Biology Reference
In-Depth Information
Chapter 3
From Modules to Models:
Advanced Analysis Methods
for Large-Scale Data
Sven Bergmann
1. Introduction
Microarrays have firmly established themselves as a standard tool in bio-
logical and biomedical research. Together with the rapid advancement of
genome sequencing projects, microarrays and related high-throughput
technologies have been key factors in the study of the more global aspects
of cellular systems biology. 1 While genomic sequence provides an inven-
tory of parts, a proper understanding of the functions and organization
of those parts requires comprehensive views of the regulatory relations
between them. 2 Genome-wide expression data offer such a global view
by providing a simultaneous read-out of the mRNA levels of all (or many)
genes in the genome.
Most microarray experiments are conducted to address specific bio-
logical issues [Fig. 1(a)]. In the simplest case, such a study may focus on
the expression response to the deletion of individual genes or to specific
cellular conditions. Already when extending the experimental setup to
include several conditions, e.g. time points along the cell cycle 3 or several
tissue samples, the sheer amount of data points necessitates computa-
tional tools to extract and organize relevant biological information.
A wide range of approaches has been developed, including numerous
clustering algorithms, statistical methods for detecting differential
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