KR20080088539A - Method for finding effective genes - Google Patents

Abstract

A method for searching effective genes is provided to enable a user to search the effective genes conveniently by minimizing user manipulation, and enable the user to understand a search result easily by displaying the search result in a table and an image. Effective gene information for a plurality of different experiment conditions is stored to a database(210), and a list of the different experiment conditions is displayed through an output device(220). A signal selecting one of the displayed experiment conditions is received from a data input device(230). Block information of a spot effective to the selected experiment condition, and the information including column/row indexes in a block are extracted from gene information stored in the database. The extracted information is displayed through an output device by using a table or a DNA(DeoxyriboNucleic Acid) chip image(240).

Description

Method for finding effective genes

The present invention relates to the use of a genomic database. In particular, it relates to a method for searching for an effective gene.

As shown in Figure 1, Estee (Expressed Sequence Tag, EST) refers to the expressed gene fragment, and refers to the part of the complementary DNA (cDNA) involved in the expression of the gene. In addition, EST is a full sequence in which a portion of an unspecified sequence is expressed in each cell, and is useful for finding a gene. EST is part of the three billion base pair sequences expressed in each cell, allowing researchers to interpret the function of genes by comparing genes of different human tissues with other microorganisms. In other words, EST (Expressed Sequence Tag) data cloned by cDNA (complementary DNA) sequencing can be compared with nucleotide sequence information of various organisms to find similarities or to estimate gene function through functional site search. Contributes to genome research.

EST is a short sequence obtained through cDNA clone analysis as shown in FIG. cDNA is a DNA that is re-transferred into double-stranded DNA by reverse transcription. Since cDNA represents a gene expressed in a protein, cDNA also represents a sequence of a gene expressed in a cell. Since EST determined the sequence by reading the sequence of each cDNA clone at the 3 'or 5' end only by an automated machine, the sequence could be somewhat inaccurate. However, in the sense that sequences can be obtained quickly and inexpensively with an automated machine, they have started to be applied to various studies.

EST discovers new genes, discovers new gene populations associated with disease, qualitative and quantitative analysis of gene expression, cloning of differentially expressed genes between tissues, and replaces the 3'UTR (Untranslated region) of EST with a new Sequence tagged It is used as an important material in various research fields, such as making a gene expression map used as a site, and analyzing a complex genome sequence by comparing with a genome sequence.

EST analysis is to analyze which gene region (EST) is expressed by what function, as shown in Figure 1, EST analysis technology is widely applied to DNA chip data analysis, SNP analysis, Motif analysis, Proteomics, new drug candidate search, etc. can do. Although EST analysis has limitations, it is very important and widely used in biotechnology research.

However, the conventional genome database requires too much manipulation in verifying the reliability of an experiment or searching for an effective gene, and it is difficult for a user to easily grasp the search result, and thus, systematically obtains information such as primers necessary for verifying the experiment. There is a problem that cannot be provided.

The problem to be solved by the present invention is to provide the convenience by minimizing the user's operation in searching for the effective gene, the effective gene search that can display the search results in a table and image so that the user can easily grasp the search results To provide a method.

In order to solve the above problems, the effective gene search method disclosed herein uses a computer system that searches a database according to an input signal received through a data input device and displays information retrieved from the database through an output device. Provides a way to search for valid genes. To this end, the present invention comprises the steps of storing the gene information valid for a plurality of different experimental conditions in the database; Displaying a list of the plurality of different experimental conditions through the output device; Receiving a selection signal for selecting any one of the plurality of different experimental conditions through the data input device; And extracting block information of spots valid for an experimental condition selected according to the selection signal, row and column indexes in the block, from the genetic information stored in the database, and extracting the extracted information through the output device. To solve the problem to be solved by the present invention including the step of displaying a table or a DNA chip image.

According to the present invention, by constructing a database by classifying the genetic information on the DNA chip according to experimental conditions, functional categories, etc., and searching by using a simple and intuitive interface, it is convenient to minimize the operation degree in searching for the effective gene Performance and display the search results in a table and image so that the user can easily understand the search results.

Genomic data is complex and its quantity and data range is wide. Thus, genomic databases must be flexible in their respective data types and values. Genomic data change quickly in nature, so you need to be able to support fast schema changes in your database. The genome database is related to various fields such as medicine, pharmacy, chemistry, biology, etc., rather than any specific field, so the method of expressing the data desired in each field is different. Therefore, even if you use a single genomic database, you must provide a variety of schemas to meet their respective requirements.

