in rat liver. A group of genes related to ischemia in rat skin,
And a group of genes related to apoptosis.

According to a third aspect of the present invention, in the first aspect of the invention, the genome database is classified based on base information, classification based on amino acid sequence, and text information for annotation classification. And a classification that includes:

According to a fourth aspect of the present invention, in the first aspect of the present invention, the pre-classified genome database can be selected by a user.

According to a sixth aspect of the present invention, in the first aspect of the present invention, the user data management unit is connected to a tagging engine included in a genome database of each category of the physiological phenomenon-related genome database, and thus a group of physiological phenomenon-related genes. Irrespective of, the user can select a genome database.

According to a sixth aspect of the present invention, in the first aspect of the present invention, the mobile terminal is connected to a user terminal via a communication network.

According to a seventh aspect of the present invention, in the first aspect of the present invention, the user data management unit further includes a charging unit for collecting a fee for the output.

The invention of claim 8 is the invention of claim 1, wherein the physiological phenomenon-related gene information includes a base sequence list of a gene of interest.
The invention according to claim 9 is a method for providing physiological phenomenon-related gene information including the expression frequency of a gene with respect to the gene information from the user, wherein the confirmation is performed by confirming the accession number of the gene information provided by the user. A step of selecting a genomic database in which a group of physiological phenomenon-related genes constituting a physiological phenomenon-related genome database is classified in advance by a user, and selecting a gene included in the genetic information provided by the user and a user A matching step of matching genes belonging to the genomic database, and a counting step of counting the number of genes in which the genes included in the gene information match the genes belonging to the selected genomic database as a result of the matching step. And using the number of the genes according to the following equation:

[0017]

(Equation 5) The method includes a calculating step of calculating a default value of the expression frequency of the gene, and an output step of outputting the calculated default value of the expression frequency of the gene to a user.

According to a ninth aspect of the present invention, in the ninth aspect,
After the calculation step, changing the number of genes belonging to the genome database selected by the user according to the selection of the user, according to the following equation,

[0019]

(Equation 6) The method further includes an optimization step of optimizing a default value of the expression frequency of the gene and calculating an optimal value.

According to an eleventh aspect of the present invention, in the ninth aspect of the present invention, the physiological phenomenon-related gene group includes a gene group associated with ischemia in mouse brain and a gene group associated with ischemia in rat liver. And a group of genes related to rat skin ischemia and a group related to apoptosis.

According to a twelfth aspect, in the ninth aspect, the genome database is classified based on base information, classification based on amino acid sequence, and text information for annotation classification. And a classification that includes:

According to a thirteenth aspect of the present invention, in the ninth aspect of the present invention, the mobile terminal is connected to a user terminal via a communication network.

The invention according to claim 14 is a procedure for confirming an accession number of a gene contained in gene information input by a user, and a procedure for allowing a user to select a pre-classified genome database of a group of physiological phenomenon-related genes. And a step of matching the gene belonging to the selected genome database with the gene contained in the gene information, and, based on the result of the matching, the gene belonging to the genome database and the gene contained in the gene information are matched. A computer-readable recording in which a program for causing a computer to execute a procedure of counting the number of genes and calculating a default value of the expression frequency of the gene according to the above formula (I) using the number of genes is recorded. It features a medium.

According to a fifteenth aspect, in the fourteenth aspect, after the step of calculating the default value of the expression frequency of the gene, the number of genes belonging to the genome database selected by the user is determined according to the user's selection. The recording medium is characterized by further executing a procedure of calculating an optimized value obtained by optimizing a default value of the expression frequency of the gene according to the above formula (II).

Each of the means described above operates as follows.

According to the first aspect of the present invention, the apparatus for providing physiological phenomenon-related gene information comprises a user data management unit for receiving the genetic information from a user, and a plurality of physiological phenomenon-related gene groups. Based on a physiological phenomenon-related genome database having a genome database in which the phenomenon-related gene group is pre-classified, and the gene information provided by a user based on the classified genome database, the gene information matches the gene belonging to the classified genome database. A calculation unit for calculating the expression frequency of the gene by counting the number of genes included in the gene information, thereby providing a physiological phenomenon including the expression frequency of the gene with respect to the gene information from the user. Related gene information can be provided.

