If you include microarray experiments in your proposal, treat them seriously with the thought and projected effort that they will require. Any criticism that can be used for other methods, such as two-hybrid assays, cDNA library screening, etc., could also be used for proposed microarray experiments. There must be follow up experiments for confirming microarray data. Different types of experiments must be used to confirm that the genes are actually induced and that they are important. It is a mistake to think that only a handful of genes will be induced by any treatment.
Important events are likely to cause very many changes in gene expression.
It is a mistake to think that all the EST clones on the microarrays encode proteins with known functions. Far fewer have been studied in any real detail. The microarrays containing up to 60,000 EST clones allow researchers to study the expression of many thousands of genes of totally unknown function. Furthermore, most EST clones have been incompletely sequenced. Therefore, it may not be possible to analyze the structure of proteins expressed by EST clones whose expression change in interesting ways.