JP2003168066A - Method for displaying relation among factor sets - Google Patents

Abstract

<P>PROBLEM TO BE SOLVED: To provide a displaying method capable of more easily judging relations among factor sets by displaying the relations among the factor sets in one table. <P>SOLUTION: The relations among the factor sets are quantized by using round-robin processing for the relations among all of factors included in the factor sets and, the results are accumulated and displayed in a spreadsheet. When a threshold is given to the quantized relations among the factors and displayed on the spreadsheet, colors and patterns are changed to sort the spreadsheet by means of digitized relations among the factors. The relations among the factor sets are displayed in one table so that the relations can be more easily judged. <P>COPYRIGHT: (C)2003,JPO

Description

Detailed Description of the Invention

[0001]

BACKGROUND OF THE INVENTION 1. Field of the Invention The present invention relates to a display method for easily displaying the relationship of each element between element sets.

[0002]

2. Description of the Related Art In recent years, advances in experimental techniques in molecular biology have enabled rapid data determination and collection of biopolymers including gene sequences. By processing such biopolymer information with an electronic computer, the quantification of the relationship such as homology with respect to a certain biopolymer assembly of a certain biopolymer is performed.

[0003]

The above-described quantification of the relationship such as homology of biopolymers is carried out in a one-to-one relationship or a one-to-many relationship. Here, there is a case where it is desired to display the quantification of the relationship between the biopolymer assembly and the biopolymer assembly. The one-to-one relationship can be easily represented as a plot on a two-dimensional plane. One-to-many relationships can be represented in the resulting list. However, many-to-many relationships are very difficult to express with these conventional methods. A first object of the present invention is to display the relationships between element sets in a single table. A second object of the present invention is to provide a display method capable of more easily determining the relationship between these element sets.

[0004]

According to the present invention, the relationship between element sets is quantified by a brute force relationship between all elements included in the element set, and the result is tabulated and displayed in a spreadsheet. By setting a threshold for the digitized element relationships, changing the color and pattern when displaying on the spreadsheet, and sorting the spreadsheet by the digitized element relationships, the relationship between the element sets Is displayed on a single table, and the relationship is displayed so that the relationship can be more easily determined.

A method for displaying a relation between element sets according to the present invention targets a first element set and a second element set, and a relation between elements in the first element set and elements in the second element set. Quantifying the sex for all pairs of elements, the elements in the first element set are arranged in the row direction, and the elements in the second element set are arranged in the column direction. It is characterized by displaying the relationship between them.

The operation of changing the arrangement order of elements in the row direction according to the quantified magnitude of the relationship and the operation of changing the order of elements in the column direction according to the quantified magnitude of the relationship are quantified. It is also possible to fix the cells whose relationship is greater than or equal to a preset threshold value, and repeat the operation alternately and sequentially for adjacent rows and columns, and display the obtained results. According to this method, a highly related element set can be displayed so that it can be visually confirmed. Calculate the average value of the quantified relationship for each row or each column, or calculate the number of cells above or below a preset threshold value, and display the row or column elements sorted in descending or ascending order of the calculated values. You may do it.

With respect to the quantified individual relationships, by calculating the average value of the relationships of a certain element to the element group,
If the average value is high, it can be recognized as an element having a relatively high relation to the entire element set. On the contrary, if the average value is low, it can be recognized as an element having a relatively low relation to the entire element set. Further, regarding the quantified individual relationships, by calculating the number of the relationships of a certain element with respect to the element set that are greater than or equal to the threshold value and the number that is less than or equal to the threshold value It is possible to rank the elements in the element set by approximating how many elements have weak relationships and rearranging the elements in the order of the number of strongly related elements.

If a threshold is set for the quantified relationship and cells having a quantified relationship higher than the threshold and cells having a lower quantified relationship are displayed in different display modes, the strength of the relationship is highlighted. You can As a different display method, for example, there is a method of changing a display color or a display pattern.

As an example, it is possible to set a threshold value for the maximum value for each quantified individual relationship and binarize the relationship depending on whether or not the maximum value is exceeded. For example, when the elements a and c have the maximum value exceeding the threshold value with respect to the element group X and the element b does not have the maximum value exceeding the threshold value, the elements a and c have the relationship with the element group X. , Element b can be determined to have no relationship.