According to the second aspect of the present invention, the physiological phenomenon-related gene group includes a mouse brain ischemia-related gene group, a rat liver ischemia-related gene group, and a rat liver ischemia-related gene group. By being composed of a group of genes related to skin ischemia and a group of genes related to apoptosis, it is possible to provide a user with genetic information related to a specific physiological phenomenon.

According to the third aspect of the present invention, the classification of the genome database includes a classification based on a nucleotide sequence,
By including a classification based on an amino acid sequence and a classification based on text information for annotation classification, it is possible to provide genetic information related to each classification.

According to the fourth aspect of the present invention, it is possible to provide gene information related to the classification of interest by allowing the user to select a pre-grouped genome database by the user.

According to the fifth aspect of the present invention, the user data management unit is connected to the tagging engine of the genome database of each category of the physiological phenomenon-related genome database, so that the user data management unit is related to the physiological phenomenon-related gene group. Instead, it is possible to select a genome database of interest to the user.

According to the sixth aspect of the present invention, since the apparatus for providing physiological phenomenon-related gene information is connected to a user computer via a communication network, it is possible to provide genetic information to a remote user. Becomes possible.

According to the seventh aspect of the present invention, it is possible to issue a bill for billing for provision of gene information by providing the user data management unit with a billing means for collecting a fee.

According to the eighth aspect of the present invention, since the physiological phenomenon-related gene information includes the base sequence of the gene of interest to the user, more specific information of the gene can be provided to the user. .

According to the ninth aspect of the present invention, there is provided a method for providing physiological phenomenon-related gene information including the frequency of gene expression in response to gene information from a user. And a selection step in which the user selects a pre-classified genome database of a physiological phenomenon-related gene group constituting the physiological phenomenon-related genome database, and a gene included in the gene information provided by the user. A matching step of matching genes belonging to the genome database selected by the user; and, as a result of the matching step, the number of genes whose genes included in the gene information match genes belonging to the selected genome database. A counting step for counting, and gene generation according to the above formula (I) using the number of genes. By consists of a calculation step of calculating the default value of the frequency, and the output step of outputting a default value of incidence of the calculated gene to a user,
It is possible to calculate the expression frequency of the gene included in the gene information from the user and provide the calculation result to the user.

According to a tenth aspect of the present invention, in the method for providing physiological phenomenon-related gene information, after the calculation step, the number of genes belonging to the genome database selected by the user is changed according to the user's selection. According to the above formula (II), the method further includes an optimization step of optimizing the default value of the expression frequency of the gene and calculating the optimal value, for example, when the value of the expression frequency of the gene is small. Can narrow down the number of related genes and provide more significant information on expression functions related to the physiological phenomenon-related genes in the genome database selected by the user.

According to the invention described in claim 11, the physiological phenomenon-related gene group includes a gene group related to ischemia in mouse brain, a gene group related to ischemia in rat liver,
By having a physiological phenomenon-related genomic database consisting of a gene group related to rat skin ischemia and a gene group related to apoptosis, it is possible to provide a user with gene information related to a specific physiological phenomenon.

According to the twelfth aspect, the classification of the genome database includes a classification based on a base sequence, a classification based on an amino acid sequence, and a classification based on text information for annotation classification. Thereby, genetic information related to each classification can be provided.

According to the thirteenth aspect of the present invention, since it is connected to the user terminal via the communication network, it is possible to provide the user at a remote place with the physiological phenomenon-related gene information.

