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Note that, the average expression profiles for all probe-sets have been taken for genes that are represented by more than one corresponding probe-set.
The clusters are summarized by the average expression profiles, per cluster, that is plotted against time (See Figure 2).
This timeline is confirmed by the data presented, implicating that most expression profiles return to baseline at 56 days, as shown by the average expression profiles (Figure 3).
The graphical representations of the average expression profiles for each of the 8 unique temporal clusters determined by cluster analysis of significant gene probe sets are shown in Figure 3.
The major biological processes identified exclusively for increased gene expressions, which all peaked between days 5 and 10 as shown by their average expression profiles (Figure 4A), consisted of a large variety of processes related to neurogenesis, skeletogenesis, cell motility, cell adhesion, vasculogenesis, and Wnt signaling, as supported by detailed information in Tables S2A and S2B.
These were used to define the average expression profiles (centroids) for each of the molecular subtypes.
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We formalized eight models to represent the average expression profile of these genes: Up-early, in which genes were expressed to their maximum level within the first 6 hrs; Up-linear, in which genes continually increased over the time-course; and Up-late, in which genes stayed constant till the 24 hr time-point.
We identified 3882 differentially expressed (DE) mRNAs; an mRNA was considered to be DE if the average expression profile of healthy donors was different from that of patients in one or more categories.
The four controls were treated as replicates and the average expression profile for each subtraction of the control data was calculated.
As an alternative approach to identify genes induced during the early stage of infection that could be associated with clearance, the average expression profile of persistently infected chimpanzees (X0234 and X0140) was compared to the average expression profile of chimp X0190 during weeks 4 and 6.
From this list of "seed genes" an "average" expression profile that best represents gametocytogenesis can be constructed, and all of the malaria genes in the genome can be relatively ranked according to their similarity to the average profile as measured by Pearson correlation.
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com