Further, a plurality of thresholds can be set.
For example, two large and small thresholds are set, and the quantified relationship is different between a cell lower than the smaller threshold, a cell intermediate between the smaller threshold and the larger threshold, and a cell higher than the larger threshold. The strength of the relationship can be highlighted by displaying in the display method.

It is also possible to display a quantified relationship histogram and set a threshold value on the histogram. According to this method, the threshold value can be easily set. Color gradation may be added and displayed according to the quantified relationship value. According to this method, the tendency of the relationship can be visualized and displayed.

Different colors may be designated for a plurality of types of quantified relationships, and the average color may be displayed. According to this method, it is possible to simultaneously visualize and display a plurality of types of relationships on one spreadsheet. The method of designating the color for each relationship may be the emphasis display of the strength or the gradation display by the threshold designation. In the above method of displaying the relationship between element sets,
When the first element set is a gene sequence group of an organism species, the second element set is a genome sequence, and the relationship between elements is a homology analysis result between sequences, comparison between genomes of different organisms can be performed.

The first element set is a gene sequence group spotted on a gene biochip, and the second element set is a gene sequence group for performing a hybridization reaction with the biochip. When the sex analysis result is used, a simulation of the biochip hybridization reaction can be performed.

If the first element set and the second element set are gene sequence groups spotted on different gene biochips, and the relationship between the elements is the result of homology analysis between genes, different chips are obtained. The relationship between can be derived. Furthermore, if the first element set and the second element set are the same gene sequence group and the relationship between the elements is the homology analysis result between genes, the gene clustering can be displayed easily.

[0015]

BEST MODE FOR CARRYING OUT THE INVENTION Embodiments of the present invention will be described below with reference to the drawings. FIG. 1 is a block diagram of a system for realizing a relationship display method between element sets according to the present invention. The system of the present invention includes a central processing unit 101 for quantifying relationships between two elements, totaling quantified relationships, displaying data, sorting processing, etc., a program memory 102 storing programs, an external storage device 103, and data. Memory 104,
A dialogue instruction input device 105 including a pointing device 151 and a keyboard 152 for inputting and selecting values to the system, and a display device 106 are provided.

In the program memory 102, an element set / relationship quantification method inquiry program 121, an inter-element relationship calculation program 122, an inter-element relationship aggregation calculation program 123, an element set comparison table display program 124,
A program memory 102 such as a threshold setting inquiry program 125 and a result sort program 126 is stored. The external storage device 103 stores element set information 13 that stores individual information of biopolymer sets existing in a sample.
1. The inter-element relationship information 132 for holding information quantifying the biopolymer element relationship, and the threshold information 133 for holding the threshold value and display color used when displaying the result, the presence or absence of gradation display, etc. Has been done. In the data memory 104, the relationship quantification parameter 141 necessary when quantifying the relationship between each element of the biopolymer, and the quantification of the relationship between the biopolymers quantified according to the relationship quantification parameter 141. Inter-organization factor relationship data 142, average value between biopolymer elements, maximum value, minimum value, number of thresholds or more,
The inter-element relationship aggregated data 143 for holding information that aggregates relationships such as the number of elements equal to or less than a threshold value is stored. The display device 106 visualizes and displays the inter-element set relationship display table and realizes interaction with the user.

FIG. 2 is a diagram showing the concept of an inter-element relationship display table. Multiple elements A01, A02, A03, A0
Element set A consisting of 4 and a plurality of elements B01, B0
When there is an element set B consisting of 2, B03, B04,
As shown by enclosing with a circle 201, the relationship between each element of these element sets is quantified by brute force. All the results thus obtained are displayed together in the spreadsheet 202.
In this table, an appropriate threshold value is designated, and the display method is performed so that the colors and patterns can be distinguished. Further, as shown in the spreadsheet 203, sorting is performed according to the quantified relationship so that the display is performed in a more easily arranged order. Further, by holding the inter-element relationship and the threshold value information used for display, it is possible to reproduce the sorting result under the same condition.