According to the fourteenth aspect, a procedure for confirming the accession number of the genetic information input by the user on a computer-readable recording medium,
A procedure for selecting a genome database in which physiological phenomenon-related genes constituting the physiological phenomenon-related genome database are classified in advance, and a procedure for comparing genes belonging to the selected genome database with genes included in the gene information, Based on the collation result, the number of genes in which the gene belonging to the genome database and the gene included in the gene information match are counted, and the expression frequency of the gene is calculated using the number of genes according to the above formula (I). By recording a program for causing a computer to execute the procedure for calculating the default value of the above, it becomes possible to provide a physiological phenomenon-related gene.

According to the fifteenth aspect, after the procedure of causing the computer-readable recording medium to calculate the default value of the gene expression establishment, the number of genes belonging to the genome database selected by the user is determined. Recording a program for causing a computer to execute a procedure of calculating an optimized value obtained by optimizing a default value of the expression frequency of the gene according to the above formula (II) while changing the value in accordance with the user's selection. For example, when the value of the expression frequency of a gene is small, the number of related genes is narrowed down, and more significant information on the expression function related to the physiological phenomenon-related gene group of the genome database selected by the user is provided. be able to.

[0041]

DETAILED DESCRIPTION OF THE PREFERRED EMBODIMENTS Next, embodiments of the present invention will be described with reference to the drawings.

FIG. 1 shows one embodiment of the present invention.
1 shows a configuration in which an apparatus for providing physiological phenomenon-related gene information is connected to a user via a communication network. User terminal 10
From ₁ to 10 _n, the genetic information of DNA chips or the like of the user is transmitted to the providing apparatus 20 of physiological phenomena related gene information via a communication network. User terminal ₁₀ 1 to 10
_n may be any ordinary or general-purpose terminal. Further, the user also transmits a signal for selecting a genome database described later via the terminal. Then, based on the gene information provided by the user and the genome database selected by the user,
The genetic information analyzed by the physiological phenomenon-related gene information providing device 20 is sent back to the user.

The gene information provided by the user is preferably gene information analyzed by a DNA chip. The DNA chip that can be used is not limited to the following, but an oligo DNA microarray (also referred to as a synthetic DNA chip) prepared by directly synthesizing DNA on a substrate is prepared in advance. DNA microarray in which DNA is fixed on a substrate (attached DN
A chip). In order to identify a gene, preferably, a synthetic DNA chip, for example, oligo DNA, from which high detection sensitivity, accuracy, and reproducibility can be obtained.
Microarray (Affymetrix, GeneChip)
Is used. In the present invention, considering the link to the Internet, it is possible to use a commercially available system incorporating a set of components necessary for gene analysis of a DNA chip. As such a system, there is a GeneChip analysis system manufactured by Affymetrix. The GeneChip analysis system includes GeneChip L as a bioinformatics tool for efficiently using the obtained gene data.
aboratory Information Management System (LIMS) and B
The eneChip Expresion Data Mining Tool (EDMTTM) is installed, and the data is used for standardization of gene-related analysis technology.
In the format specified by the Punconsortium (GATC)
The data is output to a SQL-compatible database and can be linked to the Internet.

The user is a user who wishes to predict the function of the gene group based on the result of the gene experiment performed by the user. User-supplied genetic information includes, but is not limited to, laboratory animals (eg, mice, rats, guinea pigs, rabbits, dogs, cats, pigs,
Bovine) or human-derived biological tissue (eg, blood tissue, brain tissue, heart tissue, liver tissue).

The physiological phenomenon-related gene information providing device 20 stores information such as whether the user is qualified to receive the relevant gene information. Therefore, a user who is not qualified to receive the physiological phenomenon-related gene information according to the present invention cannot perform further processing at this time.

Genes in a living body do not function independently, but interact with each other. As used herein, the term "physiological phenomenon-related gene" refers to a specific physiological phenomenon,
For example, it refers to a related gene in which a gene expressed in a living body in a certain disease state is considered to be under common control.

