The results of the in silico experiments were very different for the " equal expression" assumption.
A different picture emerged from the simulations performed using the " equal expression" assumption.
In contrast, under the " equal expression" assumption, non isoform-specific peptides are more abundant than isoform-specific peptides.
Although neither of the two pooling probability assumptions is truly realistic in a biological sense, the " equal expression" assumption arguably provides the better approximation.
The " equal expression" assumption, however, does not provide a corresponding lower bound, because it does not consider the relative expression levels between two or more AS isoforms.
The linkage between physiological and molecular models comes with the assumption that the occurrence of a phenological stage is triggered by the accumulation of adequate levels of gene expression (Assumption 5, from the Introduction).
Given this reasoning, the conclusion derived under the " equal expression" assumption, namely that AS is over-represented, or at least not under-represented in the experimental proteomics datasets, is the most plausible.
In summary, under the " equal expression" assumption the in silico experiments indicate that; (i) AS events were not under-represented in the Baerenfaller set, and; (ii) AS events were over-represented in both the Castellana- and the Merged set.
The inconsistency between the conclusions obtained under the two pooling probabilities assumptions is the result of the fact that isoform-specific peptides associated with AS events have higher pooling probabilities under the " equal pooling probability" assumption than under the " equal expression" assumption.
Under the second assumption, to which we refer as the " equal expression" assumption, two basic rules are applied: (i) all genes are represented by equal amounts of protein molecules, and; (ii) all protein isoforms from an AS locus are present in equal numbers.