FIG. 3 shows a processing flow for displaying an inter-element set comparison table on the display device 106 of FIG. 1 from the data stored in the element set information 131 of FIG. First, in step 301, an element set to be used and an inter-element relationship quantification method are set. This step
The element set A, the element set B, and the algorithm used in 201 of FIG. 2 for quantifying the inter-element relationships included in these elements are set. As an example of the element relationship quantification method used, Bla using the BLAST algorithm is used.
st2Sequence (Tatiana A. Tatusova, Thomas L. Madden
1999, "Blast2 sequenced-a new tool for comparing
protein and nucleotide sequences ", FEMS Microbiol
Lett. 174: 247-250) and ALIGN (Bill Pearson 1995) using a global alignment algorithm.

Next, the central processing unit 101 of FIG. 1 quantifies the inter-element relationships specified in step 301, and calculates the quantized inter-element relationship data 142 of FIG. 1 (step 302). ). This step is repeated until it is determined in the next step 303 that all the inter-element relationships have been quantified. Next, the individual inter-element relationships quantified in step 302 are aggregated, and the inter-element relationship aggregated data 143 of FIG. 1 is calculated (step 304). Finally, the display device 106
A comparison table between element sets is displayed in (step 305).
When the user instructs an operation such as sorting in step 306, the process returns to step 305 and the instructed sorting result is displayed.

FIG. 4 shows a processing flow when the element set / relationship quantification method inquiry program 121 inquires the element set / relationship quantification method in step 301 of FIG. First, in step 401, an inquiry is made as to whether the number S of element sets is one or two. Next, in step 402, the element set 1 is inquired. If the number of element sets S is two, the process proceeds from step 403 to step 404 to inquire about the element set 2. When the number of element sets S is 1, the inquiry about the element set 2 is not performed. Then, an inquiry is made about the element set relationship quantification method (step 405). In this step, it is decided which program that implements which algorithm will quantify the relationship. Finally, the parameters required for the algorithm and program determined in step 405 are set (step 406).

FIG. 5 shows an inter-element relationship calculation program 12
2 represents a processing flow when calculating the relationship between elements in step 302 of FIG. First, the data of the element set 1 designated in step 402 of FIG. 4 is read (step 501). If there are two set element sets S, the process proceeds from step 502 to step 503 to read the data of the element set 2 specified in step 404 of FIG. When the element set S is one, the element set 2 is not read. In the next step 504, various parameters necessary for quantifying the relationship set in step 406 of FIG. 4 are read. Then Step 505
4, the relationship quantification is repeated in a brute force manner for each element of the element set 1 and the element set 2 or each element of the element set 1 by the method of quantifying the relationship set in step 405 of FIG.

FIG. 6 shows a processing flow when the inter-element relationship aggregation calculation program 123 totals inter-element relationships in step 304 of FIG. In step 601, all the relationship data quantified in step 505 of FIG. 5 are read. In the following step 603, the maximum value, the minimum value, the average value of the quantified values in each element, the number of elements having a relationship of not less than the upper limit threshold, the number of elements having a relationship of not more than the lower limit threshold, and the like are calculated.

FIG. 7 shows an element set comparison table display program 1
Reference numeral 24 denotes a processing flow for displaying the inter-element relationship in step 305 of FIG. Step 70
1, the relationship data quantified in step 505 of FIG. 5 is read. In the following step 702, the elements are developed on the spreadsheet in the order of reading.
At this time, if it is necessary to fill the relevant cell from the relationship value, the process proceeds from step 703 to step 704 to display the relationship value and fill the cell. If there is no need to paint, step 703 to step 70
Proceed to step 5 and display only the relationship value. At the time of filling, the threshold value data table 1702 (FIG. 17) described later is referred to. These steps are repeated for all combinations of elements until the display is completed (step 706).

FIG. 8 shows a threshold setting inquiry program 125.
Shows the flow of. In step 801, as shown in FIG.
The threshold data table 1702 of No. 7 is referred to. Then, in step 802, the relationship data quantified in step 505 of FIG. 5 is read. In the following step 803, based on the data read in steps 801 and 802, the threshold value data information is displayed at the same time as the histogram of the relationship value. Next, in step 804,
Display the dialog as shown in FIGS.
Threshold setting using UI is performed. Continued Step 80
In step 5, the threshold data set by the user is reflected in the threshold data table 1702 of FIG.