FIG. 2 is a schematic diagram of a device 20 for providing physiological phenomenon-related gene information according to the present invention. The device 20 includes a user data management unit 30, an arithmetic unit 40,
And a physiological phenomenon-related genome database 50.
The user data management unit 30 receives the gene information provided by the user, and further stores data relating to the expression frequency of the gene, which will be described later, and an output unit which provides physiological phenomenon-related gene information including the expression frequency of the gene. Having. Further, the user data management unit 30
Has a charging means for charging when providing the physiological phenomenon-related gene information.

Although not shown, the output means includes a display device. The display method may be displayed in two or three dimensions in association with the physiological phenomenon-related genome database selected by the user.

The physiological phenomenon-related genome database 50
Includes a plurality of physiological phenomenon-related gene groups, and each physiological phenomenon-related gene group is classified in advance in a genome database. Specifically, the physiological phenomenon-related genome database 50 of the present invention includes a group of physiological phenomenon-related genes such as ischemia in mouse brain, ischemia in rat liver, ischemia in rat skin, and apoptosis. I have. However, those in which the function of genes in relation to physiological phenomena has been elucidated from future research results can also be added to the physiological phenomenon-related genome database according to the present invention.

The physiological phenomenon-related genome database 50 shown in FIG. 2 includes a genome database (51) in which one physiological phenomenon-related gene group is classified based on a nucleotide sequence, and a genome database (5) classified based on an amino acid sequence.
3) and a genome database (55) classified based on text information for annotation classification. The genome database based on each classification includes tagging engines 52, 54, 56, respectively. Thereby, another physiological phenomenon-related gene group can be exchanged for one based on the above classification. For example, based on the classification based on the base sequence of genes related to ischemia in mouse brain and the classification based on amino acid sequence related to ischemia in rat liver,
As described later, the expression frequency of the gene according to the present invention can be calculated. The genome databases 51, 53, and 55 based on various classifications are selected by the user who has provided the genetic information via the genome database selector 60.

The classification based on the nucleotide sequence and the classification based on the amino acid sequence are known as the K-means method and the autonomous organization model method (SOM). Such a classification method clusters the genome database of the present invention based on the Euclidean distance. The text information for annotation classification indicates a correlation with a related gene group when a search is performed using a keyword. Specifically, if a gene group related to proteolysis is used as a keyword, the gene information provided by the user is given a relevance from the classification based on the text information to a gene group contributing to a specific proteolysis. It is. further,
Based on the gene information provided by the user and the genes belonging to the pre-classified genomic database selected by the user, the arithmetic unit 40 calculates the expression frequency of the genes as described later.

The expression frequency of a gene contained in the physiological phenomenon-related gene information provided by the present invention means that the degree of gene expression is determined according to the genome database selected by the user. It indicates the ratio of expression. Further, the physiological phenomenon-related gene information provided by the present invention also includes a base sequence list of a gene of interest to a user.

Next, a method of calculating the expression frequency of a gene will be described.

The expression frequency of a gene is defined as f, the number of genes for each classification, and g as the total number of genes used in the user's experiment, based on the genome databases 51, 53, 55 pre-classified by the user. Further, assuming that the number of genes belonging to the user-selected genomic database is n, if the gene of interest is included in only k in the classification selected by the user, the expression frequency P is

[0055]

(Equation 7) And a default value of the expression frequency of the gene can be obtained.

It is interpreted that the larger the P value is, the more significant it is.
The user can obtain the association between the selected classification and the genetic information provided by the user. Specifically, the P value obtained as a result of the above calculation is a significant value if it is 20 or more, preferably 4 or more.

If the P value is 4 or less, the default value of the P value can be optimized by changing the n value by the user so that the P value becomes 4 or more. By changing the n value, according to the following equation,

[0058]

(Equation 8) It is possible to obtain a closer association between the genetic information provided by the user and the physiological phenomenon.

The P value and the optimized P value calculated as described above are stored in the user data management unit for each user. The user data unit further includes a billing means, and charges the user registered in advance for the provision of the relevant gene information in providing the P value. In providing the default or optimized P value, it is possible to provide a list of related gene information to the user, if desired.

