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Fig. 12.4 Clustered phase-phase plot transcript time course profiles for the 0.7-h (Li and Klevecz
2006 ) and 5-h (Tu et al. 2005 ) period datasets (a). The black axes represent the phase angles of the
samples, and the grey axes map these phase angles to the real time. The cluster names are given at
the side of the lower panel (b). The transcripts in these clusters were then used to cross-cluster a
collection of 1,327 transcriptome microarray hybridisations (McCord et al. 2007 ). The hue
represents the normalised rank sum where yellow to red indicates an up-regulation, and cyan to
blue represents a down-regulation of the any target hybridisation compared to the cluster. The
column numbers indicate clusters of hybridisations derived using the SOTA algorithm and plotted
in decreasing order (from left to right ) using cluster A as a reference (Machn ´ and Murray 2012 )
from two oscillation periods (Tu et al. 2005 ; Li and Klevecz 2006 ) were compared
by a Fourier transform model-based clustering approach (Machn´ and Murray
2012 ), we could define a temporal programme of five common co-expression
clusters (Fig. 12.4a ); there were also two clusters that showed differential expres-
sion between the two periods and two clusters that oscillated but with a lower
signal-noise ratio than the main consensus clusters. For brevity we will concentrate
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