The limitations to be solved in constructing genomic database system are as follows.

First, different views of a particular order must be properly representable. Second, because concepts are always changing and fluid, we need an environment that can support liquidity. Third, as the data continuously changes, it causes inconsistency and ambiguity of the data, so it is necessary to support the dynamic schema during the construction process. In other words, since concepts and schemas are constantly changing, a powerful query language is required, and a powerful pattern matching technique that can identify proper sequence and spacing of chromosomes must be provided.

Hereinafter, the configuration of the invention for clarifying the solution to the problem to be solved by the present invention will be described in detail with reference to the accompanying drawings, based on the preferred embodiment of the present invention, to give a reference numeral to the components of the drawings In the drawings, like reference numerals refer to like elements even though they are on different drawings, and it is to be noted that components of other drawings may be cited when necessary in describing the drawings.

2 is a flow chart of the effective gene search method according to the present invention.

First, valid gene information is generated for a plurality of different experimental conditions using a plurality of DNA chips (step 210). This process (process 210) is a preprocessing process, a database construction process.

Next, a list of a plurality of different experimental conditions is displayed (step 220). In this case, the list may be output in a table format and the means for selecting each item of the list may be displayed together.

When a list of a plurality of different experimental conditions is displayed, one of the plurality of different experimental conditions is selected (operation 230). At this time, the selection of the experimental condition may be a method such as clicking by using a mouse, inputting a keyboard shortcut key, directly touching the touch screen, and the like. In this case, the plurality of different experimental conditions may include COLD, COLD & ABA, SALT, SALT & ABA.

Finally, information including the block information located on the DNA chip and the row and column indexes within the block is extracted from the generated genetic information and the effective spot is selected on the DNA chip (step 240). . Preferably, this process (step 240) may include displaying on the DNA chip image information including block information of valid spots, row and column indexes within the block.

FIG. 3A illustrates a screen configuration of a gene viewer to which the effective gene search method of FIG. 2 is applied.

Gene viewer statistically analyzes 32 sets of DNA chips and shows valid gene information under 8 conditions. 3A is an initial screen of a gene viewer, in which information can be searched for eight conditions. Information retrieval can be viewed in the form of tables and images.

FIG. 3B is a screen when any one of a plurality of table views is clicked in FIG. 3A. FIG. 3C is a screen when any one of a plurality of image views is clicked in FIG. 3A. 3B and 3C show the results of genes valid for each condition in table form and image form.

3D is a screen in which the effective gene of FIG. 3A is linked with KOME annotation information.

So far I looked at the center of the preferred embodiment for the present invention. Those skilled in the art will appreciate that the present invention can be implemented in a modified form without departing from the essential features of the present invention.

Therefore, the disclosed embodiments should be considered in descriptive sense only and not for purposes of limitation. The scope of the present invention is shown in the claims rather than the foregoing description, and all differences within the equivalent scope will be construed as being included in the present invention.

1 illustrates the concept and application of Estee to which the present invention is applied.

2 is a flow chart of the effective gene search method according to the present invention.

FIG. 3A illustrates a screen configuration of a gene viewer to which the effective gene search method of FIG. 2 is applied.

FIG. 3B is a screen when any one of a plurality of table views is clicked in FIG. 3A.

FIG. 3C is a screen when any one of a plurality of image views is clicked in FIG. 3A.

3D is a screen in which the effective gene of FIG. 3A is linked with KOME annotation information.

Claims (2)

A method of searching for a valid gene using a computer system for searching a database according to an input signal received through a data input device and displaying information retrieved from the database through an output device, Storing valid genetic information for each of a plurality of different experimental conditions in the database; Displaying a list of the plurality of different experimental conditions through the output device; Receiving a selection signal for selecting any one of the plurality of different experimental conditions through the data input device; And From the gene information stored in the database, information including block information of spots valid for the experimental conditions selected according to the selection signal, row and column indexes in the block is extracted, and the extracted information is obtained through the output device. Valid gene search method comprising the step of displaying in a table or DNA chip image. According to claim 1, wherein the different experimental conditions An effective gene search method comprising COLD, COLD & ABA, SALT, SALT & ABA.

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