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These broad clusters are then fleshed out along a standard timeline of early development, highlighting gametogenesis, fertilization, cleavage, gastrulation, and axis specification (see Section 1.2).
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Broad clusters were further categorized based on their peakedness.
If this condition was not met, the broad cluster was classified as "without a peak" (see Additional file 10 for an illustration).
A broad cluster was deemed as one with a dominant peak if the TSS with the highest frequency of tag counts constituted at least 50%% of the total tag count.
These findings suggest that broad TSS clusters are not necessarily associated with the CpG type promoters in non-vertebrates.
Note that many of these clusters are annotated with broad terms such as "Signal peptide" or "Transmembrane".
A total of 328 genes were organized into 10 annotation clusters that all fit within the broad category of "Development" (top eight clusters are shown in Figure 4A).
In the first view, which abstracts the whole network, the clusters are labeled with broad biological processes such as DNA repair, rRNA processing and translation (Fig. 3A).
Figure 3 shows the result for all 4,481 promoters: the upstream cluster is enriched in single peak promoters, whereas the centered and downstream clusters are enriched in broad promoters).
In Figure 4A, which depicts the entire network, the clusters are labeled with broad biological processes such as regulation of transcription, DNA-dependent, response to heat, and embryo development ending in seed development.
Patients in clusters 1 and 3 appear to exhibit more severe psychopathology and a broader range of symptoms than those in cluster 2. Based on NEO-PI-R and MMPI-2 findings, tentative descriptions of the clusters are offered.
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