FIG. 9 shows a processing flow of the result sort program 126 when the user requests the sorting of the data compared between the different element sets in step 306 of FIG. R is the row to be sorted, C is the column to be sorted, N
Is the number of elements expanded in the row direction, and M is the number of elements expanded in the column direction. In step 901, if the sorting target row is smaller than the number of elements expanded in the row direction, sorting is performed using the element relationship value of the sorting target row as a key. At this time, the column to be sorted is compared with the column to be sorted and the locked column to make a larger column (steps 903 and 904). The locked column here refers to a column that has at least one relationship value exceeding the upper limit threshold value in the already sorted rows. This operation completes the sorting of the Rth row, so R becomes the next row (step 905). Subsequently, at step 906, if the sort target column is smaller than the number of elements developed in the column direction, the element relationship value of the sort target column is used as a key for sorting. At this time, the row to be sorted is compared with the row to be sorted and the locked row, and is set to a larger row (908, 909). The locked row here refers to a row that has at least one relationship value exceeding the upper limit threshold value in the already sorted column. This operation completes the sorting of the Cth column, so C becomes the next column (910). The above operation is repeated until the row and the column, the maximum row and the maximum column which are both expanded are reached.

FIG. 10 shows a processing flow of the result sort program 126 when the user requests the sorting of the compared data in the same element set in step 306 of FIG. Let K be the element position to be sorted and N be the total number of elements. In step 1001, the sort target element position is compared with the maximum element lock position. If the sort target element position is larger, the elements after the sort target position are sorted using the element at the sort target position as a key for both rows and columns. (Step 1002). On the contrary, if the maximum element lock position is large, the elements after the maximum element lock position are sorted using the element at the sort target position as a key in both the row and column (step 1003).
As used herein, the locked element refers to an element that has already been sorted and is located in a row or column that has at least one relationship value that exceeds the upper threshold. This operation completes the sorting of the Kth column, so K becomes the next element (step 1004). The above operation is repeated until the position of the sort target element reaches the total number of elements. Even if data is compared in the same element set, if the relationship changes depending on which element is used as a key, the sorting is performed by the method shown in FIG.

In FIG. 11, the data of the different elements are set to the upper threshold value 8
This is an example of when sorting is performed as. 1101 is data before sorting. 1102 is a result of sorting the A column and the subsequent columns with the a row as the sorting target row. Since the relation between the sorted results a and D is equal to or more than the threshold value, this cell is locked. Reference numeral 1103 denotes the result of sorting the rows b and onward, with the column D as the sorting target column. This cell is locked because the relation between the sorted results e and D is greater than or equal to the threshold value. Reference numeral 1104 denotes the result of sorting from the column C onward with the row e as the sorting target row. These cells are locked because the sorted results e and E and e and C have exceeded the threshold. A column 1105 is a result of sorting the c-th row and the subsequent rows with the E column as the sorting target column. Since the relationship between the sorted results d and E exceeds the threshold value, this cell is locked. Reference numeral 1106 denotes a result of sorting the columns A and subsequent columns with the d-th row as the sorting target row. The reason why the column C is not a target for sorting is that the cell indicating the relationship between e and C is locked in 1104. 110
Reference numeral 7 shows the result of sorting the c and subsequent rows with the C column as the sort target column. Since the relation between the sorted results b and C exceeds the threshold value, this cell is locked. 1108 is b
This is the result of sorting the rows after the column A with the row as the sorting target row. Since the relationship between the sorted result b and A exceeds the threshold value, this cell is locked. Reference numeral 1109 denotes the result of sorting the c-th row and subsequent rows with the A-column being the sorting target column.
As a result of the above operation, the sorting target row has become equal to the number of elements expanded in the row and column directions in both the row and column, so the sorting process ends.

In FIG. 12, the threshold value is set to 6 by the same method as in FIG.
This is the result of sorting by setting to. Since the locked cells are different, 1109 and 1209 will show different sort results.

