If all differentially regulated genes had been considered (large circles), there would have been many genes shared by these two studies and that is the most likely reason why the profiles from one study could be used to predict sample status from the other study.
A phylogenetic tree, constructed with the complete grape, Arabidopsis and rice R2R3MYB subfamilies, showed that many genes sharing similar functions were clustered in the same phylogenetic groups.
This suggests that many genes shared an optimal or near optimal parameter combination at the mid range of our parameter values.
As a result, many genes shared between the Stenogyne and tomato unigene sets may be relevant for fruit/embryo/seed development.
This is because the inclusive fitness of an individual is determined not only by how many genes it directly passes onto the next generation but also by how many genes shared with related individuals are also passed on (termed indirect fitness).
Motif instance data are often noisy because of redundancy and degeneracy in PSSMs, and in genome-scale expression data sets many genes may share expression profiles, but not regulatory dynamics.