Hereinafter, referring to the flowchart of FIG.
The operation of the apparatus for providing physiological phenomenon-related gene information of the present invention will be described.

Apparatus 20 for providing physiological phenomenon-related gene information
Receives the provision of genetic information from the user, and inputs user data (S10). It is assumed that the user has been registered in advance and has the qualification to receive the provision of the physiological phenomenon-related gene information of the present invention with the device 20.

In the gene information provided by the user, the accession number of each gene is confirmed (S20).
This accession number uses that of GenBank.

Next, in step 30, the user selects a pre-classified genome database of a physiological phenomenon-related gene group. As described above, there are three types of classification in the genome database.

Based on the provision of the gene information from the user and the genome database selected by the user, the arithmetic unit compares the gene information provided by the user with the gene belonging to the genome database selected by the user (S40). As a result of the collation, the number of genes whose genes included in the gene information match genes belonging to the selected genome database is counted. The default value of the expression frequency of the gene is calculated based on the expression (I) based on the count number of the matched gene (S50).

The calculation result is output to the user once. That is, the display is performed on the display device of the user. The display at that time is, as described above, two-dimensional or three-dimensional depending on the number of genome databases selected by the user.

The user selects the gene of interest,
The result is observed, and if satisfactory, the provision of the physiological phenomenon-related gene information of the present invention ends (S80).

However, if it is desired to obtain information related to physiological phenomena in another genome database based on the result, another genome database is selected in step S90, and the process returns to step S30, and the calculation is performed by the same procedure. And receive information provision.

The user can freely select the number of genes belonging to the same selected genome database without changing the genome database.
According to I), the default value of the expression frequency of the obtained gene can be optimized (S100). At that time, usually, the number of the genes is reduced, that is, the genes are narrowed down, and the user seeks a further association with the physiological phenomenon.

According to the present invention, gene information provided by a user can be recorded on an appropriate recording medium, and a genome database classified in advance can be used as comparison data. Recording media for recording include magnetic tape, CD-ROM,
All types of recording media such as a C card and a RAM can be used. Specifically, the accession number of the gene contained in the test sample from the user is confirmed. The gene belonging to the genome database selected by the user is compared with the gene included in the gene information from the user, and if they are the same, the user counts the number of genes contained in the test sample.

Next, using the number of the genes, the expression frequency of the genes is calculated by the above formula (I).

A recording medium on which a program for executing the above procedure is recorded is useful for providing physiological phenomenon-related gene information. The program includes a procedure for confirming the accession number of the genetic information input by the user,
A procedure for selecting a genome database in which a physiological phenomenon-related gene group constituting a physiological phenomenon-related genome database is classified in advance, and a procedure for comparing genes belonging to the selected genome database with genes included in the gene information, Based on the collation result, the number of genes in which the gene belonging to the genome database and the gene included in the gene information match are counted, and the expression frequency of the gene is calculated using the number of genes according to the above formula (I). Calculating a default value.

By analyzing the gene of the test sample from the user using a computer in which the above program is installed, it is possible to provide physiological phenomenon-related gene information.

Further, after the procedure for calculating the default value of the expression frequency of the gene, the program changes the number of genes belonging to the genomic database selected by the user according to the user's selection. Formula (I
According to I), the method includes a step of calculating an optimized value obtained by optimizing a default value of the expression frequency of the gene. This makes it possible to provide more relevant physiological phenomenon-related gene information.

[0074]

EXAMPLES The present invention will be further described below with reference to examples, but the present invention is not limited to the following examples.

[Example 1] A test animal was administered with a drug. The drug may be a known one, or the function of the drug may not be completely elucidated yet. Twenty-four hours after the administration, the mice were killed, the hippocampus on both sides were removed, and immediately frozen and preserved. Next, about 2 μg of Poly (A) + mRNA was extracted from 1 g of the frozen sample. afterwards,
CDNA was synthesized by reverse transcriptase, and biotin-labeled cDNA was prepared by in vitro transcription. By heat treating the labeled cRNA in the presence of Mg ²⁺ ,
It fragmented to a size of about 50mer. After labeling the internal standard,
It was added to the sample and injected into GeneChip Mu6500 (Affymetrix). After hybridization in an oven, it was washed in a Fluidic station. The chip information was captured with a GeneArray scanner. The obtained data was processed using a bioinformatics system, and the user obtained genetic information of interest.