FIG. 13 shows that the data of the same element has an upper limit threshold value of 9.
This is an example of when sorting is performed as. 1301 is data before sorting. Reference numeral 1302 denotes the result of sorting with the element A as the sorting target. When they are arranged in the descending order of the relationship with A, they are A, C, D, B, and E, so that the rows and columns are sorted in the order of A, C, D, B, and E. As a result, the relationship between A and A is greater than or equal to the threshold value, so this cell is locked. 1303 is the result of sorting the elements after C using the element C as a key. When the relationships with the elements after C are arranged in descending order, C, E, D, and B are obtained, so that both rows and columns are
After C, sorting is performed in the order of C, E, D, and B. As a result, the relationship between C and C, the relationship between C and E, and the relationship between E and C exceed the threshold value, so these cells are locked.
Reference numeral 1304 denotes the result of sorting the elements after D with the element E as a key. The elements of E are not sorted.
This is because, in 3, the cells indicating the relationship between E and C and the relationship between E and C are locked. As a result, since the relationship between E and E is greater than or equal to the threshold value, the corresponding cell is locked. Thirteen
Reference numeral 05 is a result of sorting elements after D with the element D as a key. As a result, the relationship between D and D exceeds the threshold value, and the corresponding cell is locked. As a result of performing the above operation, the sorting target position becomes equal to the number of elements, so the sorting process ends.

FIG. 14 shows that data of the same element has an upper threshold value of 7
This is an example of when sorting is performed as. Because the locked cells are different, 1305 and 1405 will show different sort results. To find the clustered element group from the sorted result, search all cells in the vertical and horizontal directions from the cells on the diagonal line from the upper left to the lower right of the table. If there is a cell that is equal to or greater than the relationship threshold value, the element for which the relationship of the cell is calculated belongs to the same cluster. Looking at the results of FIG. 13, a cluster 1306 consisting only of the element A and a cluster 130 consisting of the elements C and E
7, a cluster 1308 including only the element D and a cluster 1309 including only the element B are created. Looking at the result of FIG. 14, all the elements belong to the same cluster 1406.

FIG. 15 shows an example of a data schema holding the element set information 131. Element set table 15
01 has an element set ID for managing the element set and uniquely recognizing the element set, and an element set name data field. The element table 1502 manages the elements in the element set, and an element ID for uniquely recognizing the element, an element set ID for uniquely recognizing the element set to which the element belongs,
It has an element name and each data field of biopolymer data of the element. The element relationship aggregation table 1503 is a table that has N element IDs for identifying elements to be aggregated, aggregation items, and N sets of aggregated data.
The element information read in steps 501 and 502 of FIG. 5 is stored in these tables.

FIG. 16 shows an example of a data schema holding the inter-element relationship information 132. The inter-element relationship table 1601 is an element ID of the comparison elements 1 and 2, a relationship quantification parameter ID for uniquely recognizing a relationship quantification parameter table holding various parameter information for quantifying the relationship, It has a quantified relationship ID for uniquely recognizing a quantified relationship table holding quantified relationship information, and a threshold data ID for uniquely recognizing a threshold data table holding threshold information. The information held in the element tables 1602 and 1603 is the same as in FIG. The relationship quantification parameter table 1604 is a relationship quantification parameter ID for uniquely recognizing the relationship quantification parameter, used algorithm / program information for quantifying the relationship, and a parameter for quantifying the relationship. Holds information. The quantification relationship table 1605 includes a quantification relationship ID for uniquely recognizing the quantification relationship table, a quantification relationship name that is quantified relationship name information, and a quantification that is the relationship value. Holds the chemicalization relationship value.

FIG. 17 shows an example of a data schema for holding the threshold information 133. Inter-element relationship table 17
01 holds the threshold data ID, and this threshold data ID uniquely recognizes the threshold data table 1702.
The threshold data table includes threshold data IDs, threshold setting valid / invalid flags, gradation display flags, upper limit thresholds, lower limit thresholds, and upper limit display colors and lower limit display colors that represent colors above and below those thresholds. Hold.

FIG. 18 shows an example of the result display screen. The inter-element relationship is displayed as a spreadsheet on the display screen 1801. By designating a threshold value, a combination having a strong relationship between elements and a combination having a weak relationship are displayed in different colors and patterns. Each element name of one element set is displayed in 1802, and each element name of the other element set is displayed in 1803. When the element set is composed of highly related biopolymers, it is possible to identify elements with low relationship by looking at combinations with weak relationships. A screen 1804 shows the result after sorting. By performing sorting, cells having a threshold value or more, which are scattered before sorting, are displayed in a group of highly related cells.

