Method for visualizing data on correlation between biological events, analysis method, and database

• US 20060287831A1
• Filed: 07/12/2004
• Published: 12/21/2006
• Est. Priority Date: 10/07/2003
• Status: Abandoned Application

• Current Assignee: Reverse Proteomics Research Institute Company Limited
• Original Assignee: Reverse Proteomics Research Institute Company Limited
• Inventors: Horiuchi, Ken, Araki, Kenji, Nemoto, Masashi, Nishikawa, Tetsuo, Totiba, Motoi
• Application Number:
  US10/569,494
• Publication Number:
  US 20060287831A1
• Time in Patent Office: Days
• US Class Current: 702/19
• CPC Class Codes: G16B 20/00 ICT specially adapted for functional genomics or proteomics, e.g. genotype-phenotype associations
• CPC Class Codes: G16B 40/00 ICT specially adapted for biostatistics; ICT specially adapted for bioinformatics-related machine learning or data mining, e.g. knowledge discovery or pattern finding
• CPC Class Codes: G16B 40/30 Unsupervised data analysis
• CPC Class Codes: G16B 45/00 ICT specially adapted for bioinformatics-related data visualisation, e.g. displaying of maps or networks

Abstract

One of a plurality of data display formats with different units of correlation data that are prepared in advance is automatically selected depending on the variation of the amount of data in terms of the number of items thereof. One of a plurality of display methods with different summarization levels that are prepared in advance is also automatically selected for information (about correlation data or individual events) regarding individual cells. Information about the correlation data and individual cells is then displayed. The amount of work required to repeat the operation of observing the correlation data as a whole and the detailed observation of a small amount of data is reduced in a method for visualizing correlation data concerning two events in a matrix format.

Claims

1. A method for visualizing correlation data concerning two biological events or the correlation data and feature data regarding each event in a matrix format, the method comprising displaying correlation data concerning biological events of the same or different kinds, or the correlation data and feature data regarding each biological event in (a) one of a plurality of prepared data display formats and at (b) one of a plurality of prepared summarization levels, both of which are selected either manually or automatically depending on the number of data items in desired display data.

2. The visualizing method according to claim 1, wherein the plurality of data display formats (a) from which one is selected include:

(A) a table data display format having correlation data concerning a pair of events as a single display data unit;

(B) a table data display format having correlation data concerning clusters obtained as a result of clustering of events as a single display data unit; and

(C) a data display format having the result of statistically processing a set of correlation data as a single display data unit.

3. The method for visualizing correlation data concerning biological events according to claim 2, wherein the clustering method (B) comprises clustering based on attribute information regarding the two biological events or correlation information between the two biological events.

4. The visualizing method according to claim 2, wherein, in the table data display format (B) having correlation data concerning clusters as a single table data unit, the results are rearranged on a diagonal in order of decreasing correlation intensity from the upper left of the table.

5. The visualizing method according to claim 1, comprising a summarization method selected from the plurality of summarization levels (b) that include display or non-display of a data field, reduction of data in a data field of the character type, and reduction of data in a data field of the numeric value type.

6. The visualizing method according to claim 3, wherein the reduction of data in the data field of the character type comprises operations of extracting a part of layers of character information in a layered structure, extracting a keyword from the character data that is registered in advance, and associating the character data with a single sign, letter, or color.

7. The visualizing method according to claim 3, wherein the reduction of data in the data field of the numerical value type comprises operations of rounding a value to an arbitrary significant digit, extracting only the exponential portion of the value, and associating values in a certain range with a color.

8. The visualizing method according to claim 1, wherein the method for automatically selecting the screen display format and the summarization level of data comprises selecting a pair of a data display format and a data summarization level depending on the number of entries of the correlation data to be displayed on screen and the size of an information display region and an information display unit that are designated in advance, such that a maximum amount of information can be provided.

9. The visualizing method according to claim 1, wherein a plurality of kinds of correlation data concerning the biological events are displayed simultaneously in the cells of the matrix in an identifiable manner.

10. The visualizing method according to claim 1, wherein the correlation data concerning the biological events comprises an interaction between LMW compounds and proteins.

11. The method for visualizing correlation data concerning biological events according to claim 1, wherein, as the biological events, a structural unit is defined on the basis of atoms in a molecule or a set of atoms in a molecule for each molecule in a complex of one or more molecules, a representative position of the structural unit is defined on the basis of the coordinates of atoms of which the structural unit is composed, and information about the distance between the representative positions of the structural units is displayed in the cells in the matrix, said matrix having each of the structural units as elements in the rows and columns thereof.

12. A method for analyzing correlation information concerning two biological events, comprising extracting a feature quantity of the biological events that is common to the members of the clusters according to claim 2.

13. A method for analyzing correlation information concerning two biological events according to claim 12, wherein the feature quantity of the biological events is represented by one or a plurality of elements consisting of values or text, or a feature quantity that expresses the three-dimensional structure of a molecule.

14. A database in which the result of cluster analysis obtained by the analysis method according to claim 12 is stored together with related known information extracted from non-patent documents or patent documents, the database further having a function for searching for the known related information based on the result of cluster analysis or for the result of cluster analysis based on the known information.

15. A computer-readable recording medium in which a program for causing a computer to implement the visualizing method, analysis method, or database according to claims 1, 12 or 14 is stored.