Method of managing and displaying gene expression data
AssigneeHitachi Software Engineering Co., Ltd.
InventorsAyako Fujisaki, Noriyuki Yamamoto, Atsushi Mori
Life of this patent
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Abstract
A method visually and clearly manages and displays a large amount of gene expression data obtained using a large number of DNA chips. The types of DNA chip are displayed in a leftmost column of a matrix, parameters such as times in a time series, treatment methods, types of samples, and the like are displayed in the top row, and expression value data corresponding to the respective cells are displayed as small matrices. Treatment methods or types of samples of Channel 1 and Channel 2 are displayed in the rows and columns of the small matrices. When a cell in a small matrix is clicked, a scatter diagram for corresponding expression value data is displayed.
Claims11
A gene expression data managing and displaying method that manages and displays gene expression data including information relating to DNA chips and probes mounted on the DNA chips, gene expression value information obtained by the DNA chips, and experiment information relating to a hybridization experiment,
- the method comprising:
- a row setting step that sets a number of rows equal to a number of types of the DNA chips;
- an item setting step that determines a subject of analysis in the hybridization experiment and sets, based on the determined subject of analysis, items corresponding to the types of DNA chips;
- a column setting step that sets a number of columns equal to the number of items set in the item setting step;
- a matrix generating step that generates a matrix composed of a number of rows given by adding one to the number of rows set in the row setting step and a number of columns given by adding one to the number of columns set in the column setting step;
- a first column inserting step that inserts the types of DNA chips into respective cells in a first column of the matrix;
- a first row inserting step that inserts the items into respective cells in a first row of the matrix;
- a cell inserting step that inserts, into respective cells at intersections of columns and rows in the matrix, experiment data for a combination of a type of DNA chip in the row to which the cell belongs and an item in the column to which the cell belongs;
- and
- a matrix drawing step that draws a matrix composed of cells in which the types of DNA chip, the items, and the experiment data have been inserted.
A gene expression data managing and displaying method that extracts two specimens from each sample, marks all of the extracted specimens with two respectively different fluorescent dyes to identify organisms of the samples or treatment methods applied to the samples, and in a case where the specimens marked with one of the fluorescent dyes are set as Channel 1 and the specimens marked with another of the fluorescent dyes are set as Channel 2, manages and displays gene expression data including information relating to DNA chips and probes mounted on the DNA chips, gene expression value information obtained by the DNA chips, and experiment information relating to a hybridization experiment,
- the method comprising:
- a subject of analysis determining step that compares a number of types of treatment methods for the samples with a number of types of samples, determines that the subject of analysis is to investigate effects of the treatment methods on samples when there are more types of treatment methods for samples than types of samples, and determines that the subject of analysis is to investigate effects due to types of samples when there are not more types of treatment methods for samples than types of samples;
- a first column and row setting step that sets, when the subject of analysis determining step has determined that the subject of analysis is to investigate effects of the treatment methods on samples, a same number of columns as the number of types of treatment methods of Channel 1 and sets a same number of rows as the number of types of treatment methods of Channel 2;
- a matrix generating step that generates a matrix composed of a number of rows given by adding one to the number of rows set in the first column and row setting step and a number of columns given by adding one to the number of columns set in the first column and row setting step;
- a first column inserting step that inserts the types of treatment methods of Channel 2 into respective cells in a first column of the matrix;
- a first row inserting step that inserts the types of treatment methods of Channel 1 into respective cells in a first row of the matrix;
- a cell inserting step that inserts, into respective cells at intersections of columns and rows in the matrix, experiment data for a combination of a treatment method in the row to which the cell belongs and a treatment method in the column to which the cell belongs;
- and
- a matrix drawing step that draws a matrix composed of cells in which the types of DNA chip, the types of treatment methods, and the experiment data have been inserted.
A computer-readable program for causing a computer to carry out a gene expression data managing and displaying method comprising a row setting step that sets a number of rows equal to a number of types of the DNA chips-, an item setting step that determines a subject of analysis in the hybridization experiment and sets, based on the determined subject of analysis, items corresponding to the types of DNA chips;
- a column setting step that sets a number of columns equal to the number of items set in the item setting step, a matrix generating step that generates a matrix composed of a number of rows given by adding one to the number of rows set in the row setting step and a number of columns given by adding one to the number of columns set in the column setting step:
- a first column inserting step that inserts the types of DNA chips into respective cells in a first column of the matrix;
- a first row inserting step that inserts the items into respective cells in a first row of the matrix;
- a cell inserting step that inserts, into respective cells at intersections of columns and rows in the matrix, experiment data for a combination of a type of DNA chip in the row to which the cell belongs and an item in the column to which the cell belongs;
- and a matrix drawing step that draws a matrix composed of cells in which the types of DNA chip, the items, and the experiment data have been inserted.
A computer-readable medium storing a program comprising a row setting step that sets a number of rows equal to a number of types of the DNA chips;
- an item setting step that determines a subject of analysis in the hybridization experiment and sets, based on the determined subject of analysis, items corresponding to the types of DNA chips, a column setting step that sets a number of columns equal to the number of items set in the item setting step, a matrix generating step that generates a matrix composed of a number of rows given by adding one to the number of rows set in the row setting step and a number of columns given by adding one to the number of columns set in the column setting step;
- a first column inserting step that inserts the types of DNA chips into respective cells in a first column of the matrix;
- a first row inserting step that inserts the items into respective cells in a first row of the matrix;
- a cell inserting step that inserts, into respective cells at intersections of columns and rows in the matrix, experiment data for a combination of a type of DNA chip in the row to which the cell belongs and an item in the column to which the cell belongs;
- and a matrix drawing step that draws a matrix composed of cells in which the types of DNA chip, the items, and the experiment data have been to cause a computer to execute the program.
Dependencies are inferred from the claim text.