FIG. 19 is an example of a screen of a threshold designation auxiliary histogram. In the display unit 1901, the horizontal axis represents the relationship value,
A histogram in which the vertical axis is the number of element pairs (the number of cells in the spreadsheet) is displayed, and the set threshold value is the line 19
02 and 1903 are displayed. The threshold can be changed by dragging this line using the pointing device 151 of FIG. Reference numeral 1904 is a list for selecting the currently set relationship.
Reference numerals 1905 and 1906 indicate display colors / patterns when the thresholds are exceeded or when the thresholds are not exceeded. 190
Reference numerals 7 and 1908 represent the respective threshold values in points. This value can be changed by using the keyboard 152 of FIG. The Graph Setting ... button 1909 is a button for changing the upper limit of the Y coordinate of the graph, the histogram calculation unit, the graph shape, and the like.

FIG. 20 is a screen example of a gradation designation auxiliary histogram. A histogram is displayed on the screen 2001, and the set threshold is indicated by lines 2002 and 200.
Displayed at 3. The threshold can be changed by dragging this line using the pointing device 151 of FIG. Reference numeral 2004 is a list for selecting the currently set relationship. Reference numeral 2005 denotes a gradation state in the current setting. 2006,
Reference numerals 2007 respectively indicate upper and lower display colors of gradation. Reference numerals 2008 and 2009 respectively represent the upper limit value and the lower limit value of gradation in points. This value can be changed by using the keyboard 152 of FIG. Graph Setting ... Button 2
Reference numeral 010 is a button for changing the upper limit of the Y coordinate of the graph, the unit of histogram calculation, the graph shape, and the like. By displaying using a gradation, it is possible to display data near the boundary that is overlooked due to binarization that is above or below a threshold value. On the contrary, when the threshold value is clear, it is possible to more clearly show the presence or absence of the relationship by performing the binarized display without displaying the gradation.

When simultaneously displaying a plurality of quantified relationships, a plurality of relationship values are described in a single cell of a spreadsheet. Further, when the display color is changed by designating a threshold value or when gradation display is performed, the set display color at each relationship value is converted into an RGB value, and R,
It is displayed in a color with each of G and B as an average value. For example, the relationship of the array is calculated by two or more kinds of algorithms, and the display color of the cell whose relationship value determined by the algorithm 1 is equal to or more than the threshold value is red (R: 255, G: 0, B: 0), When the display color of a cell whose relationship value determined by Algorithm 2 is greater than or equal to the threshold value is blue (R: 0, G: 0, B: 255), a cell whose relationship exceeds the threshold value only by Algorithm 1 Is red (R: 255, G: 0, B: 0), and the cell whose relationship exceeds the threshold value only with algorithm 2 is blue (R: 0,
G: 0, B: 255), and a cell whose relationship exceeds the threshold in both algorithms is displayed in purple (R: 127, G: 0, B: 127), which is the average of the respective RGB values.
By simultaneously displaying in this way, the relationships displayed in red or blue are relationships that one algorithm cannot find, or one algorithm recognizes false positive relationships as significant. It is said that either has been done. Also, if there is an element set for which it is certain that there is a relationship, it is possible to absorb the difference in calculation of relationship values between multiple algorithms by setting the threshold value so that all related cells are displayed in purple. It is possible to Also, in the case of sorting when displaying multiple relationships at the same time, sorting is performed by specifying multiple sorting keys.

In the above method, one element set is used as a set of gene sequences of the organism species 1 and a genome sequence, and the other element set is used as a set of gene sequences of the organism type 2 and a genome sequence. By implementing it as a homology score, it becomes possible to display the comparison result at the gene sequence level between different species. For example, when a certain gene sequence of organism species 1 shows significant homology with a certain gene sequence of organism species 2, it is presumed that the corresponding genes of organism species 1 and organism species 2 have similar functions. If a gene sequence of Species 1 does not show significant homology with any gene sequence of Species 2 and shows significant homology with the genome sequence of Species 2, it is considered as a gene candidate not found in Species 2 It is possible to name. If a gene sequence of organism species 1 does not show significant homology with the gene sequence of organism species 2 or the genome sequence, it can be cited as a gene candidate involved in the difference between organism species 1 and organism 2. By using a plurality of algorithms for such homology search and displaying the results at the same time, it is possible to further improve the accuracy and perform the analysis. When displaying such an element set, the homology with the genome sequence is excluded from the sorting target, and the common gene sequence in the upper left of the table and the gene sequence different in both species in the lower right of the table are sorted. Tend to line up.

