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Because the core set approach focuses on describing the evolutionary process within a species, the initial distances can be approximated well by the pairwise differences.
We decided to include these indicators in our study, because the core set mainly reflected the secondary prevention in patients with diabetes or established CVD, neglecting the primary prevention and patient perspective, which were represented in the wider set (broad set).
Because the CORE set in the DIP database had been widely used to develop the prediction methods by the high-quality, high-throughput protein interaction data of it, and to study the properties of protein interaction networks, we selected the CORE set as the positive set for a gold standard database.
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With a typical genome size of between 115 and 170 kb and a gene complement of 100 120 unique genes (Green 2011; Wicke et al. 2011), the streptophyte plastid gene repertoire is relatively stable because retention of the core set of chloroplast genes is likely under strong selection, and gene gains are exceptional (Wicke et al. 2011).
This partitioning was performed because we suspected that tRNAs in the core set are under stronger selective constraints, whereas constraints in peripheral tRNAs are more relaxed.
In the case of sli, which Dichaete regulates in midline glia, we find some evidence of Dichaete binding, however, most of the intervals are not identified in the core set, presumably because midline glia comprise a very small fraction of the whole embryo.
Conversely, if there are fewer shared positive promoters, then the core set will be a small fraction of the universe set, because most positive promoters will not be present in all four cell types.
The core set can be empty.
Application of the core set approach to 10 sets of the terminal sequences retained 90%% of the whole sequences as the global S-core set member and did not require any local core-set trees because of random process without strong evolutionary correlations (long-branch attractions).
Continuing this process until the core set cannot be updated, we obtain the T-core set.
The last column (in core set) refers to the initial classification of the genes within the core set.
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