Biology Reference
In-Depth Information
CHAPTER 5
Applications of the SDL Global Optimization
Method in DNA Microarray Data Analysis
5.1. Leukemia Cell Line Study
5.1.1.
Introduction
In Chapter 2, we introduced our microarray study on a leukemia cell
line expressing three forms of BCR-ABL (P190, P210, and P230). The
goal of this study is to identify differences in gene expression among
the three forms of BCR-ABL. The SDL global optimization method
allows us to analyze the expression of all genes simultaneously.
5.1.2.
Datasets
Here, we analyze two sets of microarray data (P190 and P210), with the
fold changes for 21 934 mouse genes.
5.1.3.
Analysis strategies
5.1.3.1.
Data sorting based on 20 chromosome groups
(Fig. 5.1)
=
(
∑
e
(
i
,
j
)
)
/
n
(
j
).
Average change (
j
)
In this equation,
e
(
i
,
j
) are expression fold changes and
n
(
j
) are
the numbers of genes in every chromosome group;
j
=
1, 2, … , 20;
i
=
1, 2, … ,
n
(
j
).
55
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