When a gene having a complementary sequence to the spotted gene sequence is subjected to the reaction on the gene biochip, the gene having the complementary sequence binds to the gene on the biochip, Caught on. By attaching a detectable substance such as a dye to all the genes used for these reactions, it is possible to detect a gene complementary to the gene spotted on the biochip. Therefore, one element set is a gene sequence group spotted on a gene biochip, and the other element set is a gene sequence group to be subjected to a reaction with respect to this biochip. At this time, by using the relationship between these two element sets as a score of a homology search in which the complementary strand sequence of the gene sequence is also added, it is possible to simulate which spot on the biochip the gene binds to. It becomes possible to do. In the process of manufacturing a biochip, a gene group whose sequence is clear may be subjected to a reaction when determining the quality of whether or not the intended gene is spotted on the biochip. In the above method, by listing the results, theoretically, it will be combined with which spot,
It is possible to display a list of which spots are not combined.

It is possible to specify a sequence of all the spots of the gene biochip to prepare a custom-made biochip, but it is also possible to use a ready-made biochip whose sequence cannot be specified. Often, bespoke biochips are more expensive than ready-made biochips, and if ready-made biochips are available, many researchers would like to use them. Here, if the element set 1 is a gene sequence group on a certain custom-made biochip and the element set 2 is a gene sequence group on a ready-made biochip, and the relationship is displayed as a homology score of a homology search, It is possible to find out which spot of the chip can be covered by the ready-made chip. As a result, if a ready-made chip in which the spots of genes relevant to the research are covered is found, it is possible to carry out the research at a low cost with the ready-made biochip without using the custom-made chip. Similarly, even among ready-made biochips, as a set of elements with each gene sequence group as an element, homology is displayed as a relationship index, and a chip having a set more suitable for one's experiment from the relationship between chips It becomes possible to find out.

By setting two sets having the same element as the element set, calculating the relationship between the elements by brute force, displaying the list, and then sorting the elements by the algorithm described above, The element group is sorted so that the maximum value of each element is always on the diagonal line from the upper left to the lower right. Here, gene clusters can be formed on the list by a method of forming the same cluster if cells having a value equal to or higher than the reference value are in the same column or the same row.

FIG. 21 shows that the number of elements expanded in the row direction and having a quantified relationship with each element expanded in the column direction equal to or greater than a threshold value is calculated, and the row is calculated based on this number. It is an example of performing descending sort in the direction. It can be considered that the elements in the upper row have a relatively strong relationship with the element set expanded in the column direction. Reference numeral 2101 is a result display example before sorting and 2102 is a result display example after sorting.

In FIG. 22, for each element expanded in the row direction, the average value of the quantification relationship with each element expanded in the column direction is calculated, and based on this average value, the average value is calculated in the row direction. This is an example of performing descending sort. It can be considered that the elements in the upper row have a relatively strong relationship with the element set expanded in the column direction. 2201 before sorting 2
202 is an example of the result display after sorting.

[0044]

As described above, according to the present invention,
It is possible to display the quantified relationship of each element set in one table for two element sets. Further, it becomes possible to express the relationship between the element sets in a form that can be understood more easily.

[Brief description of drawings]

FIG. 1 is a configuration diagram of a system that realizes a relationship display method between element sets according to the present invention.

FIG. 2 is a conceptual diagram for displaying relationships between elements from an element set.

FIG. 3 is a diagram of a processing flow for displaying an inter-element set comparison table from the data stored in the element set information.

FIG. 4 is a diagram showing a processing flow of an element set and relationship quantification method inquiry program.

FIG. 5 is a diagram showing a processing flow of an inter-element relationship calculation program.

FIG. 6 is a diagram showing a processing flow of an inter-element relationship aggregation calculation program.

FIG. 7 is a diagram showing a processing flow of an element set comparison table display program.

FIG. 8 is a diagram showing a processing flow of a threshold setting inquiry program.

FIG. 9 is a diagram showing a processing flow of a result sort program when comparing different element sets.

FIG. 10 is a diagram showing a processing flow of a result sort program when comparing the same element sets.

