In the Bonferroni method, the P-values for each gene are multiplied by N, where N is the total number of genes being tested. This increases the P-values to such a level, that very few genes are selected within the threshold.
The Bonferroni method is highly conservative and while it reduces the number of false positives greatly, a number of truly differentially expressed genes are excluded. The Bonferroni method may be best utilized when looking for a small number of genes which are highly differentially expressed.