Thereafter, the gene information was transmitted to the apparatus for providing physiological phenomenon-related gene information of the present invention via a communication network. At that time, the user selected a genomic database that was related to mouse brain ischemia and classified based on the nucleotide sequence. FIG. 4 shows the results of the analysis of the device according to the invention.

FIG. 4 shows that clusters (CL) 1 to 30 of the genome database classified in advance on the basis of the nucleotide sequence.
And the number of genes provided by the user included in each CL is described in the number of genes constituting the cluster as a result of comparison with the genes included in the gene information from the user. This figure is displayed on the user's terminal. In it, the number of transporter-related genes and the accession number of GeneBank registration are indicated. FIG. 4 shows the expression frequencies of the transporter-related genes of each CL related to RNA synthesis, proteolysis, cell adhesion factor, DNA replication, nerve transmission, and muscle contraction. Is suggested to be associated with proteolysis.

In FIG. 4, one genomic database pre-classified based on the base sequence was selected. However, not only the base sequence but also the genomic database pre-classified based on the amino acid sequence and the annotation database were selected. It is also possible to perform analysis based on three coordinate axes by using a genome database classified based on the text information.

As described above, according to the present invention, the gene information provided by the user is presented to the physiological phenomenon-related gene information providing device, and the physiological phenomenon-related gene information is provided based on the classification of the user's interest. It is possible to do.

[Brief description of the drawings]

FIG. 1 is a diagram showing a configuration in which an apparatus for providing physiological phenomenon-related gene information according to one embodiment of the present invention is connected to a user via a communication network.

FIG. 2 is a diagram illustrating an example of a configuration of an apparatus for providing physiological phenomenon-related gene information according to the present invention.

FIG. 3 shows a flowchart in providing physiological phenomenon-related gene information according to the present invention.

FIG. 4 is a diagram showing a result of one embodiment in providing physiological phenomenon-related gene information according to the present invention.

[Explanation of symbols]

DESCRIPTION OF SYMBOLS 10 _{1-10 n} User terminal 20 Physiological phenomenon related gene information provision device 30 User data management unit 40 Operation unit 50 Physiological phenomenon genome database 51, 53, 55 Pre-classified genome database 52, 54, 56 Tagging engine 60 Genome Database selector

──────────────────────────────────────────────────続 き Continued on the front page (51) Int.Cl. ⁷ Identification symbol FI Theme coat ゛ (Reference) G01N 33/53 G01N 33/566 33/566 37/00 102 37/00 102 G06F 17/60 126Z G06F 17 / 60 126 19/00 600 19/00 600 C12N 15/00 F (72) Inventor Fumiaki Komatsu 3-10-2 Yukicho, Kawaguchi-shi, Saitama Biomedical Information Co., Ltd. F-term (reference) 4B024 AA11 AA19 AA20 BA80 CA01 HA14 HA19 4B029 AA07 AA23 FA15 5B075 KK07 KK13 KK33 KK37 ND03 ND20 ND22 ND34 NR02 NR12 PP30 PQ02 PQ20 PQ36 UU19

Claims (15)