FIG. 11 is a diagram showing an example of result sorting when there are two element sets.

FIG. 12 is a diagram showing an example of result sorting when there are two element sets.

FIG. 13 is a diagram showing an example of result sorting when there is one element set.

FIG. 14 is a diagram showing an example of result sorting when there is one element set.

FIG. 15 is a diagram showing an example of a data schema on an element set.

FIG. 16 is a diagram showing an example of a data schema of inter-element relationship information.

FIG. 17 is a diagram showing an example of a data schema of threshold information.

FIG. 18 is a diagram showing an example of a result display screen.

FIG. 19 is a diagram showing a threshold designation auxiliary histogram.

FIG. 20 is a diagram showing a gradation designation auxiliary histogram.

FIG. 21 is a view showing an example of sorting based on inter-element relationship aggregation data.

FIG. 22 is a view showing an example of sorting by inter-element relationship aggregate data.

[Explanation of symbols]

101: Central processing unit 102: Program memory 103: External storage device 104: data memory 105: Dialog instruction input device 106: Display device

Continued front page    (72) Iwa Yamashita, Inventor             6-81 Onoe-cho, Naka-ku, Yokohama-shi, Kanagawa             Hitachi Software Engineering Stock Association             In-house F-term (reference) 5E501 AC18 BA03 CA02 CB02 CB07                       DA11 DA13 EA07 EA10 FA13                       FA23 FB28

Claims (11)

[Claims] 1. A relationship between an element in the first element set and an element in the second element set is quantified for all element pairs, targeting the first element set and the second element set. And display the relationships between the corresponding elements in each cell of one spreadsheet in which the elements in the first element set are arranged in the row direction and the elements in the second element set are arranged in the column direction. A method for displaying a relationship between element sets, which is characterized by: 2. The element set relationship display method according to claim 1, wherein an operation of changing the arrangement order of elements in the row direction according to the magnitude of the quantified relationship, and the quantified relationship. The operation of changing the arrangement order of the elements in the column direction according to the magnitude of is repeated alternately for adjacent rows and columns while fixing the cells whose quantified relationship is equal to or more than a preset threshold value. A method for displaying the relationship between element sets, which is characterized by displaying the obtained results. 3. The inter-element-set relationship display method according to claim 1, wherein an average value of the quantified relationships or a number of cells equal to or greater than a preset threshold value is calculated for each row or each column. A method for displaying a relationship between element sets, characterized in that elements in rows or columns are rearranged and displayed in descending or ascending order of calculated values. 4. The element set relationship display method according to claim 1, wherein a threshold is set for the quantified relationship, and cells having a quantified relationship higher than the threshold and cells having a lower quantized relationship are selected. A method for displaying the relationship between element sets, which is characterized by displaying in different display modes. 5. The element set relationship display method according to claim 4, wherein the histogram of the quantified relationship is displayed, and a threshold value is set on the histogram. Sex display method. 6. The inter-element-set relationship display method according to claim 1, wherein the inter-element-set relationships are displayed with a color gradation depending on the value of the quantified relationship. Relationship display method. 7. The inter-element-set relationship display method according to claim 1 or 2, wherein different colors are designated for a plurality of types of quantified relationships, and the average color is displayed. A method of displaying relationships between featured element sets. 8. The method for displaying the relationship between element sets according to claim 1, wherein the first element set is a gene sequence group of a biological species, and the second element set is a genome sequence. And the relationship between the elements is a result of homology analysis between sequences. 9. The method for displaying the relationship between element sets according to any one of claims 1 to 7, wherein the first element set is a gene sequence group spotted on a gene biochip,
The second element set is a gene sequence group that carries out a hybridization reaction with respect to a biochip, and the relationship between the elements is a homology analysis result between genes. . 10. The method for displaying the relationship between element sets according to any one of claims 1 to 7, wherein the first element set and the second element set are spotted on different gene biochips, respectively. A method for displaying a relationship between element sets, which is a group of generated gene sequences, and the relationship between the elements is a homology analysis result between genes. 11. The method for displaying the relationship between element sets according to claim 1, wherein the first element set and the second element set are the same gene sequence group. A method for displaying a relationship between element sets, characterized in that the relationship between them is the result of homology analysis between genes.