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associated with a distinct type of human leukemia. The P190 form is most
often present in B-ALL, but only rarely in CML (Deininger
et al
., 2000);
whereas P210 is mainly involved in CML, and in some acute lymphoid
(Deininger
et al
., 2000) and myeloid leukemias in CML blast crisis. P230
is found in a very mild form of CML (Pane
et al
., 1996). Ph
+
B-ALL
and lymphoid blast crisis of CML account for about 20% of adult cases and
5% of childhood cases of acute B-lymphoid leukemia. Among those
patients with BCR-ABL-induced B-ALL, 50% of adults and 20% of
children carry the P210 form of BCR-ABL while the rest of the patients carry
the P190 form (Deininger
et al
., 2000; Druker
et al
., 2001a; Sawyers, 1999).
It is still not fully understood why the three forms of BCR-ABL induce
distinct diseases, but it is important to reveal the underlying mechanisms.
This chapter systematically presents how to discover useful informa-
tion based on the DNA microarray expression data collected from our
leukemia studies. Specifically, the chapter will, step by step, describe
the analysis of the microarray data obtained from our experiments study-
ing gene expression profiles for P190, P210, and P230 BCR-ABL. In
addition, data mining tasks normally include data preprocessing, data
modeling, and knowledge description. To cover this area of data mining
using our novel SDL global optimization method, we also analyze some
publicly available microarray data on leukemia to show the advantages
of our data mining method.
4.2. Experimental Design
4.2.1.
Rationale
DNA microarrays usually consist of thin glass or nylon substrates con-
taining specific DNA gene samples spotted in an array by a robotic print-
ing device (Anonymous, 2002). Researchers spread fluorescently labeled
mRNA from an experimental condition onto the DNA gene samples in the
array. This mRNA binds strongly with some DNA gene samples and
weakly with others, depending on the inherent double-helical characteris-
tics. A laser scan is done on the array and sensors to detect the fluores-
cence levels (using red and green dyes), indicating the strength with
which the sample expresses each gene. The logarithmic ratio between the
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