[Claims] An apparatus for providing physiological phenomenon-related gene information including gene expression frequency including gene expression frequency in response to gene information from a user, wherein the user data receives the gene information from a user A management unit, a physiological phenomenon-related genomic database comprising a plurality of physiological phenomenon-related gene groups, and a genomic database in which each physiological phenomenon-related gene group is pre-classified; and a user provided based on the classified genome database. An operation unit having a calculation unit that checks the gene information, counts the number of genes included in the gene information that matches the genes belonging to the classified genome database, and calculates the expression frequency of the genes. The user data management unit stores the data calculated by the arithmetic unit A storage means for storing for each, and having an output means for outputting a physiological phenomena related gene information comprising the expression frequency of the gene, provides apparatus for physiological phenomena related genetic information. 2. The group of genes related to physiological phenomena includes a group of genes related to ischemia in mouse brain, a group of genes related to ischemia in rat liver, and a group of genes related to ischemia in rat skin. The physiological information-related gene information providing apparatus according to claim 1, comprising: a group of genes related to apoptosis. 3. The classification of the genome database includes a classification based on a base sequence, a classification based on an amino acid sequence, and a classification based on text information for annotation classification. Item 2. A device for providing physiological phenomenon-related gene information according to item 1. 4. The apparatus according to claim 1, wherein the pre-classified genome database is selectable by a user. 5. The user data management unit is connected to a tagging engine of a genome database of each category of the physiological phenomenon-related genome database, so that a user can select a genome database regardless of a physiological phenomenon-related gene group. 2. The method of claim 1, wherein
The physiological information-related gene information providing device according to 1. 6. The apparatus for providing physiological phenomenon-related gene information according to claim 1, wherein the apparatus is connected to a user terminal via a communication network. 7. The apparatus according to claim 1, wherein the user data management unit further includes a charging unit for collecting a fee for the output. 8. The physiological phenomenon-related gene information includes a base sequence list of a gene of interest.
The apparatus for providing physiological phenomenon-related gene information according to claim 1. 9. A method for providing physiological phenomenon-related gene information including a gene expression frequency with respect to gene information from a user, comprising: a confirmation step of confirming an accession number of the gene information provided by the user; A selection step in which a user selects a pre-classified genome database of a physiological phenomenon-related gene group constituting a physiological phenomenon-related genome database; a gene included in the gene information provided by the user; and the genome selected by the user. A matching step of matching genes belonging to a database, and a counting step of counting the number of genes in which the genes included in the gene information and the genes belonging to the selected genome database match as a result of the matching step, Using the number of genes, according to the following equation: A method of providing physiological phenomenon-related gene information, comprising: a calculating step of calculating a default value of a gene expression frequency; and an output step of outputting the calculated default value of a gene expression frequency to a user. 10. After the calculation step, the number of genes belonging to the genome database selected by the user is changed according to the user's selection, and the number is changed according to the following equation. The method of claim 9, further comprising optimizing a default value of the expression frequency of the gene to calculate an optimal value. 11. The physiological phenomenon-related gene group includes a gene group associated with ischemia in mouse brain, a gene group associated with ischemia in rat liver, and a gene group associated with ischemia in rat skin. 10. The method for providing physiological phenomenon-related gene information according to claim 9, comprising: a group of genes related to apoptosis. 12. The classification of the genome database includes:
The method according to claim 9, further comprising a classification based on a base sequence, a classification based on an amino acid sequence, and a classification based on text information for annotation classification. . 13. The method for providing physiological phenomenon-related gene information according to claim 9, wherein the method is connected to a user terminal via a communication network. 14. A procedure for confirming an accession number of a gene contained in gene information input by a user, and a user selects a genome database in which a group of physiological phenomenon-related genes constituting the physiological phenomenon-related genome database is classified in advance. A step of causing a gene belonging to the selected genome database to be compared with a gene contained in the gene information; anda gene belonging to the genome database and a gene contained in the gene information, based on the collation result. The number of matching genes is counted, and using the number of the genes, the following formula is used. Calculating a default expression frequency of the gene;
A computer-readable recording medium on which a program for causing a computer to execute the program is recorded. 15. After the step of calculating a default value of the expression frequency of the gene, the number of genes belonging to the genome database selected by the user is changed according to the selection of the user, and the following expression is used. 4] 2. The method according to claim 1, further comprising the step of calculating an optimized value obtained by optimizing a default value of the expression frequency of the gene.
5. The recording medium according to 4.