Method of normalizing gene expression data

• US 20040063133A1
• Filed: 09/29/2003
• Published: 04/01/2004
• Est. Priority Date: 09/30/2002
• Status: Abandoned Application

• Current Assignee: Fujifilm Corporation (Fujifilm Holdings Corporation)
• Original Assignee: Fuji Photo Film Co Limited (Fujifilm Holdings Corporation)
• Inventors: Some, Masato, Ogura, Nobuhiko
• Application Number:
  US10/671,546
• Publication Number:
  US 20040063133A1
• Time in Patent Office: Days
• US Class Current: 435/6
• CPC Class Codes: C12Q 1/6809 Methods for determination or identification of nucleic acids involving differential detection
• CPC Class Codes: C12Q 2545/113 with an external standard/control, i.e. control reaction is separated from the test/target reaction
• CPC Class Codes: G16B 25/00 ICT specially adapted for hybridisation; ICT specially adapted for gene or protein expression
• CPC Class Codes: G16B 25/10 Gene or protein expression profiling; Expression-ratio estimation or normalisation

Abstract

Data concerning gene expression quantities, which have been obtained for first and second samples, are indicated with points plotted on a logarithmic coordinate system, in which a horizontal axis represents logarithms of the expression quantities obtained for the first sample, and in which a vertical axis represents logarithms of the expression quantities obtained for the second sample. A coefficient is calculated from a value of an intercept of an approximate straight line, which is obtained from approximate representation of the plotted points with a straight line having a slope of 1, on the vertical axis. The data concerning the expression quantities with respect to a plurality of genes, which expression quantities have been obtained for the second sample, are divided by the coefficient and are thus normalized.

Claims

1. A method of normalizing gene expression data wherein, in a process for comparing expression quantities with respect to a plurality of genes, which expression quantities have been obtained for a first sample, and expression quantities with respect to the plurality of the genes, which expression quantities have been obtained for a second sample, with each other, data concerning the expression quantities having been obtained for the second sample are normalized, the method comprising the steps of:

i) indicating the data concerning the expression quantities, which have been obtained for the first sample and the second sample, with points plotted on a logarithmic coordinate system, in which a horizontal axis represents logarithms of the expression quantities obtained for the first sample, and in which a vertical axis represents logarithms of the expression quantities obtained for the second sample,

ii) calculating a coefficient from a value of an intercept of an approximate straight line, which is obtained from approximate representation of the plotted points with a straight line having a slope of 1, on the vertical axis, and

iii) performing division processing for dividing the data concerning the expression quantities with respect to the plurality of the genes, which expression quantities have been obtained for the second sample, by the coefficient, whereby the data concerning the expression quantities having been obtained for the second sample are normalized.

2. A method as defined in claim 1 wherein the first sample is a sample obtained from a normal cell, and the second sample is a sample obtained from an abnormal cell.

3. A method of normalizing gene expression data wherein, in a process for comparing expression quantities with respect to a plurality of genes, which expression quantities have been obtained for a first sample, and expression quantities with respect to the plurality of the genes, which expression quantities have been obtained for a second sample, with each other, data concerning the expression quantities having been obtained for the second sample are normalized, the method comprising the steps of:

i) indicating the data concerning the expression quantities, which have been obtained for the first sample and the second sample, with points plotted on a coordinate system, in which a horizontal axis represents the expression quantities obtained for the first sample, and in which a vertical axis represents the expression quantities obtained for the second sample,

ii) calculating a value of a slope of an approximate straight line, which is obtained from approximate representation of the plotted points with a straight line passing through an origin of the coordinate system, and

iii) performing division processing for dividing the data concerning the expression quantities with respect to the plurality of the genes, which expression quantities have been obtained for the second sample, by the value of the slope of the approximate straight line, whereby the data concerning the expression quantities having been obtained for the second sample are normalized.

4. A method as defined in claim 3 wherein the first sample is a sample obtained from a normal cell, and the second sample is a sample obtained from an